Independent RNA polymerase II preinitiation complex dynamics and nucleosome turnover at promoter sites in vivo

Genome Research

Volumn 24, Issue 1, 2014, Pages 117-124

  Grimaldi, Yoselin ^a   Ferrari, Paolo ^a   Strubin, Michel ^a  

^a UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE II; TATA BINDING PROTEIN;

ANIMAL CELL; ARTICLE; CELL FUNCTION; COMPLEX FORMATION; CONTROLLED STUDY; G1 PHASE CELL CYCLE CHECKPOINT; GENE EXPRESSION; IN VIVO STUDY; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOSOME; PREINITIATION COMPLEX; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN STABILITY; TURNOVER TIME; YEAST CELL;

DNA, FUNGAL; G1 PHASE CELL CYCLE CHECKPOINTS; NUCLEOSOMES; PROMOTER REGIONS, GENETIC; RNA POLYMERASE I; RNA POLYMERASE II; RNA POLYMERASE III; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TATA-BOX BINDING PROTEIN; TRANSCRIPTION, GENETIC;

EID: 84891689852     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.157792.113     Document Type: Article

References (47)

1. Adelman K, Lis JT. 2012. Promoter-proximal pausing of RNA polymerase II: Emerging roles in metazoans. Nat Rev Genet 13: 720-731.
2. Adkins MW, Tyler JK. 2006. Transcriptional activators are dispensable for transcription in the absence of Spt6-mediated chromatin reassembly of promoter regions. Mol Cell 21: 405-416.
3. Bernstein BE, Liu CL, Humphrey EL, Perlstein EO, Schreiber SL. 2004. Global nucleosome occupancy in yeast. Genome Biol 5: R62.
4. Bhaumik SR. 2011. Distinct regulatory mechanisms of eukaryotic transcriptional activation by SAGA and TFIID. Biochim Biophys Acta 1809: 97-108.
5. Bortvin A, Winston F. 1996. Evidence that Spt6p controls chromatin structure by a direct interaction with histones. Science 272: 1473-1476.
6. Chen D, Hinkley CS, Henry RW, Huang S. 2002. TBP dynamics in living human cells: Constitutive association of TBP with mitotic chromosomes. Mol Biol Cell 13: 276-284.
7. Christova R, Oelgeschlager T. 2002. Association of human TFIID-promoter complexes with silencedmitotic chromatin in vivo. Nat Cell Biol 4: 79-82.
8. Collins GA, Lipford JR, Deshaies RJ, Tansey WP. 2009. Gal4 turnover and transcription activation. Nature 461: E7.
9. de Graaf GP, Mousson F, Geverts B, Scheer E, Tora L, Houtsmuller AB, Timmers HT. 2010. Chromatin interaction of TATA-binding protein is dynamically regulated in human cells. J Cell Sci 123: 2663-2671.
10. Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ. 2007. Dynamics of replication-independent histone turnover in budding yeast. Science 315: 1405-1408.
11. Dundr M, Hoffmann-Rohrer U, Hu Q, Grummt I, Rothblum LI, Phair RD, Misteli T. 2002. A kinetic framework for a mammalian RNA polymerase in vivo. Science 298: 1623-1626.
12. Fan X, Moqtaderi Z, Jin Y, Zhang Y, Liu XS, Struhl K. 2010. Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 39-end formation. Proc Natl Acad Sci 107: 17945-17950.
13. French SL, Osheim YN, Cioci F, Nomura M, Beyer AL. 2003. In exponentially growing Saccharomyces cerevisiae cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes. Mol Cell Biol 23: 1558-1568.
14. Gaudreau L, Schmid A, Blaschke D, Ptashne M, Horz W. 1997. RNA polymerase II holoenzyme recruitment is sufficient to remodel chromatin at the yeast PHO5 promoter. Cell 89: 55-62.
15. Giglia-Mari G, Theil AF, Mari PO, Mourgues S, Nonnekens J, Andrieux LO, De WJ, Miquel C, Wijgers N, Maas A, et al. 2009. Differentiation driven changes in the dynamic organization of Basal transcription initiation. PLoS Biol 7: e1000220.
16. Goetze H, Wittner M, Hamperl S, Hondele M, Merz K, Stoeckl U, Griesenbeck J. 2010. Alternative chromatin structures of the 35S rRNA genes in Saccharomyces cerevisiae provide a molecular basis for the selective recruitment of RNA polymerases I and II. Mol Cell Biol 30: 2028-2045.
17. Gorski SA, Snyder SK, John S, Grummt I, Misteli T. 2008. Modulation of RNA polymerase assembly dynamics in transcriptional regulation. Mol Cell 30: 486-497.
18. Gossett AJ, Lieb JD. 2012. In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae. PLoS Genet 8: e1002771.
19. Hager GL, McNally JG, Misteli T. 2009. Transcription dynamics. Mol Cell 35: 741-753.
20. Han M, Grunstein M. 1988. Nucleosome loss activates yeast downstream promoters in vivo. Cell 55: 1137-1145.
21. Haruki H, Nishikawa J, Laemmli UK. 2008. The anchor-away technique: Rapid, conditional establishment of yeast mutant phenotypes. Mol Cell 31: 925-932.
22. Imoberdorf RM, Topalidou I, Strubin M. 2006. A role for gcn5-mediated global histone acetylation in transcriptional regulation. Mol Cell Biol 26: 1610-1616.
23. Jamai A, Imoberdorf RM, Strubin M. 2007. Continuous histone H2B and transcription-dependent histone H3 exchange in yeast cells outside of replication. Mol Cell 25: 345-355.
24. Karpova TS, Kim MJ, Spriet C, Nalley K, Stasevich TJ, Kherrouche Z, Heliot L, McNally JG. 2008. Concurrent fast and slow cycling of a transcriptional activator at an endogenous promoter. Science 319: 466-469.
25. Kim J, Iyer VR. 2004. Global role of TATA box-binding protein recruitment to promoters in mediating gene expression profiles. Mol Cell Biol 24: 8104-8112.
26. Kristjuhan A, Svejstrup JQ. 2004. Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo. EMBO J 23: 4243-4252.
27. Lee CK, Shibata Y, Rao B, Strahl BD, Lieb JD. 2004. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat Genet 36: 900-905.
28. Lickwar CR, Mueller F, Hanlon SE, McNally JG, Lieb JD. 2012. Genome-wide protein DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature 484: 251-255.
29. Martens C, Krett B, Laybourn PJ. 2001. RNA polymerase II and TBP occupy the repressed CYC1 promoter. Mol Microbiol 40: 1009-1019.
30. Mencia M, Moqtaderi Z, Geisberg JV, Kuras L, Struhl K. 2002. Activatorspecific recruitment of TFIID and regulation of ribosomal protein genes in yeast. Mol Cell 9: 823-833.
31. Nalley K, Johnston SA, Kodadek T. 2006. Proteolytic turnover of the Gal4 transcription factor is not required for function in vivo. Nature 442: 1054-1057.
32. Pelechano V, Chavez S, Perez-Ortin JE. 2010. A complete set of nascent transcription rates for yeast genes. PLoS ONE 5: e15442.
33. Pokholok DK, Hannett NM, Young RA. 2002. Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Mol Cell 9: 799-809.
34. Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI, BellGW, Walker K, Rolfe PA, Herbolsheimer E, et al. 2005. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122: 517-527.
35. Rufiange A, Jacques PE, Bhat W, Robert F, Nourani A. 2007. Genome-wide replication-independent histone H3 exchange occurs predominantly at promoters and implicates H3 K56 acetylation and Asf1. Mol Cell 27: 393-405.
36. Russell J, Zomerdijk JC. 2005. RNA-polymerase-I-directed rDNA transcription, life and works. Trends Biochem Sci 30: 87-96.
37. Shandilya J, Roberts SG. 2012. The transcription cycle in eukaryotes: From productive initiation to RNA polymerase II recycling. Biochim Biophys Acta 1819: 391-400.
38. Sprouse RO, Karpova TS, Mueller F, Dasgupta A, McNally JG, Auble DT. 2008. Regulation of TATA-binding protein dynamics in living yeast cells. Proc Natl Acad Sci 105: 13304-13308.
39. Sprouse RO, Wells MN, Auble DT. 2009. TATA-binding protein variants that bypass the requirement for Mot1 in vivo. J Biol Chem 284: 4525-4535.
40. Stasevich TJ, McNally JG. 2011. Assembly of the transcription machinery: Ordered and stable, random and dynamic, or both? Chromosoma 120: 533-545.
41. van Werven FJ, van Teeffelen HA, Holstege FC, Timmers HT. 2009. Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome. Nat Struct Mol Biol 16: 1043-1048.
42. Vannini A, Cramer P. 2012. Conservation between the RNA polymerase I, II, and III transcription initiation machineries. Mol Cell 45: 439-446.
43. Xing H, Vanderford NL, Sarge KD. 2008. The TBP-PP2A mitotic complex bookmarks genes by preventing condensin action. Nat Cell Biol 10: 1318-1323.
44. Yao J, Munson KM, WebbWW, Lis JT. 2006. Dynamics of heat shock factor association with native gene loci in living cells. Nature 442: 1050-1053.
45. Yudkovsky N, Ranish JA, Hahn S. 2000. A transcription reinitiation intermediate that is stabilized by activator. Nature 408: 225-229.
46. Zanton SJ, Pugh BF. 2006. Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock. Genes Dev 20: 2250-2265.
47. Zenklusen D, Larson DR, Singer RH. 2008. Single-RNA counting reveals alternative modes of gene expression in yeast. Nat Struct Mol Biol 15: 1263-1271.