SRX5550802 2 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516347 naive-h3ac-2 2 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550803 1 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516348 naive-h3ac-1 1 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550804 4 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516349 naive-h4ac-1 4 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550805 3 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516350 naive-h3ac-3 3 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550806 6 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516351 naive-rnap2-1 6 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550807 40 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516354 esi-hos2-2 40 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550808 8 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516353 naive-rnap2-3 8 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550809 7 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516352 naive-rnap2-2 7 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550810 10 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516355 naive-input-2 10 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550811 9 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516356 naive-input-1 9 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550812 39 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516358 esi-hos2-1 39 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550813 21 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516357 esi-input-2 21 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550814 22 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516359 esi-input-3 22 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550815 23 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516360 naive-snt1-1 23 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550816 24 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516361 naive-snt1-2 24 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550817 25 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516362 naive-snt1-3 25 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550818 26 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516363 naive-snt1-1-input 26 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550819 27 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516364 naive-snt1-2-input 27 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550820 28 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516365 naive-snt1-3-input 28 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550821 29 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516366 esi-snt1-1 29 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550822 30 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516367 esi-snt1-2 30 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550823 47 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516369 naive-rap1-2-input 47 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550824 48 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516368 naive-rap1-3-input 48 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550825 45 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516370 naive-rap1-3 45 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550826 46 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516371 naive-rap1-1-input 46 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550827 43 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516373 naive-rap1-1 43 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550828 44 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516372 naive-rap1-2 44 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550829 41 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516375 esi-hos2-1-input 41 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550830 42 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516374 esi-hos2-2-input 42 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550831 49 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516376 esi-rap1-1 49 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550832 50 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516378 esi-rap1-2 50 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550833 38 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516377 naive-hos2-2-input 38 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550834 37 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516379 naive-hos2-1-input 37 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550835 20 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516380 esi-input-1 20 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550836 19 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516381 esi-rnap2-3 19 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550837 36 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516382 naive-hos2-2 36 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550838 35 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516383 naive-hos2-1 35 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550839 34 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516385 esi-snt1-3-input 34 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550840 33 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516384 esi-snt1-2-input 33 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550841 32 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516386 esi-snt1-1-input 32 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550842 31 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516387 esi-snt1-3 31 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550843 12 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516388 esi-h3ac-1 12 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550844 11 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516389 naive-input-3 11 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550845 14 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516391 esi-h3ac-3 14 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550846 13 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516390 esi-h3ac-2 13 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550847 16 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516392 esi-h4ac-2 16 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550848 15 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516395 esi-h4ac-1 15 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550849 18 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516394 esi-rnap2-1 18 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550850 17 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516393 esi-h4ac-3 17 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550851 52 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516396 esi-rap1-1-input 52 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550852 51 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516399 esi-rap1-3 51 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550853 54 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516397 esi-rap1-3-input 54 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550854 53 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516398 esi-rap1-2-input 53 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000 SRX5550855 5 SRP189056 bp0 Chromatin isolation was performed using a protocol adapted from Kuras and Struhl47. One-half litre of diploid cells were grown to mid-exponential phase per ChIP to be performed, and then fixed with 1% formaldehyde for 1 hr before collection by centrifugation. Cells were resuspended in FA lysis buffer (50 mM HEPE-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% triton X-100, 1X Roche Complete Protease Inhibitors) with 0.5% SDS added, and then lysed using acid-washed glass beads for 15 min at 50 Hz. Chromatin was then precipitated by ultracentrifugation at 237,000 x g for 30 min, then resuspended in 1 ml FA lysis buffer with 0.1% SDS. Chromatin suspension was then fragmented to predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified by centrifugation at 20,000 x g for 30 min. 10% of the resultant chromatin preparations were reserved as input controls. Pan-acetyl H3 (H3ac), pan-acetyl H4 (H4ac), and RNA Pol II ChIPs were performed using antibody-coupled Protein G Dynabeads (antibodies used, respectively: Upstate 06-599, Upstate 06-866, and Active Motif 39097). After precipitation overnight in FA buffer containing 0.1% SDS and 275 mM NaCl, H3ac and H4ac precipitations were washed once with FA buffer containing 0.1% SDS and 500 mM NaCl, once with buffer containing 0.1% SDS and 750 mM NaCl, once with wash buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE before being eluted in TE with 1% SDS at 65 C. Snt1-myc, Rap1-myc, and Hos2-myc precipitations were all performed with c-Myc affinity agarose (Sigma-Aldrich A7470) blocked with 2% BSA. After precipitation overnight in FA buffer with 0.1% SDS and 275 mM NaCl, all were washed once with FA buffer with 0.1% SDS and 275 mM NaCl, once with the same buffer but with 500 mM NaCl, one with wash buffer, and once with TE before being eluted in TE with 1% SDS at 65 C. After elution, proteinase K was added (final concentration 0.2 mg/ml) and incubated at 37 C for 2 hrs before crosslink reversal at 65 C overnight. Precipitants were then cleaned up using a standard phenol:chloroform:isoamyl alcohol extraction followed by isopropanol precipitation overnight. DNA was then resuspended in DEPC-treated water, and then the concentration was measured by Qubit spectrophotometer. Libraries for sequencing were then generated using the NEBNext Ultra II DNA Library Prep Kit, and sequencing was performed on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility. SRS4516400 naive-h4ac-2 5 ChIP-Seq GENOMIC ChIP Illumina HiSeq 4000