Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast

English version České info

It has recently become apparent that most introns are removed from pre-mRNA while the transcript is still engaged with RNA polymerase II (RNAPII). To gain insight into possible roles for chromatin in co-transcriptional splicing, we generated a genome-wide genetic interaction map in fission yeast and uncovered numerous connections between splicing and chromatin. The SWI/SNF remodeling complex is typically thought to activate gene expression by relieving barriers to polymerase elongation imposed by nucleosomes. Here we show that this remodeler is important for an early step in splicing in which Prp2, an RNA-dependent ATPase, is recruited to the assembling spliceosome to promote catalytic activation. Interestingly, introns with sub-optimal splice sites are particularly dependent on SWI/SNF, suggesting the impact of nucleosome dynamics on the kinetics of spliceosome assembly and catalysis. By monitoring nucleosome occupancy, we show significant alterations in nucleosome density in particular splicing and chromatin mutants, which generally paralleled the levels of RNAPII. Taken together, our findings challenge the notion that nucleosomes simply act as barriers to elongation; rather, we suggest that polymerase pausing at nucleosomes can activate gene expression by allowing more time for co-transcriptional splicing.

Vyšlo v časopise: Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast. PLoS Genet 11(3): e32767. doi:10.1371/journal.pgen.1005074
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005074

Souhrn

Zdroje

1. Tilgner H, Nikolaou C, Althammer S, Sammeth M, Beato M, et al. (2009) Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol 16: 996–1001. doi: 10.1038/nsmb.1658 19684599

2. Andersson R, Enroth S, Rada-Iglesias A, Wadelius C, Komorowski J (2009) Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res 19: 1732–1741. doi: 10.1101/gr.092353.109 19687145

3. Huff JT, Plocik AM, Guthrie C, Yamamoto KR (2010) Reciprocal intronic and exonic histone modification regions in humans. Nat Struct Mol Biol 17: 1495–1499. doi: 10.1038/nsmb.1924 21057525

4. Narlikar GJ, Sundaramoorthy R, Owen-Hughes T (2013) Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes. Cell 154: 490–503. doi: 10.1016/j.cell.2013.07.011 23911317

5. Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T (2011) Epigenetics in alternative pre-mRNA splicing. Cell 144: 16–26. doi: 10.1016/j.cell.2010.11.056 21215366

6. Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, et al. (2010) Regulation of alternative splicing by histone modifications. Science 327: 996–1000. doi: 10.1126/science.1184208 20133523

7. Batsche E, Yaniv M, Muchardt C (2006) The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nat Struct Mol Biol 13: 22–29. 16341228

8. Waldholm J, Wang Z, Brodin D, Tyagi A, Yu S, et al. (2011) SWI/SNF regulates the alternative processing of a specific subset of pre-mRNAs in Drosophila melanogaster. BMC Mol Biol 12: 46. doi: 10.1186/1471-2199-12-46 22047075

9. Kornblihtt AR, Schor IE, Allo M, Blencowe BJ (2009) When chromatin meets splicing. Nat Struct Mol Biol 16: 902–903. 19739285

10. Bentley DL (2014) Coupling mRNA processing with transcription in time and space. Nat Rev Genet 15: 163–175. doi: 10.1038/nrg3662 24514444

11. Kim S, Kim H, Fong N, Erickson B, Bentley DL (2011) Pre-mRNA splicing is a determinant of histone H3K36 methylation. Proc Natl Acad Sci U S A 108: 13564–13569. doi: 10.1073/pnas.1109475108 21807997

12. de Almeida SF, Grosso AR, Koch F, Fenouil R, Carvalho S, et al. (2011) Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nat Struct Mol Biol 18: 977–983. doi: 10.1038/nsmb.2123 21792193

13. Bieberstein NI, Carrillo Oesterreich F, Straube K, Neugebauer KM (2012) First exon length controls active chromatin signatures and transcription. Cell Rep 2: 62–68. doi: 10.1016/j.celrep.2012.05.019 22840397

14. Moehle EA, Ryan CJ, Krogan NJ, Kress TL, Guthrie C (2012) The yeast SR-like protein Npl3 links chromatin modification to mRNA processing. PLoS Genet 8: e1003101. doi: 10.1371/journal.pgen.1003101 23209445

15. Herissant L, Moehle EA, Bertaccini D, Van Dorsselaer A, Schaeffer-Reiss C, et al. (2014) H2B ubiquitylation modulates spliceosome assembly and function in budding yeast. Biol Cell 106: 126–138. doi: 10.1111/boc.201400003 24476359

16. Gunderson FQ, Johnson TL (2009) Acetylation by the transcriptional coactivator Gcn5 plays a novel role in co-transcriptional spliceosome assembly. PLoS Genet 5: e1000682. doi: 10.1371/journal.pgen.1000682 19834536

17. Gunderson FQ, Merkhofer EC, Johnson TL (2011) Dynamic histone acetylation is critical for cotranscriptional spliceosome assembly and spliceosomal rearrangements. Proc Natl Acad Sci U S A 108: 2004–2009. doi: 10.1073/pnas.1011982108 21245291

18. Braberg H, Jin H, Moehle EA, Chan YA, Wang S, et al. (2013) From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II. Cell 154: 775–788. doi: 10.1016/j.cell.2013.07.033 23932120

19. Moehle EA, Braberg H, Krogan NJ, Guthrie C (2014) Adventures in time and space: splicing efficiency and RNA polymerase II elongation rate. RNA Biol 11: 313–319. doi: 10.4161/rna.28646 24717535

20. Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, et al. (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415: 871–880. 11859360

21. Awan AR, Manfredo A, Pleiss JA (2013) Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans. Proc Natl Acad Sci U S A 110: 12762–12767. doi: 10.1073/pnas.1218353110 23861491

22. Moldon A, Malapeira J, Gabrielli N, Gogol M, Gomez-Escoda B, et al. (2008) Promoter-driven splicing regulation in fission yeast. Nature 455: 997–1000. doi: 10.1038/nature07325 18815595

23. Kupfer DM, Drabenstot SD, Buchanan KL, Lai H, Zhu H, et al. (2004) Introns and splicing elements of five diverse fungi. Eukaryot Cell 3: 1088–1100. 15470237

24. Schuldiner M, Collins SR, Thompson NJ, Denic V, Bhamidipati A, et al. (2005) Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell 123: 507–519. 16269340

25. Yang JJ, Sun LH, She YF, Ge JJ, Li XH, et al. (2008) [Influence of ginger-partitioned moxibustion on serum NO and plasma endothelin-1 contents in patients with primary dysmenorrhea of cold-damp stagnation type]. Zhen Ci Yan Jiu 33: 409–412. 19288904

26. Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, et al. (2008) Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science 322: 405–410. doi: 10.1126/science.1162609 18818364

27. Ryan CJ, Roguev A, Patrick K, Xu J, Jahari H, et al. (2012) Hierarchical modularity and the evolution of genetic interactomes across species. Mol Cell 46: 691–704. doi: 10.1016/j.molcel.2012.05.028 22681890

28. Beltrao P, Cagney G, Krogan NJ (2010) Quantitative genetic interactions reveal biological modularity. Cell 141: 739–745. doi: 10.1016/j.cell.2010.05.019 20510918

29. Wilmes GM, Bergkessel M, Bandyopadhyay S, Shales M, Braberg H, et al. (2008) A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol Cell 32: 735–746. doi: 10.1016/j.molcel.2008.11.012 19061648

30. Yan D, Ares M Jr. (1996) Invariant U2 RNA sequences bordering the branchpoint recognition region are essential for interaction with yeast SF3a and SF3b subunits. Mol Cell Biol 16: 818–828. 8622683

31. Dallas PB, Pacchione S, Wilsker D, Bowrin V, Kobayashi R, et al. (2000) The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. Mol Cell Biol 20: 3137–3146. 10757798

32. Lund MK, Kress TL, Guthrie C (2008) Autoregulation of Npl3, a yeast SR protein, requires a novel downstream region and serine phosphorylation. Mol Cell Biol 28: 3873–3881. doi: 10.1128/MCB.02153-07 18391019

33. Wells SE, Neville M, Haynes M, Wang J, Igel H, et al. (1996) CUS1, a suppressor of cold-sensitive U2 snRNA mutations, is a novel yeast splicing factor homologous to human SAP 145. Genes Dev 10: 220–232. 8566755

34. Maundrell K (1990) nmt1 of fission yeast. A highly transcribed gene completely repressed by thiamine. J Biol Chem 265: 10857–10864. 2358444

35. Shao W, Kim HS, Cao Y, Xu YZ, Query CC (2012) A U1-U2 snRNP interaction network during intron definition. Mol Cell Biol 32: 470–478. doi: 10.1128/MCB.06234-11 22064476

36. Warkocki Z, Odenwalder P, Schmitzova J, Platzmann F, Stark H, et al. (2009) Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components. Nat Struct Mol Biol 16: 1237–1243. doi: 10.1038/nsmb.1729 19935684

37. Ohrt T, Prior M, Dannenberg J, Odenwalder P, Dybkov O, et al. (2012) Prp2-mediated protein rearrangements at the catalytic core of the spliceosome as revealed by dcFCCS. RNA 18: 1244–1256. doi: 10.1261/rna.033316.112 22535589

38. Krishnan R, Blanco MR, Kahlscheuer ML, Abelson J, Guthrie C, et al. (2013) Biased Brownian ratcheting leads to pre-mRNA remodeling and capture prior to first-step splicing. Nat Struct Mol Biol 20: 1450–1457. doi: 10.1038/nsmb.2704 24240612

39. Kress TL, Krogan NJ, Guthrie C (2008) A single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast. Mol Cell 32: 727–734. doi: 10.1016/j.molcel.2008.11.013 19061647

40. Moore MJ, Schwartzfarb EM, Silver PA, Yu MC (2006) Differential recruitment of the splicing machinery during transcription predicts genome-wide patterns of mRNA splicing. Mol Cell 24: 903–915. 17189192

41. Vijayraghavan U, Company M, Abelson J (1989) Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae. Genes Dev 3: 1206–1216. 2676722

42. Kim DH, Edwalds-Gilbert G, Ren C, Lin RJ (1999) A mutation in a methionine tRNA gene suppresses the prp2-1 Ts mutation and causes a pre-mRNA splicing defect in Saccharomyces cerevisiae. Genetics 153: 1105–1115. 10545445

43. Roy J, Kim K, Maddock JR, Anthony JG, Woolford JL Jr. (1995) The final stages of spliceosome maturation require Spp2p that can interact with the DEAH box protein Prp2p and promote step 1 of splicing. RNA 1: 375–390. 7493316

44. Last RL, Maddock JR, Woolford JL Jr. (1987) Evidence for related functions of the RNA genes of Saccharomyces cerevisiae. Genetics 117: 619–631. 3322934

45. Infante JJ, Law GL, Young ET (2012) Analysis of nucleosome positioning using a nucleosome-scanning assay. Methods Mol Biol 833: 63–87. doi: 10.1007/978-1-61779-477-3_5 22183588

46. Soriano I, Quintales L, Antequera F (2013) Clustered regulatory elements at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe. BMC Genomics 14: 813. doi: 10.1186/1471-2164-14-813 24256300

47. Bintu L, Ishibashi T, Dangkulwanich M, Wu YY, Lubkowska L, et al. (2012) Nucleosomal elements that control the topography of the barrier to transcription. Cell 151: 738–749. doi: 10.1016/j.cell.2012.10.009 23141536

48. Hodges C, Bintu L, Lubkowska L, Kashlev M, Bustamante C (2009) Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science 325: 626–628. doi: 10.1126/science.1172926 19644123

49. Spies N, Nielsen CB, Padgett RA, Burge CB (2009) Biased chromatin signatures around polyadenylation sites and exons. Mol Cell 36: 245–254. doi: 10.1016/j.molcel.2009.10.008 19854133

50. Ast G (2004) How did alternative splicing evolve? Nat Rev Genet 5: 773–782. 15510168

51. Busch A, Hertel KJ (2012) Evolution of SR protein and hnRNP splicing regulatory factors. Wiley Interdiscip Rev RNA 3: 1–12. doi: 10.1002/wrna.100 21898828

52. Tang Z, Kuo T, Shen J, Lin RJ (2000) Biochemical and genetic conservation of fission yeast Dsk1 and human SR protein-specific kinase 1. Mol Cell Biol 20: 816–824. 10629038

53. Tang Z, Kaufer NF, Lin RJ (2002) Interactions between two fission yeast serine/arginine-rich proteins and their modulation by phosphorylation. Biochem J 368: 527–534. 12186627

54. Margaritis T, Oreal V, Brabers N, Maestroni L, Vitaliano-Prunier A, et al. (2012) Two distinct repressive mechanisms for histone 3 lysine 4 methylation through promoting 3'-end antisense transcription. PLoS Genet 8: e1002952. doi: 10.1371/journal.pgen.1002952 23028359

55. Kadosh D, Struhl K (1998) Histone deacetylase activity of Rpd3 is important for transcriptional repression in vivo. Genes Dev 12: 797–805. 9512514

56. Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, et al. (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123: 593–605. 16286008

57. Tolstorukov MY, Sansam CG, Lu P, Koellhoffer EC, Helming KC, et al. (2013) Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters. Proc Natl Acad Sci U S A 110: 10165–10170. doi: 10.1073/pnas.1302209110 23723349

58. Zhu Y, Rowley MJ, Bohmdorfer G, Wierzbicki AT (2013) A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated transcriptional silencing. Mol Cell 49: 298–309. doi: 10.1016/j.molcel.2012.11.011 23246435

59. Carrillo Oesterreich F, Preibisch S, Neugebauer KM (2010) Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. Mol Cell 40: 571–581. doi: 10.1016/j.molcel.2010.11.004 21095587

60. Alexander RD, Innocente SA, Barrass JD, Beggs JD (2010) Splicing-dependent RNA polymerase pausing in yeast. Mol Cell 40: 582–593. doi: 10.1016/j.molcel.2010.11.005 21095588

61. Kaplan CD, Jin H, Zhang IL, Belyanin A (2012) Dissection of Pol II trigger loop function and Pol II activity-dependent control of start site selection in vivo. PLoS Genet 8: e1002627. doi: 10.1371/journal.pgen.1002627 22511879

62. Versteege I, Medjkane S, Rouillard D, Delattre O (2002) A key role of the hSNF5/INI1 tumour suppressor in the control of the G1-S transition of the cell cycle. Oncogene 21: 6403–6412. 12226744

63. Collins SR, Roguev A, Krogan NJ (2010) Quantitative genetic interaction mapping using the E-MAP approach. Methods Enzymol 470: 205–231. doi: 10.1016/S0076-6879(10)70009-4 20946812

64. Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T (2008) Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol 4: e1000065. doi: 10.1371/journal.pcbi.1000065 18421374