SRX18508111 GSM6793326_r1 SRP411596 PRJNA909189 SRS15977198 GSM6793326 GSM6793326 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508112 GSM6793327_r1 SRP411596 PRJNA909189 SRS15977199 GSM6793327 GSM6793327 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508113 GSM6793328_r1 SRP411596 PRJNA909189 SRS15977200 GSM6793328 GSM6793328 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508114 GSM6793329_r1 SRP411596 PRJNA909189 SRS15977201 GSM6793329 GSM6793329 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508115 GSM6793330_r1 SRP411596 PRJNA909189 SRS15977202 GSM6793330 GSM6793330 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508116 GSM6793331_r1 SRP411596 PRJNA909189 SRS15977203 GSM6793331 GSM6793331 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508117 GSM6793332_r1 SRP411596 PRJNA909189 SRS15977204 GSM6793332 GSM6793332 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508118 GSM6793333_r1 SRP411596 PRJNA909189 SRS15977205 GSM6793333 GSM6793333 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508119 GSM6793334_r1 SRP411596 PRJNA909189 SRS15977206 GSM6793334 GSM6793334 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508120 GSM6793335_r1 SRP411596 PRJNA909189 SRS15977207 GSM6793335 GSM6793335 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508121 GSM6793336_r1 SRP411596 PRJNA909189 SRS15977208 GSM6793336 GSM6793336 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508122 GSM6793337_r1 SRP411596 PRJNA909189 SRS15977209 GSM6793337 GSM6793337 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508123 GSM6793338_r1 SRP411596 PRJNA909189 SRS15977210 GSM6793338 GSM6793338 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508124 GSM6793339_r1 SRP411596 PRJNA909189 SRS15977211 GSM6793339 GSM6793339 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508125 GSM6793340_r1 SRP411596 PRJNA909189 SRS15977212 GSM6793340 GSM6793340 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508126 GSM6793341_r1 SRP411596 PRJNA909189 SRS15977213 GSM6793341 GSM6793341 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508127 GSM6793342_r1 SRP411596 PRJNA909189 SRS15977214 GSM6793342 GSM6793342 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508128 GSM6793343_r1 SRP411596 PRJNA909189 SRS15977215 GSM6793343 GSM6793343 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508129 GSM6793344_r1 SRP411596 PRJNA909189 SRS15977216 GSM6793344 GSM6793344 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508130 GSM6793345_r1 SRP411596 PRJNA909189 SRS15977217 GSM6793345 GSM6793345 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508131 GSM6793346_r1 SRP411596 PRJNA909189 SRS15977218 GSM6793346 GSM6793346 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508132 GSM6793347_r1 SRP411596 PRJNA909189 SRS15977219 GSM6793347 GSM6793347 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508133 GSM6793348_r1 SRP411596 PRJNA909189 SRS15977220 GSM6793348 GSM6793348 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508134 GSM6793349_r1 SRP411596 PRJNA909189 SRS15977221 GSM6793349 GSM6793349 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508135 GSM6793350_r1 SRP411596 PRJNA909189 SRS15977222 GSM6793350 GSM6793350 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508136 GSM6793351_r1 SRP411596 PRJNA909189 SRS15977223 GSM6793351 GSM6793351 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000 SRX18508137 GSM6793352_r1 SRP411596 PRJNA909189 SRS15977224 GSM6793352 GSM6793352 RIP-Seq TRANSCRIPTOMIC other In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3' end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA. cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs. Illumina HiSeq 2000