SRX3205260 GSM2790399 SRP118601 PRJNA411776 SRS2531251 SAMN07687704 Hi-C GENOMIC other Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. NextSeq 500 gds 302790399 GSM2790399 GEO Accession GSM2790399 SRX3205261 GSM2790400 SRP118601 PRJNA411776 SRS2531252 SAMN07687725 Hi-C GENOMIC other Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. NextSeq 500 gds 302790400 GSM2790400 GEO Accession GSM2790400 SRX3205262 GSM2790401 SRP118601 PRJNA411776 SRS2531253 SAMN07687726 Hi-C GENOMIC other Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. NextSeq 500 gds 302790401 GSM2790401 GEO Accession GSM2790401 SRX3205263 GSM2790402 SRP118601 PRJNA411776 SRS2531254 SAMN07687727 Hi-C GENOMIC other Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. NextSeq 500 gds 302790402 GSM2790402 GEO Accession GSM2790402 SRX3205264 GSM2790403 SRP118601 PRJNA411776 SRS2531255 SAMN07687703 Hi-C GENOMIC other Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. NextSeq 500 gds 302790403 GSM2790403 GEO Accession GSM2790403 SRX3205265 GSM2790404 SRP118601 PRJNA411776 SRS2531256 SAMN07687730 Hi-C GENOMIC other Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. NextSeq 500 gds 302790404 GSM2790404 GEO Accession GSM2790404 SRX3205266 GSM2790405 SRP118601 PRJNA411776 SRS2531258 SAMN07687729 Hi-C GENOMIC other Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. NextSeq 500 gds 302790405 GSM2790405 GEO Accession GSM2790405 SRX3205267 GSM2790406 SRP118601 PRJNA411776 SRS2531257 SAMN07687728 Hi-C GENOMIC other Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. NextSeq 500 gds 302790406 GSM2790406 GEO Accession GSM2790406 SRX3205268 GSM2790407 SRP118601 PRJNA411776 SRS2531259 SAMN07687724 Hi-C GENOMIC other Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. NextSeq 500 gds 302790407 GSM2790407 GEO Accession GSM2790407 SRX3205269 GSM2790408 SRP118601 PRJNA411776 SRS2531260 SAMN07687723 Hi-C GENOMIC other Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. NextSeq 500 gds 302790408 GSM2790408 GEO Accession GSM2790408 SRX3205270 GSM2790409 SRP118601 PRJNA411776 SRS2531262 SAMN07687722 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790409 GSM2790409 GEO Accession GSM2790409 SRX3205271 GSM2790410 SRP118601 PRJNA411776 SRS2531261 SAMN07687721 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790410 GSM2790410 GEO Accession GSM2790410 SRX3205272 GSM2790411 SRP118601 PRJNA411776 SRS2531264 SAMN07687720 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790411 GSM2790411 GEO Accession GSM2790411 SRX3205273 GSM2790412 SRP118601 PRJNA411776 SRS2531263 SAMN07687719 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790412 GSM2790412 GEO Accession GSM2790412 SRX3205274 GSM2790413 SRP118601 PRJNA411776 SRS2531265 SAMN07687718 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790413 GSM2790413 GEO Accession GSM2790413 SRX3205275 GSM2790414 SRP118601 PRJNA411776 SRS2531266 SAMN07687717 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790414 GSM2790414 GEO Accession GSM2790414 SRX3205276 GSM2790415 SRP118601 PRJNA411776 SRS2531267 SAMN07687716 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790415 GSM2790415 GEO Accession GSM2790415 SRX3205277 GSM2790416 SRP118601 PRJNA411776 SRS2531268 SAMN07687715 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790416 GSM2790416 GEO Accession GSM2790416 SRX3205278 GSM2790417 SRP118601 PRJNA411776 SRS2531269 SAMN07687714 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790417 GSM2790417 GEO Accession GSM2790417 SRX3205279 GSM2790418 SRP118601 PRJNA411776 SRS2531270 SAMN07687713 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790418 GSM2790418 GEO Accession GSM2790418 SRX3205280 GSM2790419 SRP118601 PRJNA411776 SRS2531271 SAMN07687712 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790419 GSM2790419 GEO Accession GSM2790419 SRX3205281 GSM2790420 SRP118601 PRJNA411776 SRS2531272 SAMN07687711 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790420 GSM2790420 GEO Accession GSM2790420 SRX3205282 GSM2790421 SRP118601 PRJNA411776 SRS2531274 SAMN07687710 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790421 GSM2790421 GEO Accession GSM2790421 SRX3205283 GSM2790422 SRP118601 PRJNA411776 SRS2531273 SAMN07687709 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790422 GSM2790422 GEO Accession GSM2790422 SRX3205284 GSM2790423 SRP118601 PRJNA411776 SRS2531275 SAMN07687708 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790423 GSM2790423 GEO Accession GSM2790423 SRX3205285 GSM2790424 SRP118601 PRJNA411776 SRS2531276 SAMN07687707 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790424 GSM2790424 GEO Accession GSM2790424 SRX3205286 GSM2790425 SRP118601 PRJNA411776 SRS2531277 SAMN07687706 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790425 GSM2790425 GEO Accession GSM2790425 SRX3205287 GSM2790426 SRP118601 PRJNA411776 SRS2531278 SAMN07687705 ChIP-Seq GENOMIC ChIP Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash. Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C. ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash. Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates. Illumina HiSeq 2000 gds 302790426 GSM2790426 GEO Accession GSM2790426