Functional interplay between Mediator and TFIIB in preinitiation complex assembly in relation to promoter architecture

Genes and Development

Volumn 30, Issue 18, 2016, Pages 2119-2132

  Eychenne, Thomas ^a,b,c   Novikova, Elizaveta ^a,b,c   Barrault, Marie Bénédicte ^a,b,c   Alibert, Olivier ^d   Boschiero, Claire ^a,b,c   Peixeiro, Nuno ^a,b,c   Cornu, David ^a   Redeker, Virginie ^a   Kuras, Laurent ^a,b   Nicolas, Pierre ^e   Werner, Michel ^a,b,c   Soutourina, Julie ^a,b,c  

^a CNRS   (France)

^b UNIVERSITÉ PARIS SACLAY   (France)

^c SERVICE DE CHIMIE BIOORGANIQUE ET DE MARQUAGE   (France)

^d DIF   (France)

^e UR341 National Agronomical Research Institute (INRA)   (France)

Author keywords

Mediator; Preinitiation complex; Promoter architecture; RNA polymerase II transcription; Saccharomyces cerevisiae; TFIIB

Indexed keywords

TRANSCRIPTION FACTOR GAL4; TRANSCRIPTION FACTOR IIB; CHROMATIN; MEDIATOR COMPLEX; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; CHROMATIN; COMPUTER MODEL; CONTROLLED STUDY; FUNGUS MUTANT; GENE MUTATION; IN VITRO STUDY; IN VIVO STUDY; MEDIATOR; MOLECULAR DYNAMICS; MUTAGENESIS; NONHUMAN; NUCLEOSOME; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN SUBUNIT; GENETICS; METABOLISM; MUTATION; PHYSIOLOGY; PROTEIN MULTIMERIZATION; SACCHAROMYCES CEREVISIAE;

CHROMATIN; MEDIATOR COMPLEX; MUTATION; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; PROTEIN MULTIMERIZATION; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTOR TFIIB;

EID: 84990985860     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.285775.116     Document Type: Article

References (44)

1. Baek HJ, Kang YK, Roeder RG. 2006. Human Mediator enhances basal transcription by facilitating recruitment of transcription factor IIB during preinitiation complex assembly. J Biol Chem 281: 15172-15181.
2. Bourbon HM. 2008. Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex. Nucleic Acids Res 36: 3993-4008.
3. Buratowski S, Hahn S, Guarente L, Sharp PA. 1989. Five intermediate complexes in transcription initiation by RNA polymerase II. Cell 56: 549-561.
4. Cevher MA, Shi Y, Li D, Chait BT, Malik S, Roeder RG. 2014. Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit. Nat Struct Mol Biol 21: 1028-1034.
5. 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.
6. Esnault C, Ghavi-Helm Y, Brun S, Soutourina J, Van Berkum N, Boschiero C, Holstege F, Werner M. 2008. Mediator-dependent recruitment of TFIIH modules in preinitiation complex. Mol Cell 31: 337-346.
7. Eyboulet F, Cibot C, Eychenne T, Neil H, Alibert O, Werner M, Soutourina J. 2013. Mediator links transcription and DNA repair by facilitating Rad2/XPG recruitment. Genes Dev 27: 2549-2562.
8. Eyboulet F, Wydau-Dematteis S, Eychenne T, Alibert O, Neil H, Boschiero C, Nevers MC, Volland H, Cornu D, Redeker V, et al. 2015. Mediator independently orchestrates multiple steps of preinitiation complex assembly in vivo. Nucleic Acids Res 43: 9214-9231.
9. Flanagan PM, Kelleher RJ III, Sayre MH, Tschochner H, Kornberg RD. 1991. Amediator required for activation ofRNApolymerase II transcription in vitro. Nature 350: 436-438.
10. Ghavi-HelmY, Michaut M, Acker J, Aude JC, Thuriaux P,Werner M, Soutourina J. 2008. Genome-wide location analysis reveals a role of TFIIS inRNApolymerase III transcription. Genes Dev 22: 1934-1947.
11. Guglielmi B, van Berkum NL, Klapholz B, Bijma T, Boube M, Boschiero C, Bourbon HM, Holstege FC, Werner M. 2004. A high resolution protein interaction map of the yeast Mediator complex. Nucleic Acids Res 32: 5379-5391.
12. Han SJ, Lee YC, Gim BS, Ryu GH, Park SJ, Lane WS, Kim YJ. 1999. Activator-specific requirement of yeast mediator proteins for RNA polymerase II transcriptional activation. Mol Cell Biol 19: 979-988.
13. Hashimoto S, Boissel S, Zarhrate M, Rio M, Munnich A, Egly JM, Colleaux L. 2011. MED23 mutation links intellectual disability to dysregulation of immediate early gene expression. Science 333: 1161-1163.
14. He Y, Fang J, Taatjes DJ, Nogales E. 2013. Structural visualization of key steps in human transcription initiation. Nature 495: 481-486.
15. He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E. 2016. Near-atomic resolution visualization of human transcription promoter opening. Nature 533: 359-365.
16. Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA. 1998. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95: 717-728.
17. Jiang YW, Veschambre P, Erdjument-Bromage H, Tempst P, Conaway JW, Conaway RC, Kornberg RD. 1998. Mammalian mediator of transcriptional regulation and its possible role as an end-point of signal transduction pathways. Proc Natl Acad Sci 95: 8538-8543.
18. Johnson KM, Wang J, Smallwood A, Arayata C, Carey M. 2002. TFIID and human mediator coactivator complexes assemble cooperatively on promoter DNA. Genes Dev 16: 1852-1863.
19. Kang JS, Kim SH, Hwang MS, Han SJ, Lee YC, Kim YJ. 2001. The structural and functional organization of the yeast mediator complex. J Biol Chem 276: 42003-42010.
20. Kaufmann R, Straussberg R, Mandel H, Fattal-Valevski A, Ben-Zeev B, Naamati A, Shaag A, Zenvirt S, Konen O, Mimouni-Bloch A, et al. 2010. Infantile cerebral and cerebellar atrophy is associated with a mutation in the MED17 subunit of the transcription preinitiation mediator complex. Am J Hum Genet 87: 667-670.
21. Kim YJ, Bjorklund S, Li Y, Sayre MH, Kornberg RD. 1994. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77: 599-608.
22. Kornberg RD. 2005. Mediator and the mechanism of transcriptional activation. Trends Biochem Sci 30: 235-239.
23. Lacombe T, Poh SL, Barbey R, Kuras L. 2013. Mediator is an intrinsic component of the basal RNA polymerase II machinery in vivo. Nucleic Acids Res 41: 9651-9662.
24. Larivière L, Plaschka C, Seizl M, Petrotchenko EV, Wenzeck L, Borchers CH, Cramer P. 2013. Model of the Mediator middle module based on protein cross-linking. Nucleic Acids Res 41: 9266-9273.
25. Liu X, Bushnell DA, Wang D, Calero G, Kornberg RD. 2010. Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism. Science 327: 206-209.
26. Malik S, Roeder RG. 2010. The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation. Nat Rev Genet 11: 761-772.
27. Murakami K, Elmlund H, Kalisman N, Bushnell DA, Adams CM, Azubel M, Elmlund D, Levi-Kalisman Y, Liu X, Gibbons BJ, et al. 2013. Architecture of an RNA polymerase II transcription pre-initiation complex. Science 342: 1238724.
28. Murakami K, Tsai KL, Kalisman N, Bushnell DA, Asturias FJ, Kornberg RD. 2015. Structure of an RNA polymerase II preinitiation complex. Proc Natl Acad Sci 112: 13543-13548.
29. Pinto I, Ware DE, Hampsey M. 1992. The yeast SUA7 gene encodes a homolog of human transcription factor TFIIB and is required for normal start site selection in vivo. Cell 68: 977-988.
30. Plaschka C, Lariviere L, Wenzeck L, Seizl M, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, BaumeisterW, Herzog F, et al. 2015. Architecture of the RNA polymerase II-Mediator core initiation complex. Nature 518: 376-380.
31. Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P. 2016. Transcription initiation complex structures elucidate DNA opening. Nature 533: 353-358.
32. Ranish JA, Hahn S. 1996. Transcription: basal factors and activation. Curr Opin Genet Dev 6: 151-158.
33. Ranish JA, Yudkovsky N, Hahn S. 1999. Intermediates in formation and activity of the RNA polymerase II preinitiation complex: holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB. Genes Dev 13: 49-63.
34. Rhee HS, Pugh BF. 2012. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature 483: 295-301.
35. Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. 2015. Molecular architecture of the yeast Mediator complex. Elife 4: e08719.
36. Sainsbury S, Niesser J, Cramer P. 2013. Structure and function of the initially transcribing RNA polymerase II-TFIIB complex. Nature 493: 437-440.
37. Schiano C, Casamassimi A, Rienzo M, de Nigris F, Sommese L, Napoli C. 2014. Involvement of Mediator complex in malignancy. Biochim Biophys Acta 1845: 66-83.
38. Soutourina J, Wydau S, Ambroise Y, Boschiero C, Werner M. 2011. Direct interaction of RNA polymerase II and mediator required for transcription in vivo. Science 331: 1451-1454.
39. Spaeth JM, Kim NH, Boyer TG. 2011. Mediator and human disease. Semin Cell Dev Biol 22: 776-787.
40. Thompson CM, Young RA. 1995. General requirement for RNA polymerase II holoenzymes in vivo. Proc Natl Acad Sci 92: 4587-4590.
41. Tsai KL, Tomomori-Sato C, Sato S, Conaway RC, Conaway JW, Asturias FJ. 2014. Subunit architecture and functional modular rearrangements of the transcriptional mediator complex. Cell 157: 1430-1444.
42. Wang X, Sun Q, Ding Z, Ji J,Wang J, Kong X, Yang J, Cai G. 2014. Redefining the modular organization of the core Mediator complex. Cell Res 24: 796-808.
43. Wu WH, Hampsey M. 1999. An activation-specific role for transcription factor TFIIB in vivo. Proc Natl Acad Sci 96: 2764-2769.
44. Wu WH, Pinto I, Chen BS, Hampsey M. 1999. Mutational analysis of yeast TFIIB. A functional relationship between Ssu72 and Sub1/Tsp1 defined by allele-specific interactions with TFIIB. Genetics 153: 643-652.