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Review

BRD4: a general regulator of transcription elongation

, &
Pages 70-81 | Received 14 Jun 2022, Accepted 27 Jul 2022, Published online: 01 Sep 2022

References

  • Djebali S, Davis CA, Merkel A, et al. Landscape of transcription in human cells. Nature. 2012;489(7414):101–108.
  • Jensen TH, Jacquier A, Libri D. Dealing with pervasive transcription. Mol Cell. 2013;52(4):473–484.
  • Pelechano V, Steinmetz LM. Gene regulation by antisense transcription. Nat Rev Genet. 2013;14(12):880–893.
  • Cramer P. Organization and regulation of gene transcription. Nature. 2019;573(7772):45–54.
  • Wissink EM, Vihervaara A, Tippens ND, et al. Nascent RNA analyses: tracking transcription and its regulation. Nat Rev Genet. 2019;20(12):705–723.
  • Müller F, Tora L. Chromatin and DNA sequences in defining promoters for transcription initiation. Biochim Biophys Acta. 2014;1839(3):118–128.
  • Haberle V, Stark A. Eukaryotic core promoters and the functional basis of transcription initiation. Nat Rev Mol Cell Biol. 2018;19(10):621–637.
  • Danino YM, Even D, Ideses D, et al. The core promoter: at the heart of gene expression. Biochim Biophys Acta. 2015;1849:1116–1131.
  • Vos SM, Farnung L, Boehning M, et al. Structure of activated transcription complex Pol II-DSIF-PAF-SPT6. Nature. 2018;560(7720):607–612.
  • Kireeva ML, Komissarova N, Waugh DS, et al. The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex. J Biol Chem. 2000;275(9):6530–6536.
  • Cai H, Luse DS. Transcription initiation by RNA polymerase II in vitro. Properties of preinitiation, initiation, and elongation complexes. J Biol Chem. 1987;262(1):298–304.
  • Kumar A, Clerici M, Muckenfuss LM, et al. Mechanistic insights into mRNA 3’-end processing. Curr Opin Struct Biol. 2019;59:143–150.
  • Sun Y, Hamilton K, Tong L. Recent molecular insights into canonical pre-mRNA 3’-end processing. Transcription. 2020;11(2):83–96.
  • Whitelaw E, Proudfoot N. Alpha-thalassaemia caused by a poly(A) site mutation reveals that transcriptional termination is linked to 3’ end processing in the human alpha 2 globin gene. EMBO J. 1986;5(11):2915–2922.
  • Connelly S, Manley JL. A functional mRNA polyadenylation signal is required for transcription termination by RNA polymerase II. Gene Dev. 1988;2(4):440–452.
  • Eaton JD, Davidson L, Bauer DLV, et al. Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity. Gene Dev. 2018;32(2):127–139.
  • Fong N, Brannan K, Erickson B, et al. Effects of transcription elongation rate and Xrn2 exonuclease activity on RNA polymerase II termination suggest widespread kinetic competition. Mol Cell. 2015;60(2):256–267.
  • Schwalb B, Michel M, Zacher B, et al. TT-seq maps the human transient transcriptome. Science. 2016;352(6290):1225–1228.
  • Muse GW, Gilchrist DA, Nechaev S, et al. RNA polymerase is poised for activation across the genome. Nat Genet. 2007;39(12):1507–1511.
  • Zeitlinger J, Stark A, Kellis M, et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet. 2007;39(12):1512–1516.
  • Guenther MG, Levine SS, Boyer LA, et al. A chromatin landmark and transcription initiation at most promoters in human cells. Cell. 2007;130(1):77–88.
  • Stock JK, Giadrossi S, Casanova M, et al. Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nat Cell Biol. 2007;9(12):1428–1435.
  • Jonkers I, Kwak H, Lis JT. Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons. eLife. 2014;3:e02407.
  • Laitem C, Zaborowska J, Isa NF, et al. CDK9 inhibitors define elongation checkpoints at both ends of RNA polymerase II-transcribed genes. Nat Struct Mol Biol. 2015;22(5):396–403.
  • Mayer A, Di Iulio J, Maleri S, et al. Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell. 2015;161(3):541–554.
  • Rahl PB, Lin CY, Seila AC, et al. c-Myc regulates transcriptional pause release. Cell. 2010;141(3):432–445.
  • Core L, Adelman K. Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation. Genes Dev. 2019;33(15–16):960–982.
  • Gonzalez MN, Blears D, Svejstrup JQ. Causes and consequences of RNA polymerase II stalling during transcript elongation. Nat Rev Mol Cell Biol. 2021;22(1):3–21.
  • Chen FX, Smith ER, Shilatifard A. Born to run: control of transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol. 2018;19(7):464–478.
  • Dollinger R, Gilmour DS. Regulation of promoter proximal pausing of RNA polymerase II in metazoans. J Mol Biol. 2021;433(14):166897.
  • Brannan K, Kim H, Erickson B, et al. mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. Mol Cell. 2012;46(3):311–324.
  • Krebs AR, Imanci D, Hoerner L, et al. Genome-wide single-molecule footprinting reveals high RNA polymerase II turnover at paused promoters. Mol Cell. 2017;67(3):411–422.e4.
  • Kamieniarz-Gdula K, Gdula MR, Panser K, et al. Selective roles of vertebrate PCF11 in premature and full-length transcript termination. Mol Cell. 2019;74(1):158–172.e9.
  • Mayer A, Landry HM, Churchman LS. Pause & go: from the discovery of RNA polymerase pausing to its functional implications. Curr Opin Cell Biol. 2017;46:72–80.
  • Liu X, Kraus WL, Bai X. Ready, pause, go: regulation of RNA polymerase II pausing and release by cellular signaling pathways. Trends Biochem Sci. 2015;40(9):516–525.
  • Landick R. The regulatory roles and mechanism of transcriptional pausing. Biochem Soc Trans. 2006;34(6):1062–1066.
  • Gajos M, Jasnovidova O, van Bömmel A, et al. Conserved DNA sequence features underlie pervasive RNA polymerase pausing. Nucleic Acids Res. 2021;49(8):4402–4420.
  • Glover-Cutter K, Kim S, Espinosa J, et al. RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nat Struct Mol Biol. 2008;15(1):71–78.
  • Saldi T, Cortazar MA, Sheridan RM, et al. Coupling of RNA polymerase II transcription elongation with Pre-mRNA splicing. J Mol Biol. 2016;428(12):2623–2635.
  • Gehring NH, Roignant J-Y. Anything but ordinary - Emerging splicing mechanisms in eukaryotic gene regulation. Trends Genet. 2021;37(4):355–372.
  • Neugebauer KM. Nascent RNA and the coordination of splicing with transcription. Cold Spring Harb Perspect Biol. 2019;11(8):a032227.
  • Custódio N, Carmo-Fonseca M. Co-transcriptional splicing and the CTD code. Crit Rev Biochem Mol Biol. 2016;51(5):395–411.
  • Lenasi T, Barboric M. Mutual relationships between transcription and pre-mRNA processing in the synthesis of mRNA. Wiley Interdiscip Rev RNA. 2013;4(2):139–154.
  • Giono LE, Kornblihtt AR. Linking transcription, RNA polymerase II elongation and alternative splicing. Biochem J. 2020;477(16):3091–3104.
  • Peck SA, Hughes KD, Victorino JF, et al. Writing a wrong: coupled RNA polymerase II transcription and RNA quality control. Wiley Interdiscip Rev Rna. 2019;10(4):e1529.
  • de la Mata M, Alonso CR, Kadener S, et al. A slow RNA polymerase II affects alternative splicing in Vivo. Mol Cell. 2003;12(2):525–532.
  • Fong N, Kim H, Zhou Y, et al. Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Gene Dev. 2014;28(23):2663–2676.
  • Howe KJ, Kane CM, Ares M. Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. Rna. 2003;9(8):993–1006.
  • Eischer N, Arnold M, Mayer A. Emerging roles of BET proteins in transcription and co-transcriptional RNA processing. Wiley Interdiscip Rev RNA. 2022;e1734. DOI:10.1002/wrna.1734
  • Devaiah BN, Gegonne A, Singer DS. Bromodomain 4: a cellular Swiss army knife. J Leukoc Biol. 2016;100(4):679–686.
  • Taniguchi Y. The Bromodomain and Extra-terminal domain (BET) family: functional anatomy of BET paralogous proteins. Int J Mol Sci. 2016;17(11):1849.
  • S-Y W, Chiang C-M. The double bromodomain-containing chromatin adaptor Brd4 and transcriptional regulation. J Biol Chem. 2007;282(18):13141–13145.
  • Dey A, Ellenberg J, Farina A, et al. A bromodomain protein, MCAP, associates with mitotic chromosomes and affects G 2 -to-M transition. Mol Cell Biol. 2000;20(17):6537–6549.
  • Houzelstein D, Bullock SL, Lynch DE, et al. Growth and early postimplantation defects in mice deficient for the bromodomain-containing protein Brd4. Mol Cellular Biol. 2002;22(11):3794–3802.
  • Jones MH, Numata M, Shimane M. Identification and characterization of BRDT: a testis-specific gene related to the bromodomain genes RING3 and Drosophila fsh. Genomics. 1997;45(3):529–534.
  • Donczew R, Hahn S. BET family members Bdf1/2 modulate global transcription initiation and elongation in Saccharomyces cerevisiae. eLife. 2021;10:e69619.
  • Shi J, Whyte WA, Zepeda-Mendoza CJ, et al. Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. Genes Dev. 2013;27(24):2648–2662.
  • Padmanabhan A, Haldar SM. Drugging transcription in heart failure. J Physiol. 2020;598(14):3005–3014.
  • Wang C-Y, Filippakopoulos P. Beating the odds: BETS in disease. Trends Biochem Sci. 2015;40(8):468–479.
  • Jacques C, Lavaud M, Georges S, et al. BET bromodomains’ functions in bone-related pathologies. Epigenomics. 2020;12(2):127–144.
  • Belkina AC, Denis GV. BET domain co-regulators in obesity, inflammation and cancer. Nat Rev Cancer. 2012;12(7):465–477.
  • Donati B, Lorenzini E, Ciarrocchi A. BRD4 and cancer: going beyond transcriptional regulation. Mol Cancer. 2018;17(1):1–3.
  • Conrad RJ, Fozouni P, Thomas S, et al. The short isoform of BRD4 promotes HIV-1 latency by engaging repressive SWI/SNF chromatin-remodeling complexes. Mol Cell. 2017;67(6):1001–1012.e6.
  • Konuma T, Yu D, Zhao C, et al. Structural mechanism of the oxygenase JMJD6 recognition by the extraterminal (ET) domain of BRD4. Sci Rep. 2017;7(1):1–10.
  • Shaila R, Mathew ES, Matthias O, et al. The Brd4 extraterminal domain confers transcription activation independent of pTEFb by recruiting multiple proteins, including NSD3. Mol Cell Biol. 2011;31(13):2641–2652.
  • Shen C, Ipsaro JJ, Shi J, et al. NSD3-Short Is an adaptor protein that couples BRD4 to the CHD8 chromatin remodeler. Mol Cell. 2015;60(6):847–859.
  • Wai DCC, Szyszka TN, Campbell AE, et al. The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators. J Biol Chem. 2018;293(19):7160–7175.
  • Filippakopoulos P, Picaud S, Mangos M, et al. Histone recognition and large-scale structural analysis of the human bromodomain family. Cell. 2012;149(1):214–231.
  • Kanno T, Kanno Y, Siegel RM, et al. Selective recognition of acetylated histones by bromodomain proteins visualized in living cells. Mol Cell. 2004;13(1):33–43.
  • Gamsjaeger R, Webb SR, Lamonica JM, et al. Structural basis and specificity of acetylated transcription factor GATA1 recognition by BET family bromodomain protein BRD3. Mol Cell Biol. 2011;31(13):2632–2640.
  • Huang B, Yang X-D, Zhou -M-M, et al. Brd4 coactivates transcriptional activation of NF-kappaB via specific binding to acetylated RELA. Mol Cell Biol. 2009;29(5):1375–1387.
  • Lamonica JM, Deng W, Kadauke S, et al. Bromodomain protein BRD3 associates with acetylated GATA1 to promote its chromatin occupancy at erythroid target genes. Proc Natl Acad Sci. 2011;108(22):E159–68.
  • Kanno T, Kanno Y, LeRoy G, et al. BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones. Nat Struct Mol Biol. 2014;21(12):1047–1057.
  • Andrikopoulou A, Liontos M, Koutsoukos K, et al. Clinical perspectives of BET inhibition in ovarian cancer. Cell Oncol. 2021;44(2):237–249.
  • Cochran AG, Conery AR, Sims RJ. Bromodomains: a new target class for drug development. Nat Rev Drug Discov. 2019;18(8):609–628.
  • Winter GE, Mayer A, Buckley DL, et al. BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment. Mol Cell. 2017;67(1):5–18.e19.
  • Xu L, Chen Y, Mayakonda A, et al. Targetable BET proteins- and E2F1-dependent transcriptional program maintains the malignancy of glioblastoma. Proc Natl Acad Sci. 2018;115(22):E5086–E5095.
  • Bauer K, Berghoff AS, Preusser M, et al. Degradation of BRD4 - a promising treatment approach not only for hematologic but also for solid cancer. Am J Cancer Res. 2021;11(2):530–545.
  • Peterlin BM, Price DH. Controlling the elongation phase of transcription with P-TEFb. Mol Cell. 2006;23(3):297–305.
  • Price DH. P-TEFb, a cyclin-dependent kinase controlling elongation by RNA polymerase II. Mol Cellular Biol. 2000;20(8):2629–2634.
  • Sansó M, Levin RS, Lipp JJ, et al. P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates. Genes Dev. 2016;30(1):117–131.
  • Schüller R, Forné I, Straub T, et al. Heptad-Specific phosphorylation of RNA polymerase II CTD. Mol Cell. 2016;61(2):305–314.
  • Bösken CA, Farnung L, Hintermair C, et al. The structure and substrate specificity of human Cdk12/Cyclin K. Nature Commun. 2014;5(1):3505–3514.
  • Eick D, Geyer M. The RNA polymerase II carboxy-terminal domain (CTD) code. Chem Rev. 2013;113(11):8456–8490.
  • Harlen KM, Churchman LS. The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain. Nat Rev Mol Cell Biol. 2017;18(4):263–273.
  • Zaborowska J, Egloff S, Murphy S. The pol II CTD: new twists in the tail. Nat Struct Mol Biol. 2016;23(9):771–777.
  • Buratowski S. Progression through the RNA polymerase II CTD cycle. Mol Cell. 2009;36(4):541–546.
  • Egloff S. CDK9 keeps RNA polymerase II on track. Cell Mol Life Sci. 2021;78(14):5543–5567.
  • Bacon CW, D’Orso I. CDK9: a signaling hub for transcriptional control. Transcription. 2019;10(2):57–75.
  • Jeronimo C, Cois RF. The mediator complex: at the nexus of RNA polymerase II transcription. Trends Cell Biol. 2017;27(10):765–783.
  • Quaresma AJC, Bugai A, Barboric M. Cracking the control of RNA polymerase II elongation by 7SK snRNP and P-TEFb. Nucleic Acids Res. 2016;44(16):7527–7539.
  • Jang MK, Mochizuki K, Zhou M, et al. The bromodomain protein BRD4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription. Mol Cell. 2005;19(4):523–534.
  • Yang Z, Yik JHN, Chen R, et al. Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein BRD4. Mol Cell. 2005;19(4):535–545.
  • Filippakopoulos P, Qi J, Picaud S, et al. Selective inhibition of BET bromodomains. Nature. 2010;468(7327):1067–1073.
  • Nicodeme E, Jeffrey KL, Schaefer U, et al. Suppression of inflammation by a synthetic histone mimic. Nature. 2010;468(7327):1119–1123.
  • Dawson MA, Prinjha RK, Dittmann A, et al. Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. Nature. 2011;478(7370):529–533.
  • Xu Y, Vakoc CR. Targeting cancer cells with BET bromodomain inhibitors. Cold Spring Harb Perspect Med. 2017;7(7):a026674.
  • Lovén J, Hoke HA, Lin CY, et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell. 2013;153(2):320–334.
  • Micco RD, Fontanals-Cirera B, Low V, et al. Control of embryonic stem cell identity by BRD4-dependent transcriptional elongation of super-enhancer-associated pluripotency genes. Cell Rep. 2014;9(1):234–247.
  • Whyte WA, Orlando DA, Hnisz D, et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell. 2013;153(2):307–319.
  • Hnisz D, Abraham BJ, Lee TI, et al. Super-enhancers in the control of cell identity and disease. Cell. 2013;155(4):934–947.
  • Anand P, Brown JD, Lin CY, et al. BET bromodomains mediate transcriptional pause release in heart failure. Cell. 2013;154(3):569–582.
  • Bartman CR, Hamagami N, Keller CA, et al. Transcriptional burst initiation and polymerase pause release are key control points of transcriptional regulation. Mol Cell. 2019;73(3):519–532.e4.
  • Wade JT, Struhl K. The transition from transcriptional initiation to elongation. Curr Opin Genet Dev. 2008;18(2):130–136.
  • Khoueiry P, Gahlawat AW, Petretich M, et al. BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity. Epigenetics Chromatin. 2019;12(1):1–8.
  • Arnold M, Bressin A, Jasnovidova O, et al. A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3’-processing and termination. Mol Cell. 2021;81(17):3589–3603.e13.
  • Winter GE, Buckley DL, Paulk J, et al. Phthalimide conjugation as a strategy for in vivo target protein degradation. Science. 2015;348(6241):1376–1381.
  • Lu J, Qian Y, Altieri M, et al. Hijacking the E3 ubiquitin ligase cereblon to efficiently target BRD4. Chem Biol. 2015;22(6):755–763.
  • Zengerle M, Chan K-H, Ciulli A. Selective small molecule induced degradation of the BET bromodomain protein BRD4. ACS Chem Biol. 2015;10(8):1770–1777.
  • Muhar M, Ebert A, Neumann T, et al. SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. Science. 2018;360(6390):800–805.
  • Zheng B, Aoi Y, Shah AP, et al. Acute perturbation strategies in interrogating RNA polymerase II elongation factor function in gene expression. Genes Dev. 2021;35(3–4):273–285.
  • Floyd SR, Pacold ME, Huang Q, et al. The bromodomain protein BRD4 insulates chromatin from DNA damage signalling. Nature. 2013;498(7453):246–250.
  • S-Y W, Lee C-F, Lai H-T, et al. Opposing functions of BRD4 isoforms in breast cancer. Mol Cell. 2020;78(6):1114–1132.e10.
  • Hou L, Wang Y, Liu Y, et al. Paf1C regulates RNA polymerase II progression by modulating elongation rate. Proc Natl Acad Sci. 2019;116(29):14583–14592.
  • Francette AM, Tripplehorn SA, Arndt KM. The Paf1 complex: a keystone of nuclear regulation operating at the interface of transcription and chromatin. J Mol Biol. 2021;433(14):166979.
  • Liu W, Ma Q, Wong K, et al. Brd4 and JMJD6-associated anti-pause enhancers in regulation of transcriptional pause release. Cell. 2013;155(7):1581–1595.
  • Zhang W, Prakash C, Sum C, et al. Bromodomain-containing protein 4 (BRD4) regulates RNA polymerase II serine 2 phosphorylation in human CD4+ T cells*. J Biol Chem. 2012;287(51):43137–43155.
  • Eaton JD, Francis L, Davidson L, et al. A unified allosteric/torpedo mechanism for transcriptional termination on human protein-coding genes. Gene Dev. 2020;34(1–2):132–145.
  • Mandel CR, Kaneko S, Zhang H, et al. Polyadenylation factor CPSF-73 is the pre-mRNA 3’-end-processing endonuclease. Nature. 2006;444(7121):953–956.
  • Nordick K, Hoffman MG, Betz JL, et al. Direct interactions between the Paf1 complex and a cleavage and polyadenylation factor are revealed by dissociation of Paf1 from RNA polymerase II. Eukaryot Cell. 2008;7(7):1158–1167.
  • Lindstrom DL, Squazzo SL, Muster N, et al. Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Mol Cell Biol. 2003;23(4):1368–1378.
  • Mayer A, Schreieck A, Lidschreiber M, et al. The Spt5 C-terminal region recruits yeast 3′ RNA cleavage factor I. Mol Cell Biol. 2012;32(7):1321–1331.
  • Yang Y, Li W, Hoque M, et al. PAF complex plays novel subunit-specific roles in alternative cleavage and polyadenylation. Plos Genet. 2016;12(1):e1005794.
  • Bhagwat AS, Roe J-S, Mok BYL, et al. BET bromodomain inhibition releases the mediator complex from select cis-regulatory elements. Cell Rep. 2016;15(3):519–530.
  • Crump NT, Ballabio E, Godfrey L, et al. BET inhibition disrupts transcription but retains enhancer-promoter contact. Nature Commun. 2021;12(1):223.
  • Rahnamoun H, Lee J, Sun Z, et al. RNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation. Nat Struct Mol Biol. 2018;25(8):687–697.
  • Jiang YW, Veschambre P, Erdjument-Bromage H, et al. Mammalian mediator of transcriptional regulation and its possible role as an end-point of signal transduction pathways. Proc Natl Acad Sci. 1998;95(15):8538–8543.
  • Donner AJ, Ebmeier CC, Taatjes DJ, et al. CDK8 is a positive regulator of transcriptional elongation within the serum response network. Nat Struct Mol Biol. 2010;17(2):194–201.
  • Sabari BR, Dall’Agnese A, Boija A, et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science. 2018;361(6400):eaar3958.
  • Shin Y, Chang Y-C, Lee DSW, et al. Liquid nuclear condensates mechanically sense and restructure the genome. Cell. 2018;175(6):1481–1491.e13.
  • Cortazar MA, Sheridan RM, Erickson B, et al. Control of RNA Pol II speed by PNUTS-PP1 and Spt5 dephosphorylation facilitates termination by a “Sitting duck torpedo” mechanism. Mol Cell. 2019;76(6):896–908.e4.
  • Parua PK, Kalan S, Benjamin B, et al. Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II. Nature Commun. 2020;11(1):1–3.
  • Kecman T, Kuś K, Heo D-H, et al. Elongation/termination factor exchange mediated by PP1 phosphatase orchestrates transcription termination. Cell Rep. 2018;25(1):259–269.e5.
  • Chen FX, Woodfin AR, Gardini A, et al. PAF1, a molecular regulator of promoter-proximal pausing by RNA polymerase II. Cell. 2015;162(5):1003–1015.
  • Lambert J-P, Picaud S, Fujisawa T, et al. Interactome rewiring following pharmacological targeting of BET bromodomains. Mol Cell. 2019;73(3):621–638.e17.
  • Yu M, Yang W, Ni T, et al. RNA polymerase II-associated factor 1 regulates the release and phosphorylation of paused RNA polymerase II. Science. 2015;350(6266):1383–1386.
  • Nishimura K, Fukagawa T, Takisawa H, et al. An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nat Methods. 2009;6(12):917–922.
  • Nabet B, Roberts JM, Buckley DL, et al. The dTAG system for immediate and target-specific protein degradation. Nat Chem Biol. 2018;14(5):431–441.
  • Orlando DA, Chen MW, Brown VE, et al. Quantitative ChIP-Seq normalization reveals global modulation of the epigenome. Cell Rep. 2014;9(3):1163–1170.
  • Herzel L, Straube K, Neugebauer KM. Long-read sequencing of nascent RNA reveals coupling among RNA processing events. Genome Res. 2018;28(7):1008–1019.
  • Drexler HL, Choquet K, Churchman LS. Splicing kinetics and coordination revealed by direct nascent RNA sequencing through nanopores. Mol Cell. 2020;77(5):985–998.e8.
  • Churchman LS, Weissman JS. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature. 2011;469(7330):368–373.
  • Nojima T, Gomes T, Grosso ARF, et al. Mammalian NET-Seq reveals genome-wide nascent transcription coupled to RNA processing. Cell. 2015;161(3):526–540.
  • Herzog VA, Reichholf B, Neumann T, et al. Thiol-linked alkylation of RNA to assess expression dynamics. Nat Methods. 2017;14(12):1198–1204.