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Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA polymerase II transcription.

Wang, F ; El-Saafin, F ; et al.
In: Cell death and differentiation, Jg. 28 (2021-08-01), Heft 8, S. 2385-2403
academicJournal

Titel:
Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA polymerase II transcription.
Autor/in / Beteiligte Person: Wang, F ; El-Saafin, F ; Ye, T ; Stierle, M ; Negroni, L ; Durik, M ; Fischer, V ; Devys, D ; Vincent, SD ; Tora, L
Zeitschrift: Cell death and differentiation, Jg. 28 (2021-08-01), Heft 8, S. 2385-2403
Veröffentlichung: <2003->: London : Nature Publishing Group ; <i>Original Publication</i>: London : Edward Arnold, c1994-, 2021
Medientyp: academicJournal
ISSN: 1476-5403 (electronic)
DOI: 10.1038/s41418-021-00759-2
Schlagwort:
  • Animals
  • Mice
  • Transcription Factors metabolism
  • Ubiquitination
  • Gene Expression genetics
  • Histones metabolism
  • RNA Polymerase II genetics
  • RNA Polymerase II metabolism
Sonstiges:
  • Nachgewiesen in: MEDLINE
  • Sprachen: English
  • Publication Type: Journal Article
  • Language: English
  • [Cell Death Differ] 2021 Aug; Vol. 28 (8), pp. 2385-2403. <i>Date of Electronic Publication: </i>2021 Mar 17.
  • MeSH Terms: Gene Expression / *genetics ; Histones / *metabolism ; RNA Polymerase II / *genetics ; RNA Polymerase II / *metabolism ; Animals ; Mice ; Transcription Factors / metabolism ; Ubiquitination
  • References: Festuccia N, Gonzalez I, Navarro P. The epigenetic paradox of pluripotent ES cells. J Mol Biol. 2017;429:1476–503. (PMID: 2798822510.1016/j.jmb.2016.12.009) ; Osley MA. Regulation of histone H2A and H2B ubiquitylation. Brief Funct Genom Proteomic. 2006;5:179–89. (PMID: 10.1093/bfgp/ell022) ; Zhu B, Zheng Y, Pham AD, Mandal SS, Erdjument-Bromage H, Tempst P, et al. Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation. Mol Cell. 2005;20:601–11. (PMID: 1630792310.1016/j.molcel.2005.09.025) ; Shiloh Y, Shema E, Moyal L, Oren M. RNF20-RNF40: A ubiquitin-driven link between gene expression and the DNA damage response. FEBS Lett. 2011;585:2795–802. (PMID: 2182775610.1016/j.febslet.2011.07.034) ; Fierz B, Chatterjee C, McGinty RK, Bar-Dagan M, Raleigh DP, Muir TW. Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction. Nat Chem Biol. 2011;7:113–9. (PMID: 21196936307876810.1038/nchembio.501) ; Minsky N, Shema E, Field Y, Schuster M, Segal E, Oren M. Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells. Nat Cell Biol. 2008;10:483–8. (PMID: 1834498510.1038/ncb1712) ; Shema E, Tirosh I, Aylon Y, Huang J, Ye C, Moskovits N, et al. The histone H2B-specific ubiquitin ligase RNF20/hBRE1 acts as a putative tumor suppressor through selective regulation of gene expression. Genes Dev. 2008;22:2664–76. (PMID: 18832071255990510.1101/gad.1703008) ; Trujillo KM, Osley MA. A role for H2B ubiquitylation in DNA replication. Mol Cell. 2012;48:734–46. (PMID: 23103252352577210.1016/j.molcel.2012.09.019) ; Kari V, Shchebet A, Neumann H, Johnsen SA. The H2B ubiquitin ligase RNF40 cooperates with SUPT16H to induce dynamic changes in chromatin structure during DNA double-strand break repair. Cell Cycle. 2011;10:3495–504. (PMID: 2203101910.4161/cc.10.20.17769) ; Moyal L, Lerenthal Y, Gana-Weisz M, Mass G, So S, Wang SY, et al. Requirement of ATM-dependent monoubiquitylation of histone H2B for timely repair of DNA double-strand breaks. Mol Cell. 2011;41:529–42. (PMID: 21362549339714610.1016/j.molcel.2011.02.015) ; Nakamura K, Kato A, Kobayashi J, Yanagihara H, Sakamoto S, Oliveira DV, et al. Regulation of homologous recombination by RNF20-dependent H2B ubiquitination. Mol Cell. 2011;41:515–28. (PMID: 2136254810.1016/j.molcel.2011.02.002) ; Xie W, Nagarajan S, Baumgart SJ, Kosinsky RL, Najafova Z, Kari V, et al. RNF40 regulates gene expression in an epigenetic context-dependent manner. Genome Biol. 2017;18:32. (PMID: 28209164531448610.1186/s13059-017-1159-5) ; Vitaliano-Prunier A, Babour A, Herissant L, Apponi L, Margaritis T, Holstege FC, et al. H2B ubiquitylation controls the formation of export-competent mRNP. Mol Cell. 2012;45:132–9. (PMID: 22244335325952910.1016/j.molcel.2011.12.011) ; Pirngruber J, Shchebet A, Schreiber L, Shema E, Minsky N, Chapman RD, et al. CDK9 directs H2B monoubiquitination and controls replication-dependent histone mRNA 3’-end processing. EMBO Rep. 2009;10:894–900. (PMID: 19575011272667710.1038/embor.2009.108) ; Evangelista FM, Maglott-Roth A, Stierle M, Brino L, Soutoglou E, Tora L. Transcription and mRNA export machineries SAGA and TREX-2 maintain monoubiquitinated H2B balance required for DNA repair. J Cell Biol. 2018;217:3382–97. (PMID: 30054449616825610.1083/jcb.201803074) ; Pavri R, Zhu B, Li G, Trojer P, Mandal S, Shilatifard A, et al. Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. Cell. 2006;125:703–17. (PMID: 1671356310.1016/j.cell.2006.04.029) ; Chandrasekharan MB, Huang F, Sun ZW. Histone H2B ubiquitination and beyond: Regulation of nucleosome stability, chromatin dynamics and the trans-histone H3 methylation. Epigenetics. 2010;5:460–8. (PMID: 20523115323054810.4161/epi.5.6.12314) ; Bonnet J, Devys D, Tora L. Histone H2B ubiquitination: signaling not scrapping. Drug Discov Today Technol. 2014;12:e19–27. (PMID: 2502737010.1016/j.ddtec.2012.09.002) ; Bonnet J, Wang CY, Baptista T, Vincent SD, Hsiao WC, Stierle M, et al. The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription. Gene Dev. 2014;28:1999–2012. (PMID: 25228644417315810.1101/gad.250225.114) ; Fuchs G, Hollander D, Voichek Y, Ast G, Oren M. Cotranscriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate. Genome Res. 2014;24:1572–83. (PMID: 25049226419936710.1101/gr.176487.114) ; Jung I, Kim SK, Kim M, Han YM, Kim YS, Kim D, et al. H2B monoubiquitylation is a 5’-enriched active transcription mark and correlates with exon-intron structure in human cells. Genome Res. 2012;22:1026–35. (PMID: 22421545337170610.1101/gr.120634.111) ; Briggs SD, Xiao T, Sun ZW, Caldwell JA, Shabanowitz J, Hunt DF, et al. Gene silencing: trans-histone regulatory pathway in chromatin. Nature. 2002;418:498. (PMID: 1215206710.1038/nature00970) ; Dover J, Schneider J, Tawiah-Boateng MA, Wood A, Dean K, Johnston M, et al. Methylation of histone H3 by COMPASS requires ubiquitination of histone H2B by Rad6. J Biol Chem. 2002;277:28368–71. (PMID: 1207013610.1074/jbc.C200348200) ; Ng HH, Xu RM, Zhang Y, Struhl K. Ubiquitination of histone H2B by Rad6 is required for efficient Dot1-mediated methylation of histone H3 lysine 79. J Biol Chem. 2002;277:34655–7. (PMID: 1216763410.1074/jbc.C200433200) ; Sun ZW, Allis CD. Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature. 2002;418:104–8. (PMID: 1207760510.1038/nature00883) ; Lee JS, Shukla A, Schneider J, Swanson SK, Washburn MP, Florens L, et al. Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS. Cell. 2007;131:1084–96. (PMID: 1808309910.1016/j.cell.2007.09.046) ; Kim J, Kim JA, McGinty RK, Nguyen UT, Muir TW, Allis CD, et al. The n-SET domain of Set1 regulates H2B ubiquitylation-dependent H3K4 methylation. Mol Cell. 2013;49:1121–33. (PMID: 23453808361514010.1016/j.molcel.2013.01.034) ; Daniel JA, Torok MS, Sun ZW, Schieltz D, Allis CD, Yates JR 3rd, et al. Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription. J Biol Chem. 2004;279:1867–71. (PMID: 1466063410.1074/jbc.C300494200) ; Henry KW, Wyce A, Lo WS, Duggan LJ, Emre NC, Kao CF, et al. Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev. 2003;17:2648–63. (PMID: 1456367928061510.1101/gad.1144003) ; Zhao Y, Lang G, Ito S, Bonnet J, Metzger E, Sawatsubashi S, et al. A TFTC/STAGA module mediates histone H2A and H2B deubiquitination, coactivates nuclear receptors, and counteracts heterochromatin silencing. Mol Cell. 2008;29:92–101. (PMID: 1820697210.1016/j.molcel.2007.12.011) ; Zhang XY, Varthi M, Sykes SM, Phillips C, Warzecha C, Zhu W, et al. The putative cancer stem cell marker USP22 is a subunit of the human SAGA complex required for activated transcription and cell-cycle progression. Mol Cell. 2008;29:102–11. (PMID: 18206973225452210.1016/j.molcel.2007.12.015) ; Lang G, Bonnet J, Umlauf D, Karmodiya K, Koffler J, Stierle M, et al. The tightly controlled deubiquitination activity of the human SAGA complex differentially modifies distinct gene regulatory elements. Mol Cell Biol. 2011;31:3734–44. (PMID: 21746879316572210.1128/MCB.05231-11) ; Morgan MT, Wolberger C. Recognition of ubiquitinated nucleosomes. Curr Opin Struct Biol. 2017;42:75–82. (PMID: 2792320910.1016/j.sbi.2016.11.016) ; Atanassov BS, Mohan RD, Lan X, Kuang X, Lu Y, Lin K, et al. ATXN7L3 and ENY2 coordinate activity of multiple h2b deubiquitinases important for cellular proliferation and tumor growth. Mol Cell. 2016;62:558–71. (PMID: 27132940487487910.1016/j.molcel.2016.03.030) ; Bonnet J, Romier C, Tora L, Devys D. Zinc-finger UBPs: regulators of deubiquitylation. Trends Biochem Sci. 2008;33:369–75. (PMID: 1860343110.1016/j.tibs.2008.05.005) ; Atanassov BS, Evrard YA, Multani AS, Zhang Z, Tora L, Devys D, et al. Gcn5 and SAGA regulate shelterin protein turnover and telomere maintenance. Mol Cell. 2009;35:352–64. (PMID: 19683498274949210.1016/j.molcel.2009.06.015) ; Gennaro VJ, Stanek TJ, Peck AR, Sun Y, Wang F, Qie S, et al. Control of CCND1 ubiquitylation by the catalytic SAGA subunit USP22 is essential for cell cycle progression through G1 in cancer cells. Proc Natl Acad Sci USA. 2018;115:E9298–E9307. (PMID: 30224477617661510.1073/pnas.1807704115) ; Atanassov BS, Dent SY. USP22 regulates cell proliferation by deubiquitinating the transcriptional regulator FBP1. EMBO Rep. 2011;12:924–30. (PMID: 21779003316646010.1038/embor.2011.140) ; Armour SM, Bennett EJ, Braun CR, Zhang XY, McMahon SB, Gygi SP, et al. A high-confidence interaction map identifies SIRT1 as a mediator of acetylation of USP22 and the SAGA coactivator complex. Mol Cell Biol. 2013;33:1487–502. (PMID: 23382074362424910.1128/MCB.00971-12) ; Lin Z, Yang H, Kong Q, Li J, Lee SM, Gao B, et al. USP22 antagonizes p53 transcriptional activation by deubiquitinating Sirt1 to suppress cell apoptosis and is required for mouse embryonic development. Mol Cell. 2012;46:484–94. (PMID: 2254245510.1016/j.molcel.2012.03.024) ; Kobayashi T, Iwamoto Y, Takashima K, Isomura A, Kosodo Y, Kawakami K, et al. Deubiquitinating enzymes regulate Hes1 stability and neuronal differentiation. FEBS J. 2015;282:2411–23. (PMID: 2584615310.1111/febs.13290) ; Lambies G, Miceli M, Martinez-Guillamon C, Olivera-Salguero R, Pena R, Frias CP, et al. TGFbeta-activated USP27X deubiquitinase regulates cell migration and chemoresistance via stabilization of Snail1. Cancer Res. 2019;79:33–46. (PMID: 3034106610.1158/0008-5472.CAN-18-0753) ; Zhou Z, Zhang P, Hu X, Kim J, Yao F, Xiao Z, et al. USP51 promotes deubiquitination and stabilization of ZEB1. Am J Cancer Res. 2017;7:2020–31. (PMID: 291190515665849) ; Koutelou E, Wang L, Schibler AC, Chao HP, Kuang X, Lin K, et al. USP22 controls multiple signaling pathways that are essential for vasculature formation in the mouse placenta. Development. 2019;146:dev174037. (PMID: 30718289639844810.1242/dev.174037) ; Tyanova S, Temu T, Sinitcyn P, Carlson A, Hein MY, Geiger T, et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods. 2016;13:731–40. (PMID: 2734871210.1038/nmeth.3901) ; Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21. (PMID: 10.1093/bioinformatics/bts63523104886) ; Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. (PMID: 25516281430204910.1186/s13059-014-0550-8) ; El-Saafin F, Curry C, Ye T, Garnier JM, Kolb-Cheynel I, Stierle M, et al. Homozygous TAF8 mutation in a patient with intellectual disability results in undetectable TAF8 protein, but preserved RNA polymerase II transcription. Hum Mol Genet. 2018;27:2171–86. (PMID: 29648665598572510.1093/hmg/ddy126) ; Gyenis A, Umlauf D, Ujfaludi Z, Boros I, Ye T, Tora L. UVB induces a genome-wide acting negative regulatory mechanism that operates at the level of transcription initiation in human cells. PLoS Genet. 2014;10:e1004483. (PMID: 25058334410990610.1371/journal.pgen.1004483) ; Chapman RD, Heidemann M, Albert TK, Mailhammer R, Flatley A, Meisterernst M, et al. Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7. Science. 2007;318:1780–2. (PMID: 1807940410.1126/science.1145977) ; Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:R106. (PMID: 20979621321866210.1186/gb-2010-11-10-r106) ; Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, Davidson I, et al. seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res. 2011;39:e35. (PMID: 2117764510.1093/nar/gkq1287) ; Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, et al. c-Myc regulates transcriptional pause release. Cell. 2010;141:432–45. (PMID: 20434984286402210.1016/j.cell.2010.03.030) ; Kosinsky RL, Wegwitz F, Hellbach N, Dobbelstein M, Mansouri A, Vogel T, et al. Usp22 deficiency impairs intestinal epithelial lineage specification in vivo. Oncotarget. 2015;6:37906–18. (PMID: 26431380474197310.18632/oncotarget.5412) ; Martello G, Smith A. The nature of embryonic stem cells. Annu Rev Cell Dev Biol. 2014;30:647–75. (PMID: 2528811910.1146/annurev-cellbio-100913-013116) ; Hutchins AP, Yang Z, Li Y, He F, Fu X, Wang X, et al. Models of global gene expression define major domains of cell type and tissue identity. Nucleic Acids Res. 2017;45:2354–67. (PMID: 28426095538970610.1093/nar/gkx054) ; Adelman K, Lis JT. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat Rev Genet. 2012;13:720–31. (PMID: 22986266355249810.1038/nrg3293) ; Krebs AR, Imanci D, Hoerner L, Gaidatzis D, Burger L, Schubeler D. Genome-wide single-molecule footprinting reveals high RNA polymerase II turnover at paused promoters. Mol Cell. 2017;67:411–22 e414. (PMID: 28735898554895410.1016/j.molcel.2017.06.027) ; Erickson B, Sheridan RM, Cortazar M, Bentley DL. Dynamic turnover of paused Pol II complexes at human promoters. Genes Dev. 2018;32:1215–25. (PMID: 30150253612072010.1101/gad.316810.118) ; Harlen KM, Churchman LS. The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain. Nat Rev Mol Cell Biol. 2017;18:263–73. (PMID: 2824832310.1038/nrm.2017.10) ; Chen FX, Woodfin AR, Gardini A, Rickels RA, Marshall SA, Smith ER, et al. PAF1, a molecular regulator of promoter-proximal pausing by RNA polymerase II. Cell. 2015;162:1003–15. (PMID: 26279188467914410.1016/j.cell.2015.07.042) ; Vincent SD, Dunn NR, Hayashi S, Norris DP, Robertson EJ. Cell fate decisions within the mouse organizer are governed by graded Nodal signals. Genes Dev. 2003;17:1646–62. (PMID: 1284291319613610.1101/gad.1100503) ; Seruggia D, Oti M, Tripathi P, Canver MC, LeBlanc L, Di Giammartino DC, et al. TAF5L and TAF6L maintain self-renewal of embryonic stem cells via the MYC regulatory network. Mol Cell. 2019;74:1148–63 e1147. (PMID: 31005419667162810.1016/j.molcel.2019.03.025) ; Laribee RN, Fuchs SM, Strahl BD. H2B ubiquitylation in transcriptional control: a FACT-finding mission. Genes Dev. 2007;21:737–43. (PMID: 1740377510.1101/gad.1541507) ; Baptista T, Devys D. Saccharomyces cerevisiae metabolic labeling with 4-thiouracil and the quantification of newly synthesized mRNA as a proxy for RNA polymerase II activity. J Vis Exp. 2018;140:57982. ; Fleming AB, Kao CF, Hillyer C, Pikaart M, Osley MA. H2B ubiquitylation plays a role in nucleosome dynamics during transcription elongation. Mol Cell. 2008;31:57–66. (PMID: 1861404710.1016/j.molcel.2008.04.025) ; Batta K, Zhang Z, Yen K, Goffman DB, Pugh BF. Genome-wide function of H2B ubiquitylation in promoter and genic regions. Genes Dev. 2011;25:2254–65. (PMID: 22056671321923010.1101/gad.177238.111) ; Fierz B, Kilic S, Hieb AR, Luger K, Muir TW. Stability of nucleosomes containing homogenously ubiquitylated H2A and H2B prepared using semisynthesis. J Am Chem Soc. 2012;134:19548–51. (PMID: 23163596353526410.1021/ja308908p) ; Acharya D, Hainer SJ, Yoon Y, Wang F, Bach I, Rivera-Perez JA, et al. KAT-independent gene regulation by Tip60 promotes ESC Self-renewal but not pluripotency. Cell Rep. 2017;19:671–9. (PMID: 28445719548406710.1016/j.celrep.2017.04.001) ; Dorighi KM, Swigut T, Henriques T, Bhanu NV, Scruggs BS, Nady N, et al. Mll3 and Mll4 facilitate enhancer RNA synthesis and transcription from promoters independently of H3K4 monomethylation. Mol Cell. 2017;66:568–76 e564. (PMID: 28483418566213710.1016/j.molcel.2017.04.018) ; Rickels R, Herz HM, Sze CC, Cao K, Morgan MA, Collings CK, et al. Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability. Nat Genet. 2017;49:1647–53. (PMID: 28967912566321610.1038/ng.3965)
  • Grant Information: FDT201904008368 Fondation pour la Recherche Médicale (Foundation for Medical Research in France); 18-CE12-0026 Agence Nationale de la Recherche (French National Research Agency)
  • Substance Nomenclature: 0 (Histones) ; 0 (Transcription Factors) ; EC 2.7.7.- (RNA Polymerase II)
  • Entry Date(s): Date Created: 20210318 Date Completed: 20220318 Latest Revision: 20230129
  • Update Code: 20231215
  • PubMed Central ID: PMC8329007

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