Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape
Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcript...
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| Published in | Molecular cell Vol. 84; no. 8; pp. 1475 - 1495.e18 |
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| Main Authors | , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
18.04.2024
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| Subjects | |
| Online Access | Get full text |
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| Abstract | Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy.
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•SF3B1 oncogenic mutations reduce RNAPII gene-body elongation rate and promoter density•RNAPII elongation defect is linked to disruption of the early spliceosome assembly•Chromatin landscape is altered, rendering these functionally epigenetic disorders•Sin3/HDAC pathway can be therapeutically targeted in SF3B1 mutant disease
Boddu et al. reveal how common cancer-associated mutations in SF3B1, a core splicing factor, alter RNAPII transcription kinetics through impaired early spliceosome assembly. Transcription defects alter chromatin organization at gene promoters, which can be reversed by inhibiting the Sin3/HDAC complex, providing a potential therapeutic strategy. |
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| AbstractList | Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy.Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy. Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy. [Display omitted] •SF3B1 oncogenic mutations reduce RNAPII gene-body elongation rate and promoter density•RNAPII elongation defect is linked to disruption of the early spliceosome assembly•Chromatin landscape is altered, rendering these functionally epigenetic disorders•Sin3/HDAC pathway can be therapeutically targeted in SF3B1 mutant disease Boddu et al. reveal how common cancer-associated mutations in SF3B1, a core splicing factor, alter RNAPII transcription kinetics through impaired early spliceosome assembly. Transcription defects alter chromatin organization at gene promoters, which can be reversed by inhibiting the Sin3/HDAC complex, providing a potential therapeutic strategy. Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy. Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA Polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy. Boddu et. al reveal how common cancer associated mutations in SF3B1, a core splicing factor, alters RNAPII transcription kinetics through impaired early spliceosome assembly. Transcription defects alter chromatin organization at gene promoters which can be reversed by inhibiting the Sin3/HDAC complex, providing a potential therapeutic strategy. |
| Author | Chandhok, Namrata S. Ogawa, Seishi Lin, Haifan De La Peña Avalos, Bárbara Simon, Matthew D. Kupfer, Gary M. Nannya, Yasuhito Olazabal-Herrero, Anne Pillai, Manoj M. King, Darren Neugebauer, Karla M. Gupta, Abhishek K. Zimmer, Joshua T. Verma, Amit Neuenkirchen, Nils Dray, Eloise Boddu, Prajwal C. Roy, Rahul |
| AuthorAffiliation | 5. Department of Molecular Biophysics and Biochemistry, Yale University 2. Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA 4. Yale Stem Cell Center, Yale University School of Medicine 6. Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Florida, USA 9. Department of Oncology and Pediatrics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, USA 10. Division of Hemato-Oncology, Department of Medicine and Department of Developmental and Molecular Biology, Albert Einstein-Montefiore Cancer Center, New York, USA 8. Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan 7. Section of Hematology and Medical Oncology, Department of Internal Medicine and Rogel Cancer Center, University of Michigan Health, Ann Arbor, Michigan, USA 12. Department of Pathology, Yale University School of Medicine 11. Yale Center for R |
| AuthorAffiliation_xml | – name: 8. Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan – name: 11. Yale Center for RNA Science and Medicine, Yale University – name: 7. Section of Hematology and Medical Oncology, Department of Internal Medicine and Rogel Cancer Center, University of Michigan Health, Ann Arbor, Michigan, USA – name: 9. Department of Oncology and Pediatrics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, USA – name: 6. Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Florida, USA – name: 10. Division of Hemato-Oncology, Department of Medicine and Department of Developmental and Molecular Biology, Albert Einstein-Montefiore Cancer Center, New York, USA – name: 3. Department of Cell Biology, Yale University School of Medicine – name: 4. Yale Stem Cell Center, Yale University School of Medicine – name: 5. Department of Molecular Biophysics and Biochemistry, Yale University – name: 12. Department of Pathology, Yale University School of Medicine – name: 1. Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA – name: 2. Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA |
| Author_xml | – sequence: 1 givenname: Prajwal C. surname: Boddu fullname: Boddu, Prajwal C. organization: Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA – sequence: 2 givenname: Abhishek K. surname: Gupta fullname: Gupta, Abhishek K. organization: Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA – sequence: 3 givenname: Rahul surname: Roy fullname: Roy, Rahul organization: Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA – sequence: 4 givenname: Bárbara surname: De La Peña Avalos fullname: De La Peña Avalos, Bárbara organization: Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA – sequence: 5 givenname: Anne surname: Olazabal-Herrero fullname: Olazabal-Herrero, Anne organization: Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA – sequence: 6 givenname: Nils surname: Neuenkirchen fullname: Neuenkirchen, Nils organization: Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA – sequence: 7 givenname: Joshua T. surname: Zimmer fullname: Zimmer, Joshua T. organization: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA – sequence: 8 givenname: Namrata S. surname: Chandhok fullname: Chandhok, Namrata S. organization: Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA – sequence: 9 givenname: Darren surname: King fullname: King, Darren organization: Section of Hematology and Medical Oncology, Department of Internal Medicine and Rogel Cancer Center, University of Michigan Health, Ann Arbor, MI, USA – sequence: 10 givenname: Yasuhito surname: Nannya fullname: Nannya, Yasuhito organization: Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan – sequence: 11 givenname: Seishi surname: Ogawa fullname: Ogawa, Seishi organization: Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan – sequence: 12 givenname: Haifan surname: Lin fullname: Lin, Haifan organization: Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA – sequence: 13 givenname: Matthew D. surname: Simon fullname: Simon, Matthew D. organization: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA – sequence: 14 givenname: Eloise surname: Dray fullname: Dray, Eloise organization: Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA – sequence: 15 givenname: Gary M. surname: Kupfer fullname: Kupfer, Gary M. organization: Department of Oncology and Pediatrics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA – sequence: 16 givenname: Amit surname: Verma fullname: Verma, Amit organization: Division of Hemato-Oncology, Department of Medicine and Department of Developmental and Molecular Biology, Albert Einstein-Montefiore Cancer Center, New York, USA – sequence: 17 givenname: Karla M. surname: Neugebauer fullname: Neugebauer, Karla M. organization: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA – sequence: 18 givenname: Manoj M. surname: Pillai fullname: Pillai, Manoj M. email: manoj.pillai@yale.edu organization: Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/38521065$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1016/j.molcel.2006.10.030 10.1074/jbc.M105757200 10.1056/NEJMoa1103283 10.1016/j.molcel.2017.04.016 10.1016/j.molcel.2021.05.028 10.1038/nature04979 10.1101/sqb.2019.84.040402 10.1371/journal.pone.0166438 10.1182/blood.2021012652 10.1038/nbt.1754 10.1016/j.tig.2019.05.005 10.1016/j.molcel.2020.12.002 10.1126/science.abb5872 10.1101/gad.252106.114 10.1093/bioinformatics/bts635 10.1073/pnas.1419161111 10.1002/stem.2885 10.1038/s41586-022-05204-z 10.1101/gr.171405.113 10.1038/nrm.2017.63 10.1101/gad.291872.116 10.1093/bioinformatics/btt656 10.1186/s12859-020-03551-0 10.1038/ncomms10208 10.1016/j.cell.2010.10.004 10.1186/s13059-014-0550-8 10.1016/j.molcel.2019.07.037 10.1128/MCB.25.8.3305-3316.2005 10.1038/s43018-022-00384-z 10.1016/j.cell.2013.07.032 10.1038/s41588-021-00867-2 10.1182/blood-2014-04-522136 10.1038/s41586-019-1646-9 10.1101/gad.336024.119 10.1016/j.molcel.2010.01.026 10.1038/s41408-021-00584-3 10.1016/j.molcel.2022.09.001 10.1038/s41586-023-05780-8 10.1038/414929a 10.1093/bioinformatics/btw313 10.1073/pnas.1019736108 10.1016/j.molcel.2021.02.016 10.1261/rna.2192803 10.1016/j.ccell.2016.08.006 10.1186/s13072-020-00343-x 10.1016/j.cell.2019.08.055 10.1016/j.cell.2006.01.040 10.1074/jbc.M114.605816 10.1093/nar/gky1131 10.1080/10428194.2018.1452210 10.1038/nmeth.2019 10.14806/ej.17.1.200 10.1016/j.jbc.2023.104854 10.1002/cpcb.115 10.21769/BioProtoc.3035 10.1038/nmeth.1906 10.1038/s41375-020-0753-9 10.1038/onc.2016.279 10.1093/nar/gky797 10.1016/j.dnarep.2021.103182 10.1038/ng.1045 10.1093/nar/gkw257 10.1038/s41586-020-2344-3 10.1101/gr.204578.116 10.1016/j.celrep.2015.03.048 10.1038/s41576-019-0159-6 10.1186/s13072-019-0287-4 10.1128/MCB.00970-14 10.1038/s41596-019-0159-1 10.4161/nucl.29347 10.1038/s41467-020-17858-2 10.21769/BioProtoc.915 10.1371/journal.pbio.1001442 10.1038/s41588-018-0218-5 10.1101/cshperspect.a003707 10.1038/nature10496 10.1371/journal.pone.0063072 10.1016/j.molcel.2020.12.018 10.1038/nrc.2016.51 10.1101/gad.252103 10.1182/blood-2018-04-843771 10.1016/j.cell.2015.03.027 10.1038/nrm3943 10.7554/eLife.21856 10.1093/bioinformatics/btz232 10.1093/nar/gkn566 10.1093/bioinformatics/bty191 10.1101/gr.209601.116 10.1002/cpmb.128 10.1093/jmcb/mjy021 10.1038/nmeth.4396 10.1016/j.bbrc.2004.07.163 10.1016/j.molcel.2017.12.029 10.1038/nrm3417 10.1186/s12885-018-4580-6 10.1038/s41588-021-00828-9 10.1038/nmeth.1923 10.1126/science.abf1870 10.1002/0471142727.mb2701s63 10.1371/journal.pcbi.1004105 10.1083/jcb.202004079 10.1093/bioinformatics/btp352 10.1038/s41586-021-03789-5 10.1038/s41467-018-06063-x 10.1093/bioinformatics/btr026 10.1038/s41467-023-36489-x 10.1038/s41467-020-17503-y 10.1038/leu.2016.251 10.1016/j.celrep.2012.05.019 10.1038/nchembio.1859 10.1038/s41588-023-01460-5 10.1073/pnas.1506282112 10.21769/BioProtoc.2994 10.1111/febs.14700 10.1093/bioinformatics/btq033 10.1016/j.celrep.2020.108373 10.1080/21541264.2017.1281864 10.1016/j.molcel.2005.05.006 10.1016/j.molcel.2023.03.002 10.1038/mtm.2016.17 10.12688/f1000research.15931.1 10.1101/gr.253492.119 10.1073/pnas.2111703119 10.1016/j.molcel.2022.05.004 10.1101/gr.275193.120 10.1186/s13059-014-0554-4 10.1016/j.molcel.2014.01.017 10.1016/j.cell.2017.07.043 10.1016/j.molcel.2021.08.029 10.1038/nprot.2018.015 10.1038/s42003-021-02690-1 10.1074/jbc.RA118.006764 10.1093/jb/mvac049 10.1038/s41568-022-00541-7 10.1101/gr.192294.115 10.1007/978-1-4939-3578-9_16 10.1101/gad.1643208 10.1016/j.cell.2010.03.030 10.1101/pdb.prot5279 10.4161/cc.8.3.7701 10.1128/MCB.23.16.5768-5779.2003 10.1111/joim.13535 10.1038/nmeth.4582 10.1038/nature05541 10.1038/s41598-022-10188-x 10.1093/bioinformatics/btv562 10.1016/j.ccell.2015.04.006 |
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| Keywords | transcription co-transcriptional splicing DNA damage response WDR5 U2AF1 Sin3/HDAC spliceosome R-loops SF3B1 RNA polymerase II |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Author Contributions: PCB and MMP conceived and planned the study. PCB performed all the experiments with help for microscopy (AO), NGS experiments (AKG, RR), DNA fiber combing (BD, ED), in vitro splicing (RR, NN, HL), DNA replication (AO, GK) and TT-TL-seq analysis (JZ, MS). NC, DK, and AKV provided patient samples. YN and SO provided some patient RNA-seq files. PCB and MMP performed the bioinformatic analysis and wrote the manuscript. KMN provided input for the experimental design and analysis of long-read sequencing. MMP provided overall supervision for the project. |
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| References | Petryk, Kahli, d’Aubenton-Carafa, Jaszczyszyn, Shen, Silvain, Thermes, Chen, Hyrien (bib65) 2016; 7 Chen, Hu, Xia, Zhao, Li, Tyler (bib27) 2015; 36 Schmieder, Edwards (bib131) 2011; 27 Fong, Kim, Zhou, Ji, Qiu, Saldi, Diener, Jones, Fu, Bentley (bib6) 2014; 28 Gel, Díez-Villanueva, Serra, Buschbeck, Peinado, Malinverni (bib76) 2016; 32 Wiederschain, Wee, Chen, Loo, Yang, Huang, Chen, Caponigro, Yao, Lengauer (bib113) 2009; 8 Žumer, Maier, Farnung, Jaeger, Rus, Winter, Cramer (bib32) 2021; 81 Kim, Park, Jun, Lee, Jung, Kim (bib50) 2018; 41 Skene, Henikoff, Henikoff (bib152) 2018; 13 Inoue, Chew, Liu, Michel, Pangallo, D’Avino, Hitchman, North, Lee, Bitner (bib17) 2019; 574 Barbieri, Hill, Quesnel-Vallières, Zucco, Barash, Gardini (bib25) 2020; 33 Wang, Fan, Shliaha, Miele, Hendrickson, Jiang, Helin (bib79) 2023; 615 Rosa-Mercado, Zimmer, Apostolidi, Rinehart, Simon, Steitz (bib47) 2021; 81 Lin, Smith, Takahashi, Lai, Martin-Brown, Florens, Washburn, Conaway, Conaway, Shilatifard (bib67) 2010; 37 Stewart, Dykxhoorn, Palliser, Mizuno, Yu, An, Sabatini, Chen, Hahn, Sharp (bib112) 2003; 9 Zhao, Li, Qian, Liu, Fan, Liang, Hu, Wan (bib37) 2022; 172 Carey, Peterson, Smale (bib150) 2009; 2009 Clough, Pangallo, Sarchi, Ilagan, North, Bergantinos, Stolla, Naru, Nugent, Kim (bib15) 2022; 139 Promonet, Padioleau, Liu, Sanz, Biernacka, Schmitz, Skrzypczak, Sarrazin, Mettling, Rowicka (bib64) 2020; 11 Iwase, Januma, Miyamoto, Shono, Honda, Yanagisawa, Baba (bib90) 2004; 322 Meers, Tenenbaum, Henikoff (bib133) 2019; 12 Lacadie, Rosbash (bib9) 2005; 19 Loerch, Leach, Horner, Maji, Jenkins, Pulvino, Kielkopf (bib105) 2019; 294 Im, Rao, Sridhar, Bentley, Mishra, Chen, Hall, Graber, Zhang, Li (bib93) 2018; 59 Corces, Trevino, Hamilton, Greenside, Sinnott-Armstrong, Vesuna, Satpathy, Rubin, Montine, Wu (bib72) 2017; 14 Bland, Saville, Wai, Curnow, Muirhead, Nieminuszczy, Ravindran, John, Hedayat, Barker (bib106) 2023; 55 Tang, Rodriguez-Santiago, Wang, Pu, Yuste, Gupta, Moldón, Xu, Query (bib36) 2016; 30 Rahl, Lin, Seila, Flynn, McCuine, Burge, Sharp, Young (bib21) 2010; 141 Yu, Reed (bib43) 2015; 112 Chen, Deng (bib145) 2018; 8 Robinson, Thorvaldsdóttir, Winckler, Guttman, Lander, Getz, Mesirov (bib154) 2011; 29 Schep, Buenrostro, Denny, Schwartz, Sherlock, Greenleaf (bib73) 2015; 25 Fong, Saldi, Sheridan, Cortazar, Bentley (bib83) 2017; 66 Schofield, Duffy, Kiefer, Sullivan, Simon (bib26) 2018; 15 Love, Huber, Anders (bib126) 2014; 15 Le Martelot, Canella, Symul, Migliavacca, Gilardi, Liechti, Martin, Harshman, Delorenzi, Desvergne (bib81) 2012; 10 Hegazy, Cohen-Barak, Koetsier, Najor, Arvanitis, Sprecher, Green, Godsel (bib53) 2020; 89 Egan, Yuan, Craske, Labhart, Guler, Arnott, Maile, Busby, Henry, Kelly (bib151) 2016; 11 Smolka, Sanz, Hartono, Chédin (bib148) 2021; 220 Boddu, Gupta, Kim, Neugebauer, Waldman, Pillai (bib20) 2021; 4 Li, Xu, Xiao, Cong, Love, Zhang, Irizarry, Liu, Brown, Liu (bib138) 2014; 15 Pongor, Gross, Vera Alvarez, Murai, Jang, Zhang, Redon, Fu, Huang, Thakur (bib129) 2020; 13 Will, Lührmann (bib109) 2011; 3 Obeng, Chappell, Seiler, Chen, Campagna, Schmidt, Schneider, Lord, Wang, Gambe (bib99) 2016; 30 Kotovic, Lockshon, Boric, Neugebauer (bib10) 2003; 23 Kamieniarz-Gdula, Proudfoot (bib66) 2019; 35 Zhang, Aibara, Vos, Agafonov, Lührmann, Cramer (bib2) 2021; 371 Veloso, Kirkconnell, Magnuson, Biewen, Paulsen, Wilson, Ljungman (bib31) 2014; 24 Grebien, Vedadi, Getlik, Giambruno, Grover, Avellino, Skucha, Vittori, Kuznetsova, Smil (bib97) 2015; 11 Hu, Peng, Xu, Wang, Song, Chen (bib85) 2021; 81 Chathoth, Barrass, Webb, Beggs (bib103) 2014; 53 Feng, Lin, Deng, Ran, Yu, Xiang, Ye, Yao (bib8) 2023; 299 Stubbins, Karsan (bib108) 2021; 11 Segal, Fondufe-Mittendorf, Chen, Thåström, Field, Moore, Wang, Widom (bib74) 2006; 442 Duttke, Chang, Heinz, Benner (bib128) 2019; 29 Wickham (bib123) 2016 Hahne, Ivanek (bib122) 2016 Porrua, Libri (bib55) 2015; 16 Stovner, Sætrom (bib127) 2019; 35 Fong, Zhou (bib104) 2001; 414 Kizer, Phatnani, Shibata, Hall, Greenleaf, Strahl (bib84) 2005; 25 Hluchý, Gajdušková, Ruiz de los Mozos, Rájecký, Kluge, Berger, Slabá, Potěšil, Weiß, Ule (bib5) 2022; 609 Martin (bib117) 2011; 17 Castillo-Guzman, Chédin (bib61) 2021; 106 Sanz, Chédin (bib62) 2019; 14 Folco, Lei, Hsu, Reed (bib144) 2012; 64 Kesarwani, Ramirez, Gupta, Yang, Murthy, Minella, Pillai (bib24) 2017; 36 Booth, Wang, Cheung, Lis (bib30) 2016; 26 Lee, Das, Reed (bib40) 2003; 63 Fong, Sheridan, Ramachandran, Bentley (bib155) 2022; 82 Yang, Huang, Qiu, Liu, Zeng, Gao, Zheng, Hou, Wang, Yu (bib89) 2018; 10 Ventura, Kirsch, McLaughlin, Tuveson, Grimm, Lintault, Newman, Reczek, Weissleder, Jacks (bib100) 2007; 445 Stanley, Abdel-Wahab (bib101) 2022; 3 Bieberstein, Carrillo Oesterreich, Straube, Neugebauer (bib78) 2012; 2 Liao, Smyth, Shi (bib125) 2014; 30 Yoshida, Sanada, Shiraishi, Nowak, Nagata, Yamamoto, Sato, Sato-Otsubo, Kon, Nagasaki (bib12) 2011; 478 Caizzi, Monteiro-Martins, Schwalb, Lysakovskaia, Schmitzova, Sawicka, Chen, Lidschreiber, Cramer (bib4) 2021; 81 Dvinge, Kim, Abdel-Wahab, Bradley (bib14) 2016; 16 Parikh, Kim (bib75) 2013; 8 Inoue, Polaski, Taylor, Castel, Chen, Kobayashi, Hogg, Hayashi, Pineda, El Marabti (bib18) 2021; 53 Kfir, Lev-Maor, Glaich, Alajem, Datta, Sze, Meshorer, Ast (bib38) 2015; 11 Woll, Yoshizato, Hellström-Lindberg, Fioretos, Ebert, Jacobsen (bib107) 2022; 292 Saxena, Zou (bib57) 2022; 82 Kim, Bonifant, Bunz, Lane, Waldman (bib111) 2008; 36 Okamoto, Abe, Itaya, Tomida, Ishiai, Takaori-Kondo, Taoka, Isobe, Takata (bib56) 2019; 286 Ramírez, Ryan, Grüning, Bhardwaj, Kilpert, Richter, Heyne, Dündar, Manke (bib121) 2016; 44 Gu, Eils, Schlesner (bib137) 2016; 32 Muralimanoharan, Shamby, Stansbury, Schenken, de la Pena Avalos, Javanmardi, Dray, Sung, Boyer (bib58) 2022; 12 Bradley, Anczuków (bib102) 2023; 23 Bayona-Feliu, Barroso, Muñoz, Aguilera (bib147) 2021; 53 Herzel, Ottoz, Alpert, Neugebauer (bib3) 2017; 18 Castillo-Guzman, Hartono, Sanz, Chédin (bib46) 2020 Bapat, Keita, Martelly, Kang, Seet, Jacobsen, Stoilov, Hu, Crooks, Sharma (bib49) 2018; 36 Hahn, Scott (bib13) 2011; 44 Frascoli, Proietti, Grassi (bib141) 2012; 65 Yang, Bian, Zhan, Chen, Xing, Larsen, Zhang, Shi (bib35) 2023; 14 Meerbrey, Hu, Kessler, Roarty, Li, Fang, Herschkowitz, Burrows, Ciccia, Sun (bib114) 2011; 108 Gilchrist, Dos Santos, Fargo, Xie, Gao, Li, Adelman (bib70) 2010; 143 Li (bib132) 2018; 34 Zhang, Will, Bertram, Dybkov, Hartmuth, Agafonov, Hofele, Urlaub, Kastner, Lührmann (bib34) 2020; 583 Hamperl, Bocek, Saldivar, Swigut, Cimprich (bib63) 2017; 170 Skene, Henikoff (bib77) 2017; 6 Wu, Kabalane, Kahli, Petryk, Laperrousaz, Jaszczyszyn, Drillon, Nicolini, Perot, Robert (bib140) 2018; 46 Schindelin, Arganda-Carreras, Frise, Kaynig, Longair, Pietzsch, Preibisch, Rueden, Saalfeld, Schmid (bib139) 2012; 9 Shiozawa, Malcovati, Gallì, Sato-Otsubo, Kataoka, Sato, Watatani, Suzuki, Yoshizato, Yoshida (bib94) 2018; 9 Mupo, Seiler, Sathiaseelan, Pance, Yang, Agrawal, Iorio, Bautista, Pacharne, Tzelepis (bib110) 2017; 31 Li, Liu, Chen, Chen (bib42) 2018; 9 Neilsen, Chakraborty, McCall, Frodyma, Sleightholm, Fisher, Lewis (bib98) 2018; 18 Zhang, Park, Bennett, Thornton, Kim (bib134) 2021; 31 Papaemmanuil, Cazzola, Boultwood, Malcovati, Vyas, Bowen, Pellagatti, Wainscoat, Hellstrom-Lindberg, Gambacorti-Passerini (bib11) 2011; 365 Moffat, Grueneberg, Yang, Kim, Kloepfer, Hinkle, Piqani, Eisenhaure, Luo, Grenier (bib115) 2006; 124 Wingett, Andrews (bib116) 2018; 7 Roth, Heinz, Benner (bib135) 2020; 21 Reppas, Wade, Church, Struhl (bib22) 2006; 24 Bowman, Kelly (bib23) 2014; 5 Chen, Chen, Huang, Gu, Qiu, Qian, Shao, Zhang, Hu, Li (bib48) 2018; 69 Kim, Ilagan, Liang, Daubner, Lee, Ramakrishnan, Li, Chung, Micol, Murphy (bib19) 2015; 27 Nojima, Gomes, Grosso, Kimura, Dye, Dhir, Carmo-Fonseca, Proudfoot (bib44) 2015; 161 Bejar, Steensma (bib96) 2014; 124 Reimer, Neugebauer (bib28) 2020; 133 Baldwin, Morris, Mukherjee (bib153) 2021; 1 Reimer, Mimoso, Adelman, Neugebauer (bib1) 2021; 81 Lam, Kong, Huang, Vu Han, Maffa, Kasper, Yaffe (bib149) 2020; 11 Fujinaga, Luo, Schaufele, Peterlin (bib41) 2015; 290 Smith, Heger, Sudbery (bib136) 2017; 27 Quinlan, Hall (bib130) 2010; 26 Dobin, Davis, Schlesinger, Drenkow, Zaleski, Jha, Batut, Chaisson, Gingeras (bib119) 2013; 29 García-Muse, Aguilera (bib52) 2019; 179 Flomerfelt, Gress (bib59) 2016 Mas, Blanco, Ballaré, Sansó, Spill, Hu, Aoi, Le Dily, Shilatifard, Marti-Renom (bib82) 2018; 50 Merten, Hebben, Bovolenta (bib142) 2016; 3 Zatreanu, Han, Mitter, Tumini, Williams, Gregersen, Dirac-Svejstrup, Roma, Stewart, Aguilera (bib60) 2019; 76 Shen, Park, Lu, Lin, Henry, Wu, Zhou, Xing (bib124) 2014; 111 Pérez-Calero, Bayona-Feliu, Xue, Barroso, Muñoz, González-Basallote, Sung, Aguilera (bib54) 2020; 34 Langmead, Salzberg (bib118) 2012; 9 Zheng, Qi, Hu, Cao, Xu, Yin, Chen, Li, Liu, Li (bib69) 2020; 370 Gillotin (bib143) 2018; 8 Wang, Chivu, Choate, Rice, Miller, Chu, Chou, Kingsley, Petersen, Finno (bib80) 2020 Mimoso, Adelman (bib7) 2023; 83 Lieu, Liu, Ali, Wei, Penson, Zhang, An, Rabadan, Raza, Manley (bib16) 2022; 119 Carrocci, Neugebauer (bib39) 2019; 84 Ehrensberger, Kelly, Svejstrup (bib29) 2013; 154 Singh, Ahmed, Dolatshad, Tatwavedi, Schulze, Sanchi, Ryley, Dhir, Carpenter, Watt (bib51) 2020; 34 Gilchrist, Nechaev, Lee, Ghosh, Collins, Li, Gilmour, Adelman (bib71) 2008; 22 Pellagatti, Armstrong, Steeples, Sharma, Repapi, Singh, Sanchi, Radujkovic, Horn, Dolatshad (bib95) 2018; 132 Boutet-Robinet, Trouche, Canitrot (bib146) 2013; 3 Zhang, Rigo, Dybkov, Fourmann, Will, Kumar, Urlaub, Stark, Lührmann (bib33) 2021; 596 Li, Handsaker, Wysoker, Fennell, Ruan, Homer, Marth, Abecasis, Durbin (bib120) 2009; 25 Luo, Lin, Shilatifard (bib68) 2012; 13 Wysocka, Myers, Laherty, Eisenman, Herr (bib88) 2003; 17 Gori, Divieti, Demay (bib91) 2001; 276 Ernst, Kellis (bib86) 2012; 9 DeBoever, Ghia, Shepard, Rassenti, Barrett, Jepsen, Jamieson, Carson, Kipps, Frazer (bib92) 2015; 11 Szklarczyk, Gable, Lyon, Junge, Wyder, Huerta-Cepas, Simonovic, Doncheva, Morris, Bork (bib87) 2019; 47 Wissink, Vihervaara, Tippens, Lis (bib45) 2019; 20 Herzel (10.1016/j.molcel.2024.02.032_bib3) 2017; 18 Saxena (10.1016/j.molcel.2024.02.032_bib57) 2022; 82 Wang (10.1016/j.molcel.2024.02.032_bib79) 2023; 615 Im (10.1016/j.molcel.2024.02.032_bib93) 2018; 59 Zhang (10.1016/j.molcel.2024.02.032_bib134) 2021; 31 Martin (10.1016/j.molcel.2024.02.032_bib117) 2011; 17 Ramírez (10.1016/j.molcel.2024.02.032_bib121) 2016; 44 Hluchý (10.1016/j.molcel.2024.02.032_bib5) 2022; 609 Lacadie (10.1016/j.molcel.2024.02.032_bib9) 2005; 19 Yoshida (10.1016/j.molcel.2024.02.032_bib12) 2011; 478 Lam (10.1016/j.molcel.2024.02.032_bib149) 2020; 11 Singh (10.1016/j.molcel.2024.02.032_bib51) 2020; 34 Meerbrey (10.1016/j.molcel.2024.02.032_bib114) 2011; 108 Baldwin (10.1016/j.molcel.2024.02.032_bib153) 2021; 1 Bowman (10.1016/j.molcel.2024.02.032_bib23) 2014; 5 Zhao (10.1016/j.molcel.2024.02.032_bib37) 2022; 172 Porrua (10.1016/j.molcel.2024.02.032_bib55) 2015; 16 Reimer (10.1016/j.molcel.2024.02.032_bib1) 2021; 81 Fong (10.1016/j.molcel.2024.02.032_bib83) 2017; 66 Schindelin (10.1016/j.molcel.2024.02.032_bib139) 2012; 9 Bieberstein (10.1016/j.molcel.2024.02.032_bib78) 2012; 2 Mas (10.1016/j.molcel.2024.02.032_bib82) 2018; 50 Boddu (10.1016/j.molcel.2024.02.032_bib20) 2021; 4 Booth (10.1016/j.molcel.2024.02.032_bib30) 2016; 26 Fujinaga (10.1016/j.molcel.2024.02.032_bib41) 2015; 290 Obeng (10.1016/j.molcel.2024.02.032_bib99) 2016; 30 Iwase (10.1016/j.molcel.2024.02.032_bib90) 2004; 322 Schep (10.1016/j.molcel.2024.02.032_bib73) 2015; 25 Clough (10.1016/j.molcel.2024.02.032_bib15) 2022; 139 Grebien (10.1016/j.molcel.2024.02.032_bib97) 2015; 11 Hahn (10.1016/j.molcel.2024.02.032_bib13) 2011; 44 Wysocka (10.1016/j.molcel.2024.02.032_bib88) 2003; 17 Zhang (10.1016/j.molcel.2024.02.032_bib2) 2021; 371 Loerch (10.1016/j.molcel.2024.02.032_bib105) 2019; 294 Chen (10.1016/j.molcel.2024.02.032_bib48) 2018; 69 Schofield (10.1016/j.molcel.2024.02.032_bib26) 2018; 15 Li (10.1016/j.molcel.2024.02.032_bib120) 2009; 25 Gilchrist (10.1016/j.molcel.2024.02.032_bib70) 2010; 143 Fong (10.1016/j.molcel.2024.02.032_bib6) 2014; 28 Chathoth (10.1016/j.molcel.2024.02.032_bib103) 2014; 53 Petryk (10.1016/j.molcel.2024.02.032_bib65) 2016; 7 Yang (10.1016/j.molcel.2024.02.032_bib89) 2018; 10 Yu (10.1016/j.molcel.2024.02.032_bib43) 2015; 112 Fong (10.1016/j.molcel.2024.02.032_bib155) 2022; 82 Lin (10.1016/j.molcel.2024.02.032_bib67) 2010; 37 Ernst (10.1016/j.molcel.2024.02.032_bib86) 2012; 9 Chen (10.1016/j.molcel.2024.02.032_bib145) 2018; 8 Bland (10.1016/j.molcel.2024.02.032_bib106) 2023; 55 Sanz (10.1016/j.molcel.2024.02.032_bib62) 2019; 14 Love (10.1016/j.molcel.2024.02.032_bib126) 2014; 15 Pellagatti (10.1016/j.molcel.2024.02.032_bib95) 2018; 132 Kamieniarz-Gdula (10.1016/j.molcel.2024.02.032_bib66) 2019; 35 Folco (10.1016/j.molcel.2024.02.032_bib144) 2012; 64 Mimoso (10.1016/j.molcel.2024.02.032_bib7) 2023; 83 Rahl (10.1016/j.molcel.2024.02.032_bib21) 2010; 141 Luo (10.1016/j.molcel.2024.02.032_bib68) 2012; 13 Carey (10.1016/j.molcel.2024.02.032_bib150) 2009; 2009 Žumer (10.1016/j.molcel.2024.02.032_bib32) 2021; 81 Wissink (10.1016/j.molcel.2024.02.032_bib45) 2019; 20 Zhang (10.1016/j.molcel.2024.02.032_bib34) 2020; 583 Carrocci (10.1016/j.molcel.2024.02.032_bib39) 2019; 84 Papaemmanuil (10.1016/j.molcel.2024.02.032_bib11) 2011; 365 Smith (10.1016/j.molcel.2024.02.032_bib136) 2017; 27 Skene (10.1016/j.molcel.2024.02.032_bib152) 2018; 13 Segal (10.1016/j.molcel.2024.02.032_bib74) 2006; 442 Merten (10.1016/j.molcel.2024.02.032_bib142) 2016; 3 Gillotin (10.1016/j.molcel.2024.02.032_bib143) 2018; 8 Neilsen (10.1016/j.molcel.2024.02.032_bib98) 2018; 18 Inoue (10.1016/j.molcel.2024.02.032_bib17) 2019; 574 Egan (10.1016/j.molcel.2024.02.032_bib151) 2016; 11 Shen (10.1016/j.molcel.2024.02.032_bib124) 2014; 111 Stanley (10.1016/j.molcel.2024.02.032_bib101) 2022; 3 Smolka (10.1016/j.molcel.2024.02.032_bib148) 2021; 220 Zatreanu (10.1016/j.molcel.2024.02.032_bib60) 2019; 76 Le Martelot (10.1016/j.molcel.2024.02.032_bib81) 2012; 10 Lee (10.1016/j.molcel.2024.02.032_bib40) 2003; 63 Bayona-Feliu (10.1016/j.molcel.2024.02.032_bib147) 2021; 53 Barbieri (10.1016/j.molcel.2024.02.032_bib25) 2020; 33 Kizer (10.1016/j.molcel.2024.02.032_bib84) 2005; 25 Quinlan (10.1016/j.molcel.2024.02.032_bib130) 2010; 26 Boutet-Robinet (10.1016/j.molcel.2024.02.032_bib146) 2013; 3 García-Muse (10.1016/j.molcel.2024.02.032_bib52) 2019; 179 Pérez-Calero (10.1016/j.molcel.2024.02.032_bib54) 2020; 34 Wiederschain (10.1016/j.molcel.2024.02.032_bib113) 2009; 8 Hamperl (10.1016/j.molcel.2024.02.032_bib63) 2017; 170 Lieu (10.1016/j.molcel.2024.02.032_bib16) 2022; 119 Bradley (10.1016/j.molcel.2024.02.032_bib102) 2023; 23 Tang (10.1016/j.molcel.2024.02.032_bib36) 2016; 30 Zheng (10.1016/j.molcel.2024.02.032_bib69) 2020; 370 Skene (10.1016/j.molcel.2024.02.032_bib77) 2017; 6 Nojima (10.1016/j.molcel.2024.02.032_bib44) 2015; 161 Szklarczyk (10.1016/j.molcel.2024.02.032_bib87) 2019; 47 Reimer (10.1016/j.molcel.2024.02.032_bib28) 2020; 133 Langmead (10.1016/j.molcel.2024.02.032_bib118) 2012; 9 Li (10.1016/j.molcel.2024.02.032_bib138) 2014; 15 Reppas (10.1016/j.molcel.2024.02.032_bib22) 2006; 24 Moffat (10.1016/j.molcel.2024.02.032_bib115) 2006; 124 Gel (10.1016/j.molcel.2024.02.032_bib76) 2016; 32 Wu (10.1016/j.molcel.2024.02.032_bib140) 2018; 46 Ehrensberger (10.1016/j.molcel.2024.02.032_bib29) 2013; 154 Bejar (10.1016/j.molcel.2024.02.032_bib96) 2014; 124 Ventura (10.1016/j.molcel.2024.02.032_bib100) 2007; 445 Okamoto (10.1016/j.molcel.2024.02.032_bib56) 2019; 286 Rosa-Mercado (10.1016/j.molcel.2024.02.032_bib47) 2021; 81 Corces (10.1016/j.molcel.2024.02.032_bib72) 2017; 14 Bapat (10.1016/j.molcel.2024.02.032_bib49) 2018; 36 Hegazy (10.1016/j.molcel.2024.02.032_bib53) 2020; 89 Woll (10.1016/j.molcel.2024.02.032_bib107) 2022; 292 Kim (10.1016/j.molcel.2024.02.032_bib19) 2015; 27 Schmieder (10.1016/j.molcel.2024.02.032_bib131) 2011; 27 Liao (10.1016/j.molcel.2024.02.032_bib125) 2014; 30 Hu (10.1016/j.molcel.2024.02.032_bib85) 2021; 81 Robinson (10.1016/j.molcel.2024.02.032_bib154) 2011; 29 Kfir (10.1016/j.molcel.2024.02.032_bib38) 2015; 11 Kesarwani (10.1016/j.molcel.2024.02.032_bib24) 2017; 36 Gu (10.1016/j.molcel.2024.02.032_bib137) 2016; 32 Muralimanoharan (10.1016/j.molcel.2024.02.032_bib58) 2022; 12 Will (10.1016/j.molcel.2024.02.032_bib109) 2011; 3 Parikh (10.1016/j.molcel.2024.02.032_bib75) 2013; 8 Fong (10.1016/j.molcel.2024.02.032_bib104) 2001; 414 Stovner (10.1016/j.molcel.2024.02.032_bib127) 2019; 35 Roth (10.1016/j.molcel.2024.02.032_bib135) 2020; 21 Meers (10.1016/j.molcel.2024.02.032_bib133) 2019; 12 Li (10.1016/j.molcel.2024.02.032_bib42) 2018; 9 Stubbins (10.1016/j.molcel.2024.02.032_bib108) 2021; 11 Chen (10.1016/j.molcel.2024.02.032_bib27) 2015; 36 Pongor (10.1016/j.molcel.2024.02.032_bib129) 2020; 13 Zhang (10.1016/j.molcel.2024.02.032_bib33) 2021; 596 Hahne (10.1016/j.molcel.2024.02.032_bib122) 2016 Wingett (10.1016/j.molcel.2024.02.032_bib116) 2018; 7 Caizzi (10.1016/j.molcel.2024.02.032_bib4) 2021; 81 Dvinge (10.1016/j.molcel.2024.02.032_bib14) 2016; 16 Gilchrist (10.1016/j.molcel.2024.02.032_bib71) 2008; 22 Gori (10.1016/j.molcel.2024.02.032_bib91) 2001; 276 Li (10.1016/j.molcel.2024.02.032_bib132) 2018; 34 Stewart (10.1016/j.molcel.2024.02.032_bib112) 2003; 9 Castillo-Guzman (10.1016/j.molcel.2024.02.032_bib61) 2021; 106 Wickham (10.1016/j.molcel.2024.02.032_bib123) 2016 Veloso (10.1016/j.molcel.2024.02.032_bib31) 2014; 24 Flomerfelt (10.1016/j.molcel.2024.02.032_bib59) 2016 Shiozawa (10.1016/j.molcel.2024.02.032_bib94) 2018; 9 Duttke (10.1016/j.molcel.2024.02.032_bib128) 2019; 29 Wang (10.1016/j.molcel.2024.02.032_bib80) 2020 Kim (10.1016/j.molcel.2024.02.032_bib111) 2008; 36 Frascoli (10.1016/j.molcel.2024.02.032_bib141) 2012; 65 Feng (10.1016/j.molcel.2024.02.032_bib8) 2023; 299 Yang (10.1016/j.molcel.2024.02.032_bib35) 2023; 14 Castillo-Guzman (10.1016/j.molcel.2024.02.032_bib46) 2020 DeBoever (10.1016/j.molcel.2024.02.032_bib92) 2015; 11 Mupo (10.1016/j.molcel.2024.02.032_bib110) 2017; 31 Kotovic (10.1016/j.molcel.2024.02.032_bib10) 2003; 23 Kim (10.1016/j.molcel.2024.02.032_bib50) 2018; 41 Inoue (10.1016/j.molcel.2024.02.032_bib18) 2021; 53 Dobin (10.1016/j.molcel.2024.02.032_bib119) 2013; 29 Promonet (10.1016/j.molcel.2024.02.032_bib64) 2020; 11 36891287 - bioRxiv. 2023 Feb 26:2023.02.25.530019. doi: 10.1101/2023.02.25.530019. |
| References_xml | – volume: 25 start-page: 3305 year: 2005 end-page: 3316 ident: bib84 article-title: A Novel Domain in Set2 Mediates RNA Polymerase II Interaction and Couples Histone H3 K36 Methylation with Transcript Elongation publication-title: Mol. Cell. Biol. – volume: 478 start-page: 64 year: 2011 end-page: 69 ident: bib12 article-title: Frequent pathway mutations of splicing machinery in myelodysplasia publication-title: Nature – volume: 31 start-page: 720 year: 2017 end-page: 727 ident: bib110 article-title: Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts publication-title: Leukemia – volume: 25 start-page: 1757 year: 2015 end-page: 1770 ident: bib73 article-title: Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions publication-title: Genome Res. – volume: 17 start-page: 896 year: 2003 end-page: 911 ident: bib88 article-title: Human Sin3 deacetylase and trithorax-related Set1/Ash2 histone H3-K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1 publication-title: Genes Dev. – volume: 2009 year: 2009 ident: bib150 article-title: Chromatin Immunoprecipitation (ChIP) publication-title: Cold Spring Harb. Protoc. – volume: 18 start-page: 637 year: 2017 end-page: 650 ident: bib3 article-title: Splicing and transcription touch base: co-transcriptional spliceosome assembly and function publication-title: Nat. Rev. Mol. Cell Biol. – volume: 414 start-page: 929 year: 2001 end-page: 933 ident: bib104 article-title: Stimulatory effect of splicing factors on transcriptional elongation publication-title: Nature – volume: 106 start-page: 103182 year: 2021 ident: bib61 article-title: Defining R-loop classes and their contributions to genome instability publication-title: DNA Repair – volume: 8 start-page: 8 year: 2018 ident: bib145 article-title: Cell Synchronization by Double Thymidine Block publication-title: Bio Protoc. – volume: 36 start-page: 1663 year: 2018 end-page: 1675 ident: bib49 article-title: Myeloid Disease Mutations of Splicing Factor SRSF2 Cause G2-M Arrest and Skewed Differentiation of Human Hematopoietic Stem and Progenitor Cells publication-title: Stem Cells – volume: 179 start-page: 604 year: 2019 end-page: 618 ident: bib52 article-title: R Loops: From Physiological to Pathological Roles publication-title: Cell – volume: 20 start-page: 705 year: 2019 end-page: 723 ident: bib45 article-title: Nascent RNA analyses: tracking transcription and its regulation publication-title: Nat. Rev. Genet. – volume: 442 start-page: 772 year: 2006 end-page: 778 ident: bib74 article-title: A genomic code for nucleosome positioning publication-title: Nature – volume: 9 start-page: 215 year: 2012 end-page: 216 ident: bib86 article-title: ChromHMM: automating chromatin-state discovery and characterization publication-title: Nat. Methods – volume: 21 start-page: 214 year: 2020 ident: bib135 article-title: ARTDeco: automatic readthrough transcription detection publication-title: BMC Bioinformatics – volume: 84 start-page: 11 year: 2019 end-page: 20 ident: bib39 article-title: Pre-mRNA Splicing in the Nuclear Landscape publication-title: Cold Spring Harb. Symp. Quant. Biol. – volume: 22 start-page: 1921 year: 2008 end-page: 1933 ident: bib71 article-title: NELF-mediated stalling of RNAPII can enhance gene expression by blocking promoter-proximal nucleosome assembly publication-title: Genes Dev. – volume: 322 start-page: 601 year: 2004 end-page: 608 ident: bib90 article-title: Characterization of BHC80 in BRAF–HDAC complex, involved in neuron-specific gene repression publication-title: Biochem. Biophys. Res. Commun. – volume: 81 start-page: 4425 year: 2021 end-page: 4439.e6 ident: bib85 article-title: SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape publication-title: Mol. Cell – volume: 8 year: 2013 ident: bib75 article-title: The Effect of an Intervening Promoter Nucleosome on Gene Expression publication-title: PLoS ONE – volume: 33 start-page: 108373 year: 2020 ident: bib25 article-title: Rapid and Scalable Profiling of Nascent RNA with fastGRO publication-title: Cell Rep. – volume: 10 start-page: 285 year: 2018 end-page: 301 ident: bib89 article-title: LSD1 coordinates with the SIN3A/HDAC complex and maintains sensitivity to chemotherapy in breast cancer publication-title: J. Mol. Cell Biol. – volume: 112 start-page: 8608 year: 2015 end-page: 8613 ident: bib43 article-title: FUS functions in coupling transcription to splicing by mediating an interaction between RNAP II and U1snRNP publication-title: Proc. Natl. Acad. Sci. USA – volume: 17 start-page: 10 year: 2011 ident: bib117 article-title: Cutadapt removes adapter sequences from high-throughput sequencing reads publication-title: EMBnet J. – volume: 59 start-page: 2952 year: 2018 end-page: 2962 ident: bib93 article-title: Distinct transcriptomic and exomic abnormalities within myelodysplastic syndrome marrow cells publication-title: Leuk. Lymphoma – volume: 124 start-page: 2793 year: 2014 end-page: 2803 ident: bib96 article-title: Recent developments in myelodysplastic syndromes publication-title: Blood – volume: 12 start-page: 42 year: 2019 ident: bib133 article-title: Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling publication-title: Epigenetics Chromatin – volume: 69 start-page: 412 year: 2018 end-page: 425.e6 ident: bib48 article-title: The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations publication-title: Mol. Cell – volume: 11 year: 2015 ident: bib92 article-title: Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers publication-title: PLoS Comput. Biol. – volume: 55 start-page: 1311 year: 2023 end-page: 1323 ident: bib106 article-title: SF3B1 hotspot mutations confer sensitivity to PARP inhibition by eliciting a defective replication stress response publication-title: Nat. Genet. – volume: 23 start-page: 5768 year: 2003 end-page: 5779 ident: bib10 article-title: Cotranscriptional Recruitment of the U1snRNP to Intron-Containing Genes in Yeast publication-title: Mol. Cell. Biol. – volume: 14 start-page: 897 year: 2023 ident: bib35 article-title: Mechanisms of the RNA helicases DDX42 and DDX46 in human U2snRNP assembly publication-title: Nat. Commun. – volume: 16 start-page: 190 year: 2015 end-page: 202 ident: bib55 article-title: Transcription termination and the control of the transcriptome: why, where and how to stop publication-title: Nat. Rev. Mol. Cell Biol. – volume: 615 start-page: 339 year: 2023 end-page: 348 ident: bib79 article-title: H3K4me3 regulates RNA polymerase II promoter-proximal pause-release publication-title: Nature – volume: 53 start-page: 779 year: 2014 end-page: 790 ident: bib103 article-title: A Splicing-Dependent Transcriptional Checkpoint Associated with Prespliceosome Formation publication-title: Mol. Cell – volume: 9 start-page: 493 year: 2003 end-page: 501 ident: bib112 article-title: Lentivirus-delivered stable gene silencing by RNAi in primary cells publication-title: RNA – volume: 31 start-page: 1290 year: 2021 end-page: 1295 ident: bib134 article-title: Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N publication-title: Genome Res. – volume: 34 start-page: 3094 year: 2018 end-page: 3100 ident: bib132 article-title: Minimap2: pairwise alignment for nucleotide sequences publication-title: Bioinformatics – volume: 26 start-page: 799 year: 2016 end-page: 811 ident: bib30 article-title: Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast publication-title: Genome Res. – volume: 371 start-page: 305 year: 2021 end-page: 309 ident: bib2 article-title: Structure of a transcribing RNA polymerase II–U1snRNP complex publication-title: Science – volume: 133 start-page: e128 year: 2020 ident: bib28 article-title: Preparation of Mammalian Nascent RNA for Long Read Sequencing publication-title: Curr. Protoc. Mol. Biol. – volume: 111 start-page: E5593 year: 2014 end-page: E5601 ident: bib124 article-title: rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data publication-title: Proc. Natl. Acad. Sci. USA – volume: 596 start-page: 296 year: 2021 end-page: 300 ident: bib33 article-title: Structural insights into how Prp5 proofreads the pre-mRNA branch site publication-title: Nature – volume: 30 start-page: 404 year: 2016 end-page: 417 ident: bib99 article-title: Physiologic Expression of Sf3b1 K700E Causes Impaired Erythropoiesis, Aberrant Splicing, and Sensitivity to Therapeutic Spliceosome Modulation publication-title: Cancer Cell – volume: 34 start-page: 898 year: 2020 end-page: 912 ident: bib54 article-title: UAP56/DDX39B is a major cotranscriptional RNA–DNA helicase that unwinds harmful R loops genome-wide publication-title: Genes Dev. – volume: 29 start-page: 24 year: 2011 end-page: 26 ident: bib154 article-title: Integrative genomics viewer publication-title: Nat. Biotechnol. – volume: 66 start-page: 546 year: 2017 end-page: 557.e3 ident: bib83 article-title: RNA RNAPII Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction publication-title: Mol. Cell – volume: 4 start-page: 1184 year: 2021 ident: bib20 article-title: Generation of scalable cancer models by combining AAV-intron-trap, CRISPR/Cas9, and inducible Cre-recombinase publication-title: Commun. Biol. – volume: 108 start-page: 3665 year: 2011 end-page: 3670 ident: bib114 article-title: The pINDUCER lentiviral toolkit for inducible RNA interference in vitro and in vivo publication-title: Proc. Natl. Acad. Sci. USA – volume: 27 start-page: 617 year: 2015 end-page: 630 ident: bib19 article-title: SRSF2 Mutations Contribute to Myelodysplasia by Mutant-Specific Effects on Exon Recognition publication-title: Cancer Cell – volume: 37 start-page: 429 year: 2010 end-page: 437 ident: bib67 article-title: AFF4, a Component of the ELL/P-TEFb Elongation Complex and a Shared Subunit of MLL Chimeras, Can Link Transcription Elongation to Leukemia publication-title: Mol. Cell – start-page: 211 year: 2016 end-page: 220 ident: bib59 article-title: Analysis of Cell Proliferation and Homeostasis Using EdU Labeling publication-title: T-Cell Development Methods in Molecular Biology – volume: 276 start-page: 46515 year: 2001 end-page: 46522 ident: bib91 article-title: Cloning and Characterization of a Novel WD-40 Repeat Protein That Dramatically Accelerates Osteoblastic Differentiation publication-title: J. Biol. Chem. – volume: 132 start-page: 1225 year: 2018 end-page: 1240 ident: bib95 article-title: Impact of spliceosome mutations on RNA splicing in myelodysplasia: dysregulated genes/pathways and clinical associations publication-title: Blood – volume: 14 start-page: 959 year: 2017 end-page: 962 ident: bib72 article-title: An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues publication-title: Nat. Methods – volume: 1 year: 2021 ident: bib153 article-title: An Easy, Cost-Effective, and Scalable Method to Deplete Human Ribosomal RNA for RNA-seq publication-title: Curr. Protoc. – volume: 143 start-page: 540 year: 2010 end-page: 551 ident: bib70 article-title: Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation publication-title: Cell – volume: 9 start-page: 357 year: 2012 end-page: 359 ident: bib118 article-title: Fast gapped-read alignment with Bowtie 2 publication-title: Nat. Methods – volume: 286 start-page: 139 year: 2019 end-page: 150 ident: bib56 article-title: FANCD 2 protects genome stability by recruiting RNA processing enzymes to resolve R-loops during mild replication stress publication-title: FEBS J. – volume: 35 start-page: 4392 year: 2019 end-page: 4393 ident: bib127 article-title: epic2 efficiently finds diffuse domains in ChIP-seq data publication-title: Bioinformatics – year: 2016 ident: bib123 article-title: ggplot2: Elegant Graphics for Data Analysis – volume: 9 start-page: 676 year: 2012 end-page: 682 ident: bib139 article-title: Fiji: an open-source platform for biological-image analysis publication-title: Nat. Methods – volume: 35 start-page: 553 year: 2019 end-page: 564 ident: bib66 article-title: Transcriptional Control by Premature Termination: A Forgotten Mechanism publication-title: Trends Genet. – volume: 370 start-page: eabb5872 year: 2020 ident: bib69 article-title: Identification of Integrator-PP2A complex (INTAC), an RNA polymerase II phosphatase publication-title: Science – volume: 6 year: 2017 ident: bib77 article-title: An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites publication-title: eLife – volume: 11 year: 2016 ident: bib151 article-title: An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition publication-title: PLoS ONE – volume: 11 start-page: 3940 year: 2020 ident: bib64 article-title: Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites publication-title: Nat. Commun. – volume: 13 start-page: 543 year: 2012 end-page: 547 ident: bib68 article-title: The super elongation complex (SEC) family in transcriptional control publication-title: Nat. Rev. Mol. Cell Biol. – volume: 290 start-page: 1829 year: 2015 end-page: 1836 ident: bib41 article-title: Visualization of Positive Transcription Elongation Factor b (P-TEFb) Activation in Living Cells publication-title: J. Biol. Chem. – volume: 9 start-page: 3649 year: 2018 ident: bib94 article-title: Aberrant splicing and defective mRNA production induced by somatic spliceosome mutations in myelodysplasia publication-title: Nat. Commun. – volume: 82 start-page: 2298 year: 2022 end-page: 2314 ident: bib57 article-title: Hallmarks of DNA replication stress publication-title: Mol. Cell – start-page: 335 year: 2016 end-page: 351 ident: bib122 article-title: Visualizing Genomic Data Using Gviz and Bioconductor publication-title: Statistical Genomics Methods in Molecular Biology – volume: 29 start-page: 1836 year: 2019 end-page: 1846 ident: bib128 article-title: Identification and dynamic quantification of regulatory elements using total RNA publication-title: Genome Res. – volume: 3 start-page: 3 year: 2013 ident: bib146 article-title: Neutral comet assay publication-title: Bio Protoc. – volume: 15 start-page: 554 year: 2014 ident: bib138 article-title: MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens publication-title: Genome Biol. – volume: 76 start-page: 57 year: 2019 end-page: 69.e9 ident: bib60 article-title: Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome Stability publication-title: Mol. Cell – volume: 5 start-page: 224 year: 2014 end-page: 236 ident: bib23 article-title: RNA Polymerase II transcription elongation and RNAPII CTD Ser2 phosphorylation: A tail of two kinases publication-title: Nucleus – volume: 15 start-page: 221 year: 2018 end-page: 225 ident: bib26 article-title: TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding publication-title: Nat. Methods – volume: 7 start-page: 10208 year: 2016 ident: bib65 article-title: Replication landscape of the human genome publication-title: Nat. Commun. – volume: 299 start-page: 104854 year: 2023 ident: bib8 article-title: The U1 antisense morpholino oligonucleotide (AMO) disrupts U1snRNP structure to promote intronic PCPA modification of pre-mRNAs publication-title: J. Biol. Chem. – volume: 11 start-page: 4083 year: 2020 ident: bib149 article-title: BRD4 prevents the accumulation of R-loops and protects against transcription–replication collision events and DNA damage publication-title: Nat. Commun. – volume: 11 start-page: 571 year: 2015 end-page: 578 ident: bib97 article-title: Pharmacological targeting of the Wdr5-MLL interaction in C/EBPα N-terminal leukemia publication-title: Nat. Chem. Biol. – volume: 3 start-page: 536 year: 2022 end-page: 546 ident: bib101 article-title: Dysregulation and therapeutic targeting of RNA splicing in cancer publication-title: Nat. Cancer – volume: 63 start-page: 27.1 year: 2003 ident: bib40 article-title: Agarose Gel Separation/Isolation of RNA -Protein Complexes publication-title: CP Mol. Biol. – volume: 27 start-page: 491 year: 2017 end-page: 499 ident: bib136 article-title: UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy publication-title: Genome Res. – volume: 53 start-page: 707 year: 2021 end-page: 718 ident: bib18 article-title: Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition publication-title: Nat. Genet. – volume: 11 start-page: 618 year: 2015 end-page: 629 ident: bib38 article-title: SF3B1 Association with Chromatin Determines Splicing Outcomes publication-title: Cell Rep. – volume: 34 start-page: 2525 year: 2020 end-page: 2530 ident: bib51 article-title: SF3B1 mutations induce R-loop accumulation and DNA damage in MDS and leukemia cells with therapeutic implications publication-title: Leukemia – volume: 82 start-page: 3632 year: 2022 end-page: 3645.e4 ident: bib155 article-title: The pausing zone and control of RNA polymerase II elongation by Spt5: Implications for the pause-release model publication-title: Mol. Cell – volume: 25 start-page: 2078 year: 2009 end-page: 2079 ident: bib120 article-title: The Sequence Alignment/Map format and SAMtools publication-title: Bioinformatics – volume: 13 start-page: 21 year: 2020 ident: bib129 article-title: BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks publication-title: Epigenetics Chromatin – volume: 139 start-page: 2038 year: 2022 end-page: 2049 ident: bib15 article-title: Coordinated missplicing of TMEM14C and ABCB7 causes ring sideroblast formation in SF3B1-mutant myelodysplastic syndrome publication-title: Blood – volume: 30 start-page: 2710 year: 2016 end-page: 2723 ident: bib36 article-title: SF3B1/Hsh155 HEAT motif mutations affect interaction with the spliceosomal ATPase Prp5, resulting in altered branch site selectivity in pre-mRNA splicing publication-title: Genes Dev. – volume: 81 start-page: 502 year: 2021 end-page: 513.e4 ident: bib47 article-title: Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression publication-title: Mol. Cell – volume: 81 start-page: 1920 year: 2021 end-page: 1934.e9 ident: bib4 article-title: Efficient RNA polymerase II pause release requires U2snRNP function publication-title: Mol. Cell – volume: 46 start-page: 10157 year: 2018 end-page: 10172 ident: bib140 article-title: Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions publication-title: Nucleic Acids Res. – volume: 26 start-page: 841 year: 2010 end-page: 842 ident: bib130 article-title: BEDTools: a flexible suite of utilities for comparing genomic features publication-title: Bioinformatics – volume: 365 start-page: 1384 year: 2011 end-page: 1395 ident: bib11 article-title: Somatic publication-title: N. Engl. J. Med. – volume: 89 year: 2020 ident: bib53 article-title: Proximity Ligation Assay for Detecting Protein-Protein Interactions and Protein Modifications in Cells and Tissues in Situ publication-title: Curr. Protoc. Cell Biol. – volume: 23 start-page: 135 year: 2023 end-page: 155 ident: bib102 article-title: RNA splicing dysregulation and the hallmarks of cancer publication-title: Nat. Rev. Cancer – volume: 50 start-page: 1452 year: 2018 end-page: 1462 ident: bib82 article-title: Promoter bivalency favors an open chromatin architecture in embryonic stem cells publication-title: Nat. Genet. – volume: 27 start-page: 863 year: 2011 end-page: 864 ident: bib131 article-title: Quality control and preprocessing of metagenomic datasets publication-title: Bioinformatics – volume: 170 start-page: 774 year: 2017 end-page: 786.e19 ident: bib63 article-title: Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses publication-title: Cell – volume: 32 start-page: 2847 year: 2016 end-page: 2849 ident: bib137 article-title: Complex heatmaps reveal patterns and correlations in multidimensional genomic data publication-title: Bioinformatics – volume: 83 start-page: 1264 year: 2023 end-page: 1279.e10 ident: bib7 article-title: U1snRNP increases RNA RNAPII elongation rate to enable synthesis of long genes publication-title: Mol. Cell – volume: 16 start-page: 413 year: 2016 end-page: 430 ident: bib14 article-title: RNA splicing factors as oncoproteins and tumour suppressors publication-title: Nat. Rev. Cancer – volume: 2 start-page: 62 year: 2012 end-page: 68 ident: bib78 article-title: First Exon Length Controls Active Chromatin Signatures and Transcription publication-title: Cell Rep. – volume: 3 year: 2011 ident: bib109 article-title: Spliceosome Structure and Function publication-title: Cold Spring Harbor Perspect. Biol. – volume: 15 start-page: 550 year: 2014 ident: bib126 article-title: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 publication-title: Genome Biol. – volume: 124 start-page: 1283 year: 2006 end-page: 1298 ident: bib115 article-title: A Lentiviral RNAi Library for Human and Mouse Genes Applied to an Arrayed Viral High-Content Screen publication-title: Cell – volume: 292 start-page: 262 year: 2022 end-page: 277 ident: bib107 article-title: Targeting stem cells in myelodysplastic syndromes and acute myeloid leukemia publication-title: J. Intern. Med. – volume: 220 year: 2021 ident: bib148 article-title: Recognition of RNA by the S9.6 antibody creates pervasive artifacts when imaging RNA:DNA hybrids publication-title: J. Cell Biol. – volume: 24 start-page: 747 year: 2006 end-page: 757 ident: bib22 article-title: The Transition between Transcriptional Initiation and Elongation in E. coli Is Highly Variable and Often Rate Limiting publication-title: Mol. Cell – volume: 47 start-page: D607 year: 2019 end-page: D613 ident: bib87 article-title: STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets publication-title: Nucleic Acids Res. – year: 2020 ident: bib80 article-title: Interdependence between histone marks and steps in RNAPII transcription (Genomics) publication-title: bioRxiv – volume: 445 start-page: 661 year: 2007 end-page: 665 ident: bib100 article-title: Restoration of p53 function leads to tumour regression in vivo publication-title: Nature – volume: 7 start-page: 1338 year: 2018 ident: bib116 article-title: FastQ Screen: A tool for multi-genome mapping and quality control publication-title: F1000Res – volume: 30 start-page: 923 year: 2014 end-page: 930 ident: bib125 article-title: featureCounts: an efficient general purpose program for assigning sequence reads to genomic features publication-title: Bioinformatics – volume: 154 start-page: 713 year: 2013 end-page: 715 ident: bib29 article-title: Mechanistic Interpretation of Promoter-Proximal Peaks and RNAPII Density Maps publication-title: Cell – volume: 81 start-page: 3096 year: 2021 end-page: 3109.e8 ident: bib32 article-title: Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo publication-title: Mol. Cell – volume: 53 start-page: 1050 year: 2021 end-page: 1063 ident: bib147 article-title: The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts publication-title: Nat. Genet. – volume: 9 start-page: 88 year: 2018 end-page: 94 ident: bib42 article-title: P-TEFb: Finding its ways to release promoter-proximally paused RNA polymerase II publication-title: Transcription – volume: 64 start-page: 4140 year: 2012 ident: bib144 article-title: Small-scale Nuclear Extracts for Functional Assays of Gene-expression Machineries publication-title: J. Vis. Exp. (JoVE) – volume: 36 start-page: e127 year: 2008 ident: bib111 article-title: Epitope tagging of endogenous genes in diverse human cell lines publication-title: Nucleic Acids Res. – volume: 13 start-page: 1006 year: 2018 end-page: 1019 ident: bib152 article-title: Targeted in situ genome-wide profiling with high efficiency for low cell numbers publication-title: Nat. Protoc. – volume: 10 year: 2012 ident: bib81 article-title: Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles publication-title: PLoS Biol. – volume: 8 start-page: 498 year: 2009 end-page: 504 ident: bib113 article-title: Single-vector inducible lentiviral RNAi system for oncology target validation publication-title: Cell Cycle – volume: 81 start-page: 998 year: 2021 end-page: 1012.e7 ident: bib1 article-title: Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis publication-title: Mol. Cell – volume: 14 start-page: 1734 year: 2019 end-page: 1755 ident: bib62 article-title: High-resolution, strand-specific R-loop mapping via S9.6-based DNA–RNA immunoprecipitation and high-throughput sequencing publication-title: Nat. Protoc. – volume: 8 year: 2018 ident: bib143 article-title: Isolation of Chromatin-bound Proteins from Subcellular Fractions for Biochemical Analysis publication-title: Bio Protoc. – year: 2020 ident: bib46 article-title: SF3B1-targeted Splicing Inhibition Triggers Global Alterations in Transcriptional Dynamics and R-Loop Metabolism publication-title: bioRxiv – volume: 583 start-page: 310 year: 2020 end-page: 313 ident: bib34 article-title: Molecular architecture of the human 17S U2snRNP publication-title: Nature – volume: 65 start-page: 3736 year: 2012 ident: bib141 article-title: Phenotypic Analysis and Isolation of Murine Hematopoietic Stem Cells and Lineage-committed Progenitors publication-title: J. Vis. Exp. (JoVE) – volume: 141 start-page: 432 year: 2010 end-page: 445 ident: bib21 article-title: c-Myc Regulates Transcriptional Pause Release publication-title: Cell – volume: 11 start-page: 193 year: 2021 ident: bib108 article-title: Differentiation therapy for myeloid malignancies: beyond cytotoxicity publication-title: Blood Cancer J. – volume: 41 start-page: 733 year: 2018 end-page: 741 ident: bib50 article-title: Integrative Profiling of Alternative Splicing Induced by U2AF1 S34F Mutation in Lung Adenocarcinoma Reveals a Mechanistic Link to Mitotic Stress publication-title: Mol. Cells – volume: 12 start-page: 6169 year: 2022 ident: bib58 article-title: Aberrant R-loop-induced replication stress in MED12-mutant uterine fibroids publication-title: Sci. Rep. – volume: 32 start-page: 289 year: 2016 end-page: 291 ident: bib76 article-title: regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests. Bioinformatics, btv562 publication-title: Bioinformatics – volume: 18 start-page: 673 year: 2018 ident: bib98 article-title: WDR5 supports colon cancer cells by promoting methylation of H3K4 and suppressing DNA damage publication-title: BMC Cancer – volume: 3 start-page: 16017 year: 2016 ident: bib142 article-title: Production of lentiviral vectors publication-title: Mol. Ther. Methods Clin. Dev. – volume: 44 start-page: W160 year: 2016 end-page: W165 ident: bib121 article-title: deepTools2: a next generation web server for deep-sequencing data analysis publication-title: Nucleic Acids Res. – volume: 36 start-page: 662 year: 2015 end-page: 667 ident: bib27 article-title: The Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses publication-title: Mol. Cell. Biol. – volume: 44 start-page: 9 year: 2011 end-page: 10 ident: bib13 article-title: Spliceosome mutations in hematopoietic malignancies publication-title: Nat. Genet. – volume: 119 year: 2022 ident: bib16 article-title: SF3B1 mutant-induced missplicing of MAP3K7 causes anemia in myelodysplastic syndromes publication-title: Proc. Natl. Acad. Sci. USA – volume: 574 start-page: 432 year: 2019 end-page: 436 ident: bib17 article-title: Spliceosomal disruption of the non-canonical BAF complex in cancer publication-title: Nature – volume: 29 start-page: 15 year: 2013 end-page: 21 ident: bib119 article-title: STAR: ultrafast universal RNA-seq aligner publication-title: Bioinformatics – volume: 161 start-page: 526 year: 2015 end-page: 540 ident: bib44 article-title: Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing publication-title: Cell – volume: 28 start-page: 2663 year: 2014 end-page: 2676 ident: bib6 article-title: Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate publication-title: Genes Dev. – volume: 172 start-page: 117 year: 2022 end-page: 126 ident: bib37 article-title: Cancer-associated mutations in publication-title: J. Biochem. – volume: 19 start-page: 65 year: 2005 end-page: 75 ident: bib9 article-title: Cotranscriptional Spliceosome Assembly Dynamics and the Role of U1snRNA:5′ss Base Pairing in Yeast publication-title: Mol. Cell – volume: 609 start-page: 829 year: 2022 end-page: 834 ident: bib5 article-title: CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1 publication-title: Nature – volume: 36 start-page: 1123 year: 2017 end-page: 1133 ident: bib24 article-title: Cancer-associated SF3B1 mutants recognize otherwise inaccessible cryptic 3′ splice sites within RNA secondary structures publication-title: Oncogene – volume: 294 start-page: 2892 year: 2019 end-page: 2902 ident: bib105 article-title: The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface publication-title: J. Biol. Chem. – volume: 24 start-page: 896 year: 2014 end-page: 905 ident: bib31 article-title: Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications publication-title: Genome Res. – volume: 24 start-page: 747 year: 2006 ident: 10.1016/j.molcel.2024.02.032_bib22 article-title: The Transition between Transcriptional Initiation and Elongation in E. coli Is Highly Variable and Often Rate Limiting publication-title: Mol. Cell doi: 10.1016/j.molcel.2006.10.030 – volume: 276 start-page: 46515 year: 2001 ident: 10.1016/j.molcel.2024.02.032_bib91 article-title: Cloning and Characterization of a Novel WD-40 Repeat Protein That Dramatically Accelerates Osteoblastic Differentiation publication-title: J. Biol. Chem. doi: 10.1074/jbc.M105757200 – volume: 365 start-page: 1384 year: 2011 ident: 10.1016/j.molcel.2024.02.032_bib11 article-title: Somatic SF3B1 Mutation in Myelodysplasia with Ring Sideroblasts publication-title: N. Engl. J. Med. doi: 10.1056/NEJMoa1103283 – volume: 66 start-page: 546 year: 2017 ident: 10.1016/j.molcel.2024.02.032_bib83 article-title: RNA RNAPII Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction publication-title: Mol. Cell doi: 10.1016/j.molcel.2017.04.016 – volume: 81 start-page: 3096 year: 2021 ident: 10.1016/j.molcel.2024.02.032_bib32 article-title: Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo publication-title: Mol. Cell doi: 10.1016/j.molcel.2021.05.028 – volume: 442 start-page: 772 year: 2006 ident: 10.1016/j.molcel.2024.02.032_bib74 article-title: A genomic code for nucleosome positioning publication-title: Nature doi: 10.1038/nature04979 – volume: 84 start-page: 11 year: 2019 ident: 10.1016/j.molcel.2024.02.032_bib39 article-title: Pre-mRNA Splicing in the Nuclear Landscape publication-title: Cold Spring Harb. Symp. Quant. Biol. doi: 10.1101/sqb.2019.84.040402 – volume: 11 year: 2016 ident: 10.1016/j.molcel.2024.02.032_bib151 article-title: An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition publication-title: PLoS ONE doi: 10.1371/journal.pone.0166438 – volume: 139 start-page: 2038 year: 2022 ident: 10.1016/j.molcel.2024.02.032_bib15 article-title: Coordinated missplicing of TMEM14C and ABCB7 causes ring sideroblast formation in SF3B1-mutant myelodysplastic syndrome publication-title: Blood doi: 10.1182/blood.2021012652 – volume: 29 start-page: 24 year: 2011 ident: 10.1016/j.molcel.2024.02.032_bib154 article-title: Integrative genomics viewer publication-title: Nat. Biotechnol. doi: 10.1038/nbt.1754 – volume: 35 start-page: 553 year: 2019 ident: 10.1016/j.molcel.2024.02.032_bib66 article-title: Transcriptional Control by Premature Termination: A Forgotten Mechanism publication-title: Trends Genet. doi: 10.1016/j.tig.2019.05.005 – volume: 64 start-page: 4140 year: 2012 ident: 10.1016/j.molcel.2024.02.032_bib144 article-title: Small-scale Nuclear Extracts for Functional Assays of Gene-expression Machineries publication-title: J. Vis. Exp. (JoVE) – volume: 81 start-page: 502 year: 2021 ident: 10.1016/j.molcel.2024.02.032_bib47 article-title: Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression publication-title: Mol. Cell doi: 10.1016/j.molcel.2020.12.002 – year: 2020 ident: 10.1016/j.molcel.2024.02.032_bib80 article-title: Interdependence between histone marks and steps in RNAPII transcription (Genomics) publication-title: bioRxiv – volume: 370 start-page: eabb5872 year: 2020 ident: 10.1016/j.molcel.2024.02.032_bib69 article-title: Identification of Integrator-PP2A complex (INTAC), an RNA polymerase II phosphatase publication-title: Science doi: 10.1126/science.abb5872 – volume: 28 start-page: 2663 year: 2014 ident: 10.1016/j.molcel.2024.02.032_bib6 article-title: Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate publication-title: Genes Dev. doi: 10.1101/gad.252106.114 – volume: 29 start-page: 15 year: 2013 ident: 10.1016/j.molcel.2024.02.032_bib119 article-title: STAR: ultrafast universal RNA-seq aligner publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts635 – volume: 111 start-page: E5593 year: 2014 ident: 10.1016/j.molcel.2024.02.032_bib124 article-title: rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1419161111 – volume: 36 start-page: 1663 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib49 article-title: Myeloid Disease Mutations of Splicing Factor SRSF2 Cause G2-M Arrest and Skewed Differentiation of Human Hematopoietic Stem and Progenitor Cells publication-title: Stem Cells doi: 10.1002/stem.2885 – volume: 609 start-page: 829 year: 2022 ident: 10.1016/j.molcel.2024.02.032_bib5 article-title: CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1 publication-title: Nature doi: 10.1038/s41586-022-05204-z – volume: 24 start-page: 896 year: 2014 ident: 10.1016/j.molcel.2024.02.032_bib31 article-title: Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications publication-title: Genome Res. doi: 10.1101/gr.171405.113 – volume: 18 start-page: 637 year: 2017 ident: 10.1016/j.molcel.2024.02.032_bib3 article-title: Splicing and transcription touch base: co-transcriptional spliceosome assembly and function publication-title: Nat. Rev. Mol. Cell Biol. doi: 10.1038/nrm.2017.63 – volume: 30 start-page: 2710 year: 2016 ident: 10.1016/j.molcel.2024.02.032_bib36 article-title: SF3B1/Hsh155 HEAT motif mutations affect interaction with the spliceosomal ATPase Prp5, resulting in altered branch site selectivity in pre-mRNA splicing publication-title: Genes Dev. doi: 10.1101/gad.291872.116 – volume: 30 start-page: 923 year: 2014 ident: 10.1016/j.molcel.2024.02.032_bib125 article-title: featureCounts: an efficient general purpose program for assigning sequence reads to genomic features publication-title: Bioinformatics doi: 10.1093/bioinformatics/btt656 – year: 2020 ident: 10.1016/j.molcel.2024.02.032_bib46 article-title: SF3B1-targeted Splicing Inhibition Triggers Global Alterations in Transcriptional Dynamics and R-Loop Metabolism publication-title: bioRxiv – volume: 21 start-page: 214 year: 2020 ident: 10.1016/j.molcel.2024.02.032_bib135 article-title: ARTDeco: automatic readthrough transcription detection publication-title: BMC Bioinformatics doi: 10.1186/s12859-020-03551-0 – volume: 7 start-page: 10208 year: 2016 ident: 10.1016/j.molcel.2024.02.032_bib65 article-title: Replication landscape of the human genome publication-title: Nat. Commun. doi: 10.1038/ncomms10208 – volume: 143 start-page: 540 year: 2010 ident: 10.1016/j.molcel.2024.02.032_bib70 article-title: Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation publication-title: Cell doi: 10.1016/j.cell.2010.10.004 – volume: 15 start-page: 550 year: 2014 ident: 10.1016/j.molcel.2024.02.032_bib126 article-title: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 publication-title: Genome Biol. doi: 10.1186/s13059-014-0550-8 – volume: 76 start-page: 57 year: 2019 ident: 10.1016/j.molcel.2024.02.032_bib60 article-title: Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome Stability publication-title: Mol. Cell doi: 10.1016/j.molcel.2019.07.037 – volume: 25 start-page: 3305 year: 2005 ident: 10.1016/j.molcel.2024.02.032_bib84 article-title: A Novel Domain in Set2 Mediates RNA Polymerase II Interaction and Couples Histone H3 K36 Methylation with Transcript Elongation publication-title: Mol. Cell. Biol. doi: 10.1128/MCB.25.8.3305-3316.2005 – volume: 3 start-page: 536 year: 2022 ident: 10.1016/j.molcel.2024.02.032_bib101 article-title: Dysregulation and therapeutic targeting of RNA splicing in cancer publication-title: Nat. Cancer doi: 10.1038/s43018-022-00384-z – volume: 154 start-page: 713 year: 2013 ident: 10.1016/j.molcel.2024.02.032_bib29 article-title: Mechanistic Interpretation of Promoter-Proximal Peaks and RNAPII Density Maps publication-title: Cell doi: 10.1016/j.cell.2013.07.032 – volume: 53 start-page: 1050 year: 2021 ident: 10.1016/j.molcel.2024.02.032_bib147 article-title: The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts publication-title: Nat. Genet. doi: 10.1038/s41588-021-00867-2 – volume: 124 start-page: 2793 year: 2014 ident: 10.1016/j.molcel.2024.02.032_bib96 article-title: Recent developments in myelodysplastic syndromes publication-title: Blood doi: 10.1182/blood-2014-04-522136 – volume: 574 start-page: 432 year: 2019 ident: 10.1016/j.molcel.2024.02.032_bib17 article-title: Spliceosomal disruption of the non-canonical BAF complex in cancer publication-title: Nature doi: 10.1038/s41586-019-1646-9 – volume: 34 start-page: 898 year: 2020 ident: 10.1016/j.molcel.2024.02.032_bib54 article-title: UAP56/DDX39B is a major cotranscriptional RNA–DNA helicase that unwinds harmful R loops genome-wide publication-title: Genes Dev. doi: 10.1101/gad.336024.119 – volume: 37 start-page: 429 year: 2010 ident: 10.1016/j.molcel.2024.02.032_bib67 article-title: AFF4, a Component of the ELL/P-TEFb Elongation Complex and a Shared Subunit of MLL Chimeras, Can Link Transcription Elongation to Leukemia publication-title: Mol. Cell doi: 10.1016/j.molcel.2010.01.026 – volume: 11 start-page: 193 year: 2021 ident: 10.1016/j.molcel.2024.02.032_bib108 article-title: Differentiation therapy for myeloid malignancies: beyond cytotoxicity publication-title: Blood Cancer J. doi: 10.1038/s41408-021-00584-3 – volume: 82 start-page: 3632 year: 2022 ident: 10.1016/j.molcel.2024.02.032_bib155 article-title: The pausing zone and control of RNA polymerase II elongation by Spt5: Implications for the pause-release model publication-title: Mol. Cell doi: 10.1016/j.molcel.2022.09.001 – volume: 615 start-page: 339 year: 2023 ident: 10.1016/j.molcel.2024.02.032_bib79 article-title: H3K4me3 regulates RNA polymerase II promoter-proximal pause-release publication-title: Nature doi: 10.1038/s41586-023-05780-8 – volume: 414 start-page: 929 year: 2001 ident: 10.1016/j.molcel.2024.02.032_bib104 article-title: Stimulatory effect of splicing factors on transcriptional elongation publication-title: Nature doi: 10.1038/414929a – volume: 32 start-page: 2847 year: 2016 ident: 10.1016/j.molcel.2024.02.032_bib137 article-title: Complex heatmaps reveal patterns and correlations in multidimensional genomic data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btw313 – volume: 108 start-page: 3665 year: 2011 ident: 10.1016/j.molcel.2024.02.032_bib114 article-title: The pINDUCER lentiviral toolkit for inducible RNA interference in vitro and in vivo publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1019736108 – volume: 81 start-page: 1920 year: 2021 ident: 10.1016/j.molcel.2024.02.032_bib4 article-title: Efficient RNA polymerase II pause release requires U2snRNP function publication-title: Mol. Cell doi: 10.1016/j.molcel.2021.02.016 – volume: 9 start-page: 493 year: 2003 ident: 10.1016/j.molcel.2024.02.032_bib112 article-title: Lentivirus-delivered stable gene silencing by RNAi in primary cells publication-title: RNA doi: 10.1261/rna.2192803 – volume: 30 start-page: 404 year: 2016 ident: 10.1016/j.molcel.2024.02.032_bib99 article-title: Physiologic Expression of Sf3b1 K700E Causes Impaired Erythropoiesis, Aberrant Splicing, and Sensitivity to Therapeutic Spliceosome Modulation publication-title: Cancer Cell doi: 10.1016/j.ccell.2016.08.006 – volume: 13 start-page: 21 year: 2020 ident: 10.1016/j.molcel.2024.02.032_bib129 article-title: BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks publication-title: Epigenetics Chromatin doi: 10.1186/s13072-020-00343-x – volume: 179 start-page: 604 year: 2019 ident: 10.1016/j.molcel.2024.02.032_bib52 article-title: R Loops: From Physiological to Pathological Roles publication-title: Cell doi: 10.1016/j.cell.2019.08.055 – volume: 124 start-page: 1283 year: 2006 ident: 10.1016/j.molcel.2024.02.032_bib115 article-title: A Lentiviral RNAi Library for Human and Mouse Genes Applied to an Arrayed Viral High-Content Screen publication-title: Cell doi: 10.1016/j.cell.2006.01.040 – volume: 290 start-page: 1829 year: 2015 ident: 10.1016/j.molcel.2024.02.032_bib41 article-title: Visualization of Positive Transcription Elongation Factor b (P-TEFb) Activation in Living Cells publication-title: J. Biol. Chem. doi: 10.1074/jbc.M114.605816 – volume: 47 start-page: D607 year: 2019 ident: 10.1016/j.molcel.2024.02.032_bib87 article-title: STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets publication-title: Nucleic Acids Res. doi: 10.1093/nar/gky1131 – volume: 59 start-page: 2952 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib93 article-title: Distinct transcriptomic and exomic abnormalities within myelodysplastic syndrome marrow cells publication-title: Leuk. Lymphoma doi: 10.1080/10428194.2018.1452210 – volume: 9 start-page: 676 year: 2012 ident: 10.1016/j.molcel.2024.02.032_bib139 article-title: Fiji: an open-source platform for biological-image analysis publication-title: Nat. Methods doi: 10.1038/nmeth.2019 – volume: 17 start-page: 10 year: 2011 ident: 10.1016/j.molcel.2024.02.032_bib117 article-title: Cutadapt removes adapter sequences from high-throughput sequencing reads publication-title: EMBnet J. doi: 10.14806/ej.17.1.200 – volume: 299 start-page: 104854 year: 2023 ident: 10.1016/j.molcel.2024.02.032_bib8 article-title: The U1 antisense morpholino oligonucleotide (AMO) disrupts U1snRNP structure to promote intronic PCPA modification of pre-mRNAs publication-title: J. Biol. Chem. doi: 10.1016/j.jbc.2023.104854 – volume: 89 year: 2020 ident: 10.1016/j.molcel.2024.02.032_bib53 article-title: Proximity Ligation Assay for Detecting Protein-Protein Interactions and Protein Modifications in Cells and Tissues in Situ publication-title: Curr. Protoc. Cell Biol. doi: 10.1002/cpcb.115 – volume: 8 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib143 article-title: Isolation of Chromatin-bound Proteins from Subcellular Fractions for Biochemical Analysis publication-title: Bio Protoc. doi: 10.21769/BioProtoc.3035 – volume: 9 start-page: 215 year: 2012 ident: 10.1016/j.molcel.2024.02.032_bib86 article-title: ChromHMM: automating chromatin-state discovery and characterization publication-title: Nat. Methods doi: 10.1038/nmeth.1906 – volume: 34 start-page: 2525 year: 2020 ident: 10.1016/j.molcel.2024.02.032_bib51 article-title: SF3B1 mutations induce R-loop accumulation and DNA damage in MDS and leukemia cells with therapeutic implications publication-title: Leukemia doi: 10.1038/s41375-020-0753-9 – volume: 36 start-page: 1123 year: 2017 ident: 10.1016/j.molcel.2024.02.032_bib24 article-title: Cancer-associated SF3B1 mutants recognize otherwise inaccessible cryptic 3′ splice sites within RNA secondary structures publication-title: Oncogene doi: 10.1038/onc.2016.279 – volume: 46 start-page: 10157 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib140 article-title: Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions publication-title: Nucleic Acids Res. doi: 10.1093/nar/gky797 – volume: 106 start-page: 103182 year: 2021 ident: 10.1016/j.molcel.2024.02.032_bib61 article-title: Defining R-loop classes and their contributions to genome instability publication-title: DNA Repair doi: 10.1016/j.dnarep.2021.103182 – volume: 44 start-page: 9 year: 2011 ident: 10.1016/j.molcel.2024.02.032_bib13 article-title: Spliceosome mutations in hematopoietic malignancies publication-title: Nat. Genet. doi: 10.1038/ng.1045 – volume: 44 start-page: W160 year: 2016 ident: 10.1016/j.molcel.2024.02.032_bib121 article-title: deepTools2: a next generation web server for deep-sequencing data analysis publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkw257 – volume: 583 start-page: 310 year: 2020 ident: 10.1016/j.molcel.2024.02.032_bib34 article-title: Molecular architecture of the human 17S U2snRNP publication-title: Nature doi: 10.1038/s41586-020-2344-3 – volume: 26 start-page: 799 year: 2016 ident: 10.1016/j.molcel.2024.02.032_bib30 article-title: Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast publication-title: Genome Res. doi: 10.1101/gr.204578.116 – volume: 11 start-page: 618 year: 2015 ident: 10.1016/j.molcel.2024.02.032_bib38 article-title: SF3B1 Association with Chromatin Determines Splicing Outcomes publication-title: Cell Rep. doi: 10.1016/j.celrep.2015.03.048 – volume: 20 start-page: 705 year: 2019 ident: 10.1016/j.molcel.2024.02.032_bib45 article-title: Nascent RNA analyses: tracking transcription and its regulation publication-title: Nat. Rev. Genet. doi: 10.1038/s41576-019-0159-6 – volume: 12 start-page: 42 year: 2019 ident: 10.1016/j.molcel.2024.02.032_bib133 article-title: Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling publication-title: Epigenetics Chromatin doi: 10.1186/s13072-019-0287-4 – volume: 36 start-page: 662 year: 2015 ident: 10.1016/j.molcel.2024.02.032_bib27 article-title: The Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses publication-title: Mol. Cell. Biol. doi: 10.1128/MCB.00970-14 – volume: 14 start-page: 1734 year: 2019 ident: 10.1016/j.molcel.2024.02.032_bib62 article-title: High-resolution, strand-specific R-loop mapping via S9.6-based DNA–RNA immunoprecipitation and high-throughput sequencing publication-title: Nat. Protoc. doi: 10.1038/s41596-019-0159-1 – volume: 5 start-page: 224 year: 2014 ident: 10.1016/j.molcel.2024.02.032_bib23 article-title: RNA Polymerase II transcription elongation and RNAPII CTD Ser2 phosphorylation: A tail of two kinases publication-title: Nucleus doi: 10.4161/nucl.29347 – volume: 11 start-page: 3940 year: 2020 ident: 10.1016/j.molcel.2024.02.032_bib64 article-title: Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites publication-title: Nat. Commun. doi: 10.1038/s41467-020-17858-2 – year: 2016 ident: 10.1016/j.molcel.2024.02.032_bib123 – volume: 3 start-page: 3 year: 2013 ident: 10.1016/j.molcel.2024.02.032_bib146 article-title: Neutral comet assay publication-title: Bio Protoc. doi: 10.21769/BioProtoc.915 – volume: 10 year: 2012 ident: 10.1016/j.molcel.2024.02.032_bib81 article-title: Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles publication-title: PLoS Biol. doi: 10.1371/journal.pbio.1001442 – volume: 50 start-page: 1452 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib82 article-title: Promoter bivalency favors an open chromatin architecture in embryonic stem cells publication-title: Nat. Genet. doi: 10.1038/s41588-018-0218-5 – volume: 3 year: 2011 ident: 10.1016/j.molcel.2024.02.032_bib109 article-title: Spliceosome Structure and Function publication-title: Cold Spring Harbor Perspect. Biol. doi: 10.1101/cshperspect.a003707 – volume: 478 start-page: 64 year: 2011 ident: 10.1016/j.molcel.2024.02.032_bib12 article-title: Frequent pathway mutations of splicing machinery in myelodysplasia publication-title: Nature doi: 10.1038/nature10496 – volume: 8 year: 2013 ident: 10.1016/j.molcel.2024.02.032_bib75 article-title: The Effect of an Intervening Promoter Nucleosome on Gene Expression publication-title: PLoS ONE doi: 10.1371/journal.pone.0063072 – volume: 81 start-page: 998 year: 2021 ident: 10.1016/j.molcel.2024.02.032_bib1 article-title: Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis publication-title: Mol. Cell doi: 10.1016/j.molcel.2020.12.018 – volume: 16 start-page: 413 year: 2016 ident: 10.1016/j.molcel.2024.02.032_bib14 article-title: RNA splicing factors as oncoproteins and tumour suppressors publication-title: Nat. Rev. Cancer doi: 10.1038/nrc.2016.51 – volume: 17 start-page: 896 year: 2003 ident: 10.1016/j.molcel.2024.02.032_bib88 article-title: Human Sin3 deacetylase and trithorax-related Set1/Ash2 histone H3-K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1 publication-title: Genes Dev. doi: 10.1101/gad.252103 – volume: 132 start-page: 1225 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib95 article-title: Impact of spliceosome mutations on RNA splicing in myelodysplasia: dysregulated genes/pathways and clinical associations publication-title: Blood doi: 10.1182/blood-2018-04-843771 – volume: 161 start-page: 526 year: 2015 ident: 10.1016/j.molcel.2024.02.032_bib44 article-title: Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing publication-title: Cell doi: 10.1016/j.cell.2015.03.027 – volume: 16 start-page: 190 year: 2015 ident: 10.1016/j.molcel.2024.02.032_bib55 article-title: Transcription termination and the control of the transcriptome: why, where and how to stop publication-title: Nat. Rev. Mol. Cell Biol. doi: 10.1038/nrm3943 – volume: 6 year: 2017 ident: 10.1016/j.molcel.2024.02.032_bib77 article-title: An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites publication-title: eLife doi: 10.7554/eLife.21856 – volume: 35 start-page: 4392 year: 2019 ident: 10.1016/j.molcel.2024.02.032_bib127 article-title: epic2 efficiently finds diffuse domains in ChIP-seq data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btz232 – volume: 36 start-page: e127 year: 2008 ident: 10.1016/j.molcel.2024.02.032_bib111 article-title: Epitope tagging of endogenous genes in diverse human cell lines publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkn566 – volume: 34 start-page: 3094 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib132 article-title: Minimap2: pairwise alignment for nucleotide sequences publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty191 – volume: 27 start-page: 491 year: 2017 ident: 10.1016/j.molcel.2024.02.032_bib136 article-title: UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy publication-title: Genome Res. doi: 10.1101/gr.209601.116 – volume: 133 start-page: e128 year: 2020 ident: 10.1016/j.molcel.2024.02.032_bib28 article-title: Preparation of Mammalian Nascent RNA for Long Read Sequencing publication-title: Curr. Protoc. Mol. Biol. doi: 10.1002/cpmb.128 – volume: 10 start-page: 285 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib89 article-title: LSD1 coordinates with the SIN3A/HDAC complex and maintains sensitivity to chemotherapy in breast cancer publication-title: J. Mol. Cell Biol. doi: 10.1093/jmcb/mjy021 – volume: 14 start-page: 959 year: 2017 ident: 10.1016/j.molcel.2024.02.032_bib72 article-title: An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues publication-title: Nat. Methods doi: 10.1038/nmeth.4396 – volume: 322 start-page: 601 year: 2004 ident: 10.1016/j.molcel.2024.02.032_bib90 article-title: Characterization of BHC80 in BRAF–HDAC complex, involved in neuron-specific gene repression publication-title: Biochem. Biophys. Res. Commun. doi: 10.1016/j.bbrc.2004.07.163 – volume: 69 start-page: 412 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib48 article-title: The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations publication-title: Mol. Cell doi: 10.1016/j.molcel.2017.12.029 – volume: 13 start-page: 543 year: 2012 ident: 10.1016/j.molcel.2024.02.032_bib68 article-title: The super elongation complex (SEC) family in transcriptional control publication-title: Nat. Rev. Mol. Cell Biol. doi: 10.1038/nrm3417 – volume: 18 start-page: 673 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib98 article-title: WDR5 supports colon cancer cells by promoting methylation of H3K4 and suppressing DNA damage publication-title: BMC Cancer doi: 10.1186/s12885-018-4580-6 – volume: 53 start-page: 707 year: 2021 ident: 10.1016/j.molcel.2024.02.032_bib18 article-title: Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition publication-title: Nat. Genet. doi: 10.1038/s41588-021-00828-9 – volume: 9 start-page: 357 year: 2012 ident: 10.1016/j.molcel.2024.02.032_bib118 article-title: Fast gapped-read alignment with Bowtie 2 publication-title: Nat. Methods doi: 10.1038/nmeth.1923 – volume: 371 start-page: 305 year: 2021 ident: 10.1016/j.molcel.2024.02.032_bib2 article-title: Structure of a transcribing RNA polymerase II–U1snRNP complex publication-title: Science doi: 10.1126/science.abf1870 – volume: 63 start-page: 27.1 year: 2003 ident: 10.1016/j.molcel.2024.02.032_bib40 article-title: Agarose Gel Separation/Isolation of RNA -Protein Complexes publication-title: CP Mol. Biol. doi: 10.1002/0471142727.mb2701s63 – volume: 11 year: 2015 ident: 10.1016/j.molcel.2024.02.032_bib92 article-title: Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers publication-title: PLoS Comput. Biol. doi: 10.1371/journal.pcbi.1004105 – volume: 220 year: 2021 ident: 10.1016/j.molcel.2024.02.032_bib148 article-title: Recognition of RNA by the S9.6 antibody creates pervasive artifacts when imaging RNA:DNA hybrids publication-title: J. Cell Biol. doi: 10.1083/jcb.202004079 – volume: 25 start-page: 2078 year: 2009 ident: 10.1016/j.molcel.2024.02.032_bib120 article-title: The Sequence Alignment/Map format and SAMtools publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp352 – volume: 596 start-page: 296 year: 2021 ident: 10.1016/j.molcel.2024.02.032_bib33 article-title: Structural insights into how Prp5 proofreads the pre-mRNA branch site publication-title: Nature doi: 10.1038/s41586-021-03789-5 – volume: 9 start-page: 3649 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib94 article-title: Aberrant splicing and defective mRNA production induced by somatic spliceosome mutations in myelodysplasia publication-title: Nat. Commun. doi: 10.1038/s41467-018-06063-x – volume: 27 start-page: 863 year: 2011 ident: 10.1016/j.molcel.2024.02.032_bib131 article-title: Quality control and preprocessing of metagenomic datasets publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr026 – volume: 14 start-page: 897 year: 2023 ident: 10.1016/j.molcel.2024.02.032_bib35 article-title: Mechanisms of the RNA helicases DDX42 and DDX46 in human U2snRNP assembly publication-title: Nat. Commun. doi: 10.1038/s41467-023-36489-x – volume: 1 year: 2021 ident: 10.1016/j.molcel.2024.02.032_bib153 article-title: An Easy, Cost-Effective, and Scalable Method to Deplete Human Ribosomal RNA for RNA-seq publication-title: Curr. Protoc. – volume: 11 start-page: 4083 year: 2020 ident: 10.1016/j.molcel.2024.02.032_bib149 article-title: BRD4 prevents the accumulation of R-loops and protects against transcription–replication collision events and DNA damage publication-title: Nat. Commun. doi: 10.1038/s41467-020-17503-y – volume: 31 start-page: 720 year: 2017 ident: 10.1016/j.molcel.2024.02.032_bib110 article-title: Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts publication-title: Leukemia doi: 10.1038/leu.2016.251 – volume: 2 start-page: 62 year: 2012 ident: 10.1016/j.molcel.2024.02.032_bib78 article-title: First Exon Length Controls Active Chromatin Signatures and Transcription publication-title: Cell Rep. doi: 10.1016/j.celrep.2012.05.019 – volume: 11 start-page: 571 year: 2015 ident: 10.1016/j.molcel.2024.02.032_bib97 article-title: Pharmacological targeting of the Wdr5-MLL interaction in C/EBPα N-terminal leukemia publication-title: Nat. Chem. Biol. doi: 10.1038/nchembio.1859 – volume: 55 start-page: 1311 year: 2023 ident: 10.1016/j.molcel.2024.02.032_bib106 article-title: SF3B1 hotspot mutations confer sensitivity to PARP inhibition by eliciting a defective replication stress response publication-title: Nat. Genet. doi: 10.1038/s41588-023-01460-5 – volume: 112 start-page: 8608 year: 2015 ident: 10.1016/j.molcel.2024.02.032_bib43 article-title: FUS functions in coupling transcription to splicing by mediating an interaction between RNAP II and U1snRNP publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1506282112 – volume: 8 start-page: 8 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib145 article-title: Cell Synchronization by Double Thymidine Block publication-title: Bio Protoc. doi: 10.21769/BioProtoc.2994 – volume: 286 start-page: 139 year: 2019 ident: 10.1016/j.molcel.2024.02.032_bib56 article-title: FANCD 2 protects genome stability by recruiting RNA processing enzymes to resolve R-loops during mild replication stress publication-title: FEBS J. doi: 10.1111/febs.14700 – volume: 26 start-page: 841 year: 2010 ident: 10.1016/j.molcel.2024.02.032_bib130 article-title: BEDTools: a flexible suite of utilities for comparing genomic features publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq033 – volume: 33 start-page: 108373 year: 2020 ident: 10.1016/j.molcel.2024.02.032_bib25 article-title: Rapid and Scalable Profiling of Nascent RNA with fastGRO publication-title: Cell Rep. doi: 10.1016/j.celrep.2020.108373 – volume: 9 start-page: 88 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib42 article-title: P-TEFb: Finding its ways to release promoter-proximally paused RNA polymerase II publication-title: Transcription doi: 10.1080/21541264.2017.1281864 – volume: 19 start-page: 65 year: 2005 ident: 10.1016/j.molcel.2024.02.032_bib9 article-title: Cotranscriptional Spliceosome Assembly Dynamics and the Role of U1snRNA:5′ss Base Pairing in Yeast publication-title: Mol. Cell doi: 10.1016/j.molcel.2005.05.006 – volume: 65 start-page: 3736 year: 2012 ident: 10.1016/j.molcel.2024.02.032_bib141 article-title: Phenotypic Analysis and Isolation of Murine Hematopoietic Stem Cells and Lineage-committed Progenitors publication-title: J. Vis. Exp. (JoVE) – volume: 83 start-page: 1264 year: 2023 ident: 10.1016/j.molcel.2024.02.032_bib7 article-title: U1snRNP increases RNA RNAPII elongation rate to enable synthesis of long genes publication-title: Mol. Cell doi: 10.1016/j.molcel.2023.03.002 – volume: 3 start-page: 16017 year: 2016 ident: 10.1016/j.molcel.2024.02.032_bib142 article-title: Production of lentiviral vectors publication-title: Mol. Ther. Methods Clin. Dev. doi: 10.1038/mtm.2016.17 – volume: 7 start-page: 1338 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib116 article-title: FastQ Screen: A tool for multi-genome mapping and quality control publication-title: F1000Res doi: 10.12688/f1000research.15931.1 – volume: 29 start-page: 1836 year: 2019 ident: 10.1016/j.molcel.2024.02.032_bib128 article-title: Identification and dynamic quantification of regulatory elements using total RNA publication-title: Genome Res. doi: 10.1101/gr.253492.119 – volume: 119 year: 2022 ident: 10.1016/j.molcel.2024.02.032_bib16 article-title: SF3B1 mutant-induced missplicing of MAP3K7 causes anemia in myelodysplastic syndromes publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.2111703119 – volume: 82 start-page: 2298 year: 2022 ident: 10.1016/j.molcel.2024.02.032_bib57 article-title: Hallmarks of DNA replication stress publication-title: Mol. Cell doi: 10.1016/j.molcel.2022.05.004 – volume: 41 start-page: 733 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib50 article-title: Integrative Profiling of Alternative Splicing Induced by U2AF1 S34F Mutation in Lung Adenocarcinoma Reveals a Mechanistic Link to Mitotic Stress publication-title: Mol. Cells – volume: 31 start-page: 1290 year: 2021 ident: 10.1016/j.molcel.2024.02.032_bib134 article-title: Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N publication-title: Genome Res. doi: 10.1101/gr.275193.120 – volume: 15 start-page: 554 year: 2014 ident: 10.1016/j.molcel.2024.02.032_bib138 article-title: MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens publication-title: Genome Biol. doi: 10.1186/s13059-014-0554-4 – volume: 53 start-page: 779 year: 2014 ident: 10.1016/j.molcel.2024.02.032_bib103 article-title: A Splicing-Dependent Transcriptional Checkpoint Associated with Prespliceosome Formation publication-title: Mol. Cell doi: 10.1016/j.molcel.2014.01.017 – volume: 170 start-page: 774 year: 2017 ident: 10.1016/j.molcel.2024.02.032_bib63 article-title: Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses publication-title: Cell doi: 10.1016/j.cell.2017.07.043 – volume: 81 start-page: 4425 year: 2021 ident: 10.1016/j.molcel.2024.02.032_bib85 article-title: SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape publication-title: Mol. Cell doi: 10.1016/j.molcel.2021.08.029 – volume: 13 start-page: 1006 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib152 article-title: Targeted in situ genome-wide profiling with high efficiency for low cell numbers publication-title: Nat. Protoc. doi: 10.1038/nprot.2018.015 – volume: 4 start-page: 1184 year: 2021 ident: 10.1016/j.molcel.2024.02.032_bib20 article-title: Generation of scalable cancer models by combining AAV-intron-trap, CRISPR/Cas9, and inducible Cre-recombinase publication-title: Commun. Biol. doi: 10.1038/s42003-021-02690-1 – volume: 294 start-page: 2892 year: 2019 ident: 10.1016/j.molcel.2024.02.032_bib105 article-title: The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface publication-title: J. Biol. Chem. doi: 10.1074/jbc.RA118.006764 – volume: 172 start-page: 117 year: 2022 ident: 10.1016/j.molcel.2024.02.032_bib37 article-title: Cancer-associated mutations in SF3B1 disrupt the interaction between SF3B1 and DDX42 publication-title: J. Biochem. doi: 10.1093/jb/mvac049 – volume: 23 start-page: 135 year: 2023 ident: 10.1016/j.molcel.2024.02.032_bib102 article-title: RNA splicing dysregulation and the hallmarks of cancer publication-title: Nat. Rev. Cancer doi: 10.1038/s41568-022-00541-7 – volume: 25 start-page: 1757 year: 2015 ident: 10.1016/j.molcel.2024.02.032_bib73 article-title: Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions publication-title: Genome Res. doi: 10.1101/gr.192294.115 – start-page: 335 year: 2016 ident: 10.1016/j.molcel.2024.02.032_bib122 article-title: Visualizing Genomic Data Using Gviz and Bioconductor doi: 10.1007/978-1-4939-3578-9_16 – start-page: 211 year: 2016 ident: 10.1016/j.molcel.2024.02.032_bib59 article-title: Analysis of Cell Proliferation and Homeostasis Using EdU Labeling – volume: 22 start-page: 1921 year: 2008 ident: 10.1016/j.molcel.2024.02.032_bib71 article-title: NELF-mediated stalling of RNAPII can enhance gene expression by blocking promoter-proximal nucleosome assembly publication-title: Genes Dev. doi: 10.1101/gad.1643208 – volume: 141 start-page: 432 year: 2010 ident: 10.1016/j.molcel.2024.02.032_bib21 article-title: c-Myc Regulates Transcriptional Pause Release publication-title: Cell doi: 10.1016/j.cell.2010.03.030 – volume: 2009 year: 2009 ident: 10.1016/j.molcel.2024.02.032_bib150 article-title: Chromatin Immunoprecipitation (ChIP) publication-title: Cold Spring Harb. Protoc. doi: 10.1101/pdb.prot5279 – volume: 8 start-page: 498 year: 2009 ident: 10.1016/j.molcel.2024.02.032_bib113 article-title: Single-vector inducible lentiviral RNAi system for oncology target validation publication-title: Cell Cycle doi: 10.4161/cc.8.3.7701 – volume: 23 start-page: 5768 year: 2003 ident: 10.1016/j.molcel.2024.02.032_bib10 article-title: Cotranscriptional Recruitment of the U1snRNP to Intron-Containing Genes in Yeast publication-title: Mol. Cell. Biol. doi: 10.1128/MCB.23.16.5768-5779.2003 – volume: 292 start-page: 262 year: 2022 ident: 10.1016/j.molcel.2024.02.032_bib107 article-title: Targeting stem cells in myelodysplastic syndromes and acute myeloid leukemia publication-title: J. Intern. Med. doi: 10.1111/joim.13535 – volume: 15 start-page: 221 year: 2018 ident: 10.1016/j.molcel.2024.02.032_bib26 article-title: TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding publication-title: Nat. Methods doi: 10.1038/nmeth.4582 – volume: 445 start-page: 661 year: 2007 ident: 10.1016/j.molcel.2024.02.032_bib100 article-title: Restoration of p53 function leads to tumour regression in vivo publication-title: Nature doi: 10.1038/nature05541 – volume: 12 start-page: 6169 year: 2022 ident: 10.1016/j.molcel.2024.02.032_bib58 article-title: Aberrant R-loop-induced replication stress in MED12-mutant uterine fibroids publication-title: Sci. Rep. doi: 10.1038/s41598-022-10188-x – volume: 32 start-page: 289 year: 2016 ident: 10.1016/j.molcel.2024.02.032_bib76 article-title: regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests. Bioinformatics, btv562 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv562 – volume: 27 start-page: 617 year: 2015 ident: 10.1016/j.molcel.2024.02.032_bib19 article-title: SRSF2 Mutations Contribute to Myelodysplasia by Mutant-Specific Effects on Exon Recognition publication-title: Cancer Cell doi: 10.1016/j.ccell.2015.04.006 – reference: 36891287 - bioRxiv. 2023 Feb 26:2023.02.25.530019. doi: 10.1101/2023.02.25.530019. |
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| SubjectTerms | Animals Chromatin - genetics co-transcriptional splicing DNA damage response Humans Mice Mutation Neoplasms Phosphoproteins - genetics Phosphoproteins - metabolism R-loops RNA polymerase II RNA Polymerase II - genetics RNA Polymerase II - metabolism RNA Splicing - genetics RNA Splicing Factors - genetics RNA Splicing Factors - metabolism SF3B1 Sin3/HDAC spliceosome transcription U2AF1 WDR5 |
| Title | Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape |
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