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The Nucleosome Acidic Patch Regulates the H2B K123 Monoubiquitylation Cascade and Transcription Elongation in


Chromatin, a complex of DNA wrapped around histone proteins, impacts all DNA-templated processes, including gene expression. Cells employ various strategies to alter chromatin structure and control access to the genetic material. Nucleosomes, the building blocks of chromatin, are subject to a myriad of modifications on their constituent histone proteins. One highly conserved modification with important connections to human health is the addition of ubiquitin to histone H2B. H2B ubiquitylation modulates chromatin structure during gene transcription and acts as a master regulator for downstream histone modifications. The proteins that promote H2B ubiquitylation have been identified; however, little is known about how these proteins interface with the nucleosome. Here, we exploited the genetic tools of budding yeast to reveal features of the nucleosome that are required for H2B ubiquitylation. Our genetic screen identified amino acids on the nucleosome acidic patch, a negatively charged region on the nucleosome surface, as being important for this process. The acidic patch is critical for regulating chromatin transactions, and, in our study, we identified roles for the acidic patch throughout transcription. Our data reveal that the acidic patch recruits histone modifiers, regulates histone modifications within the H2B ubiquitylation cascade, and maintains transcriptional fidelity.


Vyšlo v časopise: The Nucleosome Acidic Patch Regulates the H2B K123 Monoubiquitylation Cascade and Transcription Elongation in. PLoS Genet 11(8): e32767. doi:10.1371/journal.pgen.1005420
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005420

Souhrn

Chromatin, a complex of DNA wrapped around histone proteins, impacts all DNA-templated processes, including gene expression. Cells employ various strategies to alter chromatin structure and control access to the genetic material. Nucleosomes, the building blocks of chromatin, are subject to a myriad of modifications on their constituent histone proteins. One highly conserved modification with important connections to human health is the addition of ubiquitin to histone H2B. H2B ubiquitylation modulates chromatin structure during gene transcription and acts as a master regulator for downstream histone modifications. The proteins that promote H2B ubiquitylation have been identified; however, little is known about how these proteins interface with the nucleosome. Here, we exploited the genetic tools of budding yeast to reveal features of the nucleosome that are required for H2B ubiquitylation. Our genetic screen identified amino acids on the nucleosome acidic patch, a negatively charged region on the nucleosome surface, as being important for this process. The acidic patch is critical for regulating chromatin transactions, and, in our study, we identified roles for the acidic patch throughout transcription. Our data reveal that the acidic patch recruits histone modifiers, regulates histone modifications within the H2B ubiquitylation cascade, and maintains transcriptional fidelity.


Zdroje

1. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389: 251–260. 9305837

2. Zentner GE, Henikoff S (2013) Regulation of nucleosome dynamics by histone modifications. Nat Struct Mol Biol 20: 259–266. doi: 10.1038/nsmb.2470 23463310

3. Fischle W, Wang Y, Allis CD (2003) Histone and chromatin cross-talk. Curr Opin Cell Biol 15: 172–183. 12648673

4. Fuchs G, Oren M (2014) Writing and reading H2B monoubiquitylation. Biochim Biophys Acta 1839: 694–701. doi: 10.1016/j.bbagrm.2014.01.002 24412854

5. Robzyk K, Recht J, Osley MA (2000) Rad6-dependent ubiquitination of histone H2B in yeast. Science 287: 501–504. 10642555

6. Hwang WW, Venkatasubrahmanyam S, Ianculescu AG, Tong A, Boone C, et al. (2003) A conserved RING finger protein required for histone H2B monoubiquitination and cell size control. Mol Cell 11: 261–266. 12535538

7. Wood A, Krogan NJ, Dover J, Schneider J, Heidt J, et al. (2003) Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter. Mol Cell 11: 267–274. 12535539

8. Kim J, Hake SB, Roeder RG (2005) The human homolog of yeast BRE1 functions as a transcriptional coactivator through direct activator interactions. Mol Cell 20: 759–770. 16337599

9. Kim J, Guermah M, McGinty RK, Lee JS, Tang Z, et al. (2009) RAD6-Mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells. Cell 137: 459–471. doi: 10.1016/j.cell.2009.02.027 19410543

10. Sun ZW, Allis CD (2002) Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418: 104–108. 12077605

11. Dover J, Schneider J, Tawiah-Boateng MA, Wood A, Dean K, et al. (2002) Methylation of histone H3 by COMPASS requires ubiquitination of histone H2B by Rad6. J Biol Chem 277: 28368–28371. 12070136

12. Briggs SD, Xiao T, Sun ZW, Caldwell JA, Shabanowitz J, et al. (2002) Gene silencing: trans-histone regulatory pathway in chromatin. Nature 418: 498. 12152067

13. Latham JA, Dent SY (2007) Cross-regulation of histone modifications. Nat Struct Mol Biol 14: 1017–1024. 17984964

14. Lu X, Simon MD, Chodaparambil JV, Hansen JC, Shokat KM, et al. (2008) The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure. Nat Struct Mol Biol 15: 1122–1124. doi: 10.1038/nsmb.1489 18794842

15. Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, et al. (2005) Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol 3: e328. 16122352

16. Portela A, Esteller M (2010) Epigenetic modifications and human disease. Nat Biotechnol 28: 1057–1068. doi: 10.1038/nbt.1685 20944598

17. Wood A, Schneider J, Dover J, Johnston M, Shilatifard A (2005) The Bur1/Bur2 complex is required for histone H2B monoubiquitination by Rad6/Bre1 and histone methylation by COMPASS. Mol Cell 20: 589–599. 16307922

18. Pavri R, Zhu B, Li G, Trojer P, Mandal S, et al. (2006) Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. Cell 125: 703–717. 16713563

19. Fleming AB, Kao CF, Hillyer C, Pikaart M, Osley MA (2008) H2B ubiquitylation plays a role in nucleosome dynamics during transcription elongation. Mol Cell 31: 57–66. doi: 10.1016/j.molcel.2008.04.025 18614047

20. Ng HH, Dole S, Struhl K (2003) The Rtf1 component of the Paf1 transcriptional elongation complex is required for ubiquitination of histone H2B. J Biol Chem 278: 33625–33628. 12876293

21. Wood A, Schneider J, Dover J, Johnston M, Shilatifard A (2003) The Paf1 complex is essential for histone monoubiquitination by the Rad6-Bre1 complex, which signals for histone methylation by COMPASS and Dot1p. J Biol Chem 278: 34739–34742. 12876294

22. Warner MH, Roinick KL, Arndt KM (2007) Rtf1 is a multifunctional component of the Paf1 complex that regulates gene expression by directing cotranscriptional histone modification. Mol Cell Biol 27: 6103–6115. 17576814

23. Piro AS, Mayekar MK, Warner MH, Davis CP, Arndt KM (2012) Small region of Rtf1 protein can substitute for complete Paf1 complex in facilitating global histone H2B ubiquitylation in yeast. Proc Natl Acad Sci U S A 109: 10837–10842. doi: 10.1073/pnas.1116994109 22699496

24. Braun MA, Costa PJ, Crisucci EM, Arndt KM (2007) Identification of Rkr1, a nuclear RING domain protein with functional connections to chromatin modification in Saccharomyces cerevisiae. Mol Cell Biol 27: 2800–2811. 17283062

25. Bengtson MH, Joazeiro CA (2010) Role of a ribosome-associated E3 ubiquitin ligase in protein quality control. Nature 467: 470–473. doi: 10.1038/nature09371 20835226

26. Brandman O, Stewart-Ornstein J, Wong D, Larson A, Williams CC, et al. (2012) A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress. Cell 151: 1042–1054. doi: 10.1016/j.cell.2012.10.044 23178123

27. Nakanishi S, Sanderson BW, Delventhal KM, Bradford WD, Staehling-Hampton K, et al. (2008) A comprehensive library of histone mutants identifies nucleosomal residues required for H3K4 methylation. Nat Struct Mol Biol 15: 881–888. doi: 10.1038/nsmb.1454 18622391

28. Kalashnikova AA, Porter-Goff ME, Muthurajan UM, Luger K, Hansen JC (2013) The role of the nucleosome acidic patch in modulating higher order chromatin structure. J R Soc Interface 10: 20121022. doi: 10.1098/rsif.2012.1022 23446052

29. Wilkins BJ, Rall NA, Ostwal Y, Kruitwagen T, Hiragami-Hamada K, et al. (2014) A cascade of histone modifications induces chromatin condensation in mitosis. Science 343: 77–80. doi: 10.1126/science.1244508 24385627

30. McGinty RK, Tan S (2015) Nucleosome structure and function. Chem Rev 115: 2255–2273. doi: 10.1021/cr500373h 25495456

31. Wozniak GG, Strahl BD (2014) Catalysis-dependent stabilization of Bre1 fine-tunes histone H2B ubiquitylation to regulate gene transcription. Genes Dev 28: 1647–1652. doi: 10.1101/gad.243121.114 25085417

32. Chandrasekharan MB, Huang F, Sun ZW (2009) Ubiquitination of histone H2B regulates chromatin dynamics by enhancing nucleosome stability. Proc Natl Acad Sci U S A 106: 16686–16691. doi: 10.1073/pnas.0907862106 19805358

33. Batta K, Zhang Z, Yen K, Goffman DB, Pugh BF (2011) Genome-wide function of H2B ubiquitylation in promoter and genic regions. Genes Dev 25: 2254–2265. doi: 10.1101/gad.177238.111 22056671

34. Ferreira H, Somers J, Webster R, Flaus A, Owen-Hughes T (2007) Histone tails and the H3 alphaN helix regulate nucleosome mobility and stability. Mol Cell Biol 27: 4037–4048. 17387148

35. White CL, Suto RK, Luger K (2001) Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. EMBO J 20: 5207–5218. 11566884

36. Kaplan CD, Laprade L, Winston F (2003) Transcription elongation factors repress transcription initiation from cryptic sites. Science 301: 1096–1099. 12934008

37. Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, et al. (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123: 581–592. 16286007

38. Joshi AA, Struhl K (2005) Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol Cell 20: 971–978. 16364921

39. Hainer SJ, Pruneski JA, Mitchell RD, Monteverde RM, Martens JA (2011) Intergenic transcription causes repression by directing nucleosome assembly. Genes Dev 25: 29–40. doi: 10.1101/gad.1975011 21156811

40. Pruneski JA, Hainer SJ, Petrov KO, Martens JA (2011) The Paf1 complex represses SER3 transcription in Saccharomyces cerevisiae by facilitating intergenic transcription-dependent nucleosome occupancy of the SER3 promoter. Eukaryot Cell 10: 1283–1294. doi: 10.1128/EC.05141-11 21873510

41. Wyrick JJ, Kyriss MN, Davis WB (2012) Ascending the nucleosome face: recognition and function of structured domains in the histone H2A-H2B dimer. Biochim Biophys Acta 1819: 892–901. doi: 10.1016/j.bbagrm.2012.04.001 22521324

42. Terzi N, Churchman LS, Vasiljeva L, Weissman J, Buratowski S (2011) H3K4 trimethylation by Set1 promotes efficient termination by the Nrd1-Nab3-Sen1 pathway. Mol Cell Biol 31: 3569–3583. doi: 10.1128/MCB.05590-11 21709022

43. Tomson BN, Davis CP, Warner MH, Arndt KM (2011) Identification of a role for histone H2B ubiquitylation in noncoding RNA 3'-end formation through mutational analysis of Rtf1 in Saccharomyces cerevisiae. Genetics 188: 273–289. doi: 10.1534/genetics.111.128645 21441211

44. Tomson BN, Crisucci EM, Heisler LE, Gebbia M, Nislow C, et al. (2013) Effects of the Paf1 complex and histone modifications on snoRNA 3'-end formation reveal broad and locus-specific regulation. Mol Cell Biol 33: 170–182. doi: 10.1128/MCB.01233-12 23109428

45. Daniel JA, Torok MS, Sun ZW, Schieltz D, Allis CD, et al. (2004) Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription. J Biol Chem 279: 1867–1871. 14660634

46. Henry KW, Wyce A, Lo WS, Duggan LJ, Emre NC, et al. (2003) Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev 17: 2648–2663. 14563679

47. Emre NC, Ingvarsdottir K, Wyce A, Wood A, Krogan NJ, et al. (2005) Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal Sir2 association and gene silencing. Mol Cell 17: 585–594. 15721261

48. Schulze JM, Hentrich T, Nakanishi S, Gupta A, Emberly E, et al. (2011) Splitting the task: Ubp8 and Ubp10 deubiquitinate different cellular pools of H2BK123. Genes Dev 25: 2242–2247. doi: 10.1101/gad.177220.111 22056669

49. Xiao T, Kao CF, Krogan NJ, Sun ZW, Greenblatt JF, et al. (2005) Histone H2B ubiquitylation is associated with elongating RNA polymerase II. Mol Cell Biol 25: 637–651. 15632065

50. Wier AD, Mayekar MK, Heroux A, Arndt KM, VanDemark AP (2013) Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin. Proc Natl Acad Sci U S A 110: 17290–17295. doi: 10.1073/pnas.1314754110 24101474

51. Mayekar MK, Gardner RG, Arndt KM (2013) The recruitment of the Saccharomyces cerevisiae Paf1 complex to active genes requires a domain of Rtf1 that directly interacts with the Spt4-Spt5 complex. Mol Cell Biol 33: 3259–3273. doi: 10.1128/MCB.00270-13 23775116

52. Belotserkovskaya R, Oh S, Bondarenko VA, Orphanides G, Studitsky VM, et al. (2003) FACT facilitates transcription-dependent nucleosome alteration. Science 301: 1090–1093. 12934006

53. Soares LM, Radman-Livaja M, Lin SG, Rando OJ, Buratowski S (2014) Feedback control of Set1 protein levels is important for proper H3K4 methylation patterns. Cell Rep 6: 961–972. doi: 10.1016/j.celrep.2014.02.017 24613354

54. Thornton JL, Westfield GH, Takahashi YH, Cook M, Gao X, et al. (2014) Context dependency of Set1/COMPASS-mediated histone H3 Lys4 trimethylation. Genes Dev 28: 115–120. doi: 10.1101/gad.232215.113 24402317

55. Mason PB, Struhl K (2005) Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol Cell 17: 831–840. 15780939

56. Schwabish MA, Struhl K (2004) Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II. Mol Cell Biol 24: 10111–10117. 15542822

57. Mason PB, Struhl K (2003) The FACT complex travels with elongating RNA polymerase II and is important for the fidelity of transcriptional initiation in vivo. Mol Cell Biol 23: 8323–8333. 14585989

58. Mattiroli F, Uckelmann M, Sahtoe DD, van Dijk WJ, Sixma TK (2014) The nucleosome acidic patch plays a critical role in RNF168-dependent ubiquitination of histone H2A. Nat Commun 5: 3291. doi: 10.1038/ncomms4291 24518117

59. Leung JW, Agarwal P, Canny MD, Gong F, Robison AD, et al. (2014) Nucleosome acidic patch promotes RNF168- and RING1B/BMI1-dependent H2AX and H2A ubiquitination and DNA damage signaling. PLoS Genet 10: e1004178. doi: 10.1371/journal.pgen.1004178 24603765

60. McGinty RK, Henrici RC, Tan S (2014) Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome. Nature 514: 591–596. doi: 10.1038/nature13890 25355358

61. Turco E, Gallego LD, Schneider M, Kohler A (2015) Monoubiquitination of histone H2B is intrinsic to the Bre1 RING domain-Rad6 interaction and augmented by a second Rad6-binding site on Bre1. J Biol Chem 290: 5298–5310. doi: 10.1074/jbc.M114.626788 25548288

62. Zheng S, Wyrick JJ, Reese JC (2010) Novel trans-tail regulation of H2B ubiquitylation and H3K4 methylation by the N terminus of histone H2A. Mol Cell Biol 30: 3635–3645. doi: 10.1128/MCB.00324-10 20498280

63. Liu Y, Warfield L, Zhang C, Luo J, Allen J, et al. (2009) Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex. Mol Cell Biol 29: 4852–4863. doi: 10.1128/MCB.00609-09 19581288

64. Zhou K, Kuo WH, Fillingham J, Greenblatt JF (2009) Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5. Proc Natl Acad Sci U S A 106: 6956–6961. doi: 10.1073/pnas.0806302106 19365074

65. Wu L, Li L, Zhou B, Qin Z, Dou Y (2014) H2B ubiquitylation promotes RNA Pol II processivity via PAF1 and pTEFb. Mol Cell 54: 920–931. doi: 10.1016/j.molcel.2014.04.013 24837678

66. Marazzi I, Ho JS, Kim J, Manicassamy B, Dewell S, et al. (2012) Suppression of the antiviral response by an influenza histone mimic. Nature 483: 428–433. doi: 10.1038/nature10892 22419161

67. Chu X, Qin X, Xu H, Li L, Wang Z, et al. (2013) Structural insights into Paf1 complex assembly and histone binding. Nucleic Acids Res 41: 10619–10629. doi: 10.1093/nar/gkt819 24038468

68. Basnet H, Su XB, Tan Y, Meisenhelder J, Merkurjev D, et al. (2014) Tyrosine phosphorylation of histone H2A by CK2 regulates transcriptional elongation. Nature 516: 267–271. doi: 10.1038/nature13736 25252977

69. Nakanishi S, Lee JS, Gardner KE, Gardner JM, Takahashi YH, et al. (2009) Histone H2BK123 monoubiquitination is the critical determinant for H3K4 and H3K79 trimethylation by COMPASS and Dot1. J Cell Biol 186: 371–377. doi: 10.1083/jcb.200906005 19667127

70. Chandrasekharan MB, Huang F, Chen YC, Sun ZW (2010) Histone H2B C-terminal helix mediates trans-histone H3K4 methylation independent of H2B ubiquitination. Mol Cell Biol 30: 3216–3232. doi: 10.1128/MCB.01008-09 20439497

71. Fingerman IM, Li HC, Briggs SD (2007) A charge-based interaction between histone H4 and Dot1 is required for H3K79 methylation and telomere silencing: identification of a new trans-histone pathway. Genes Dev 21: 2018–2029. 17675446

72. Klucevsek KM, Braun MA, Arndt KM (2012) The Paf1 complex subunit Rtf1 buffers cells against the toxic effects of [PSI+] and defects in Rkr1-dependent protein quality control in Saccharomyces cerevisiae. Genetics 191: 1107–1118. doi: 10.1534/genetics.112.141713 22595241

73. Winston F, Dollard C, Ricupero-Hovasse SL (1995) Construction of a set of convenient Saccharomyces cerevisiae strains that are isogenic to S288C. Yeast 11: 53–55. 7762301

74. Ausubel FM BR, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (1988) Current protocols in molecular biology. New York, NY: Wiley-Interscience.

75. Moqtaderi Z, Struhl K (2008) Expanding the repertoire of plasmids for PCR-mediated epitope tagging in yeast. Yeast 25: 287–292. doi: 10.1002/yea.1581 18338317

76. Cox JS, Chapman RE, Walter P (1997) The unfolded protein response coordinates the production of endoplasmic reticulum protein and endoplasmic reticulum membrane. Mol Biol Cell 8: 1805–1814. 9307975

77. Squazzo SL, Costa PJ, Lindstrom DL, Kumer KE, Simic R, et al. (2002) The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO J 21: 1764–1774. 11927560

78. Shirra MK, Rogers SE, Alexander DE, Arndt KM (2005) The Snf1 protein kinase and Sit4 protein phosphatase have opposing functions in regulating TATA-binding protein association with the Saccharomyces cerevisiae INO1 promoter. Genetics 169: 1957–1972. 15716495

79. Swanson MS, Malone EA, Winston F (1991) SPT5, an essential gene important for normal transcription in Saccharomyces cerevisiae, encodes an acidic nuclear protein with a carboxy-terminal repeat. Mol Cell Biol 11: 4286. 2072920

80. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402–408. 11846609

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