Genome-Wide Occupancy Profile of Mediator and the Srb8-11 Module Reveals Interactions with Coding Regions

Molecular Cell

Volumn 22, Issue 2, 2006, Pages 169-178

  Zhu, Xuefeng ^a   Wirén, Marianna ^a,b   Sinha, Indranil ^a,b   Rasmussen, Nina N ^c   Linder, Tomas ^a   Holmberg, Steen ^c   Ekwall, Karl ^a,b   Gustafsson, Claes M ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

^b School of Life Sciences Södertörn University   (Sweden)

^c INSTITUTE OF MOLECULAR BIOLOGY   (Armenia)

Author keywords

DNA

Indexed keywords

ARTICLE; BINDING AFFINITY; CHROMATIN IMMUNOPRECIPITATION; DNA MICROARRAY; DOWN REGULATION; EUKARYOTE; GENE INTERACTION; GENE LOCATION; GENE SEQUENCE; GENETIC CODE; GENETIC TRANSCRIPTION; GENOMICS; MOLECULAR INTERACTION; NONHUMAN; OPEN READING FRAME; PROMOTER REGION; TEMPERATURE SENSITIVITY; TRANSCRIPTION INITIATION; YEAST;

ALLELES; CHROMATIN IMMUNOPRECIPITATION; DNA, FUNGAL; DNA, INTERGENIC; DOWN-REGULATION; GENE EXPRESSION PROFILING; GENES, FUNGAL; GENOME, FUNGAL; NUCLEIC ACID AMPLIFICATION TECHNIQUES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OPEN READING FRAMES; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE PROTEINS; TRANSCRIPTION, GENETIC;

EUKARYOTA; SCHIZOSACCHAROMYCES POMBE;

EID: 33646075157     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2006.03.032     Document Type: Article

References (44)

1. Andrau J.-C., van de Pasch L., Lijnzaad P., Bijma T., Koerkamp M.G., van de Peppel J., Wener M., and Hostege F.C.P. Genome-wide location of the coactivator mediator: binding without activation and transient Cdk8 interaction on DNA. Mol. Cell 22 (2006) 179-192 this issue
2. Borggrefe T., Davis R., Erdjument-Bromage H., Tempst P., and Kornberg R. A complex of the Srb8, 9, 10, and 11 transcriptional regulatory proteins from yeast. J. Biol. Chem. 27 (2002) 44202-44207
3. Boyer T.G., Martin M.E., Lees E., Ricciardi R.P., and Berk A.J. Mammalian Srb/Mediator complex is targeted by adenovirus E1A protein. Nature 399 (1999) 276-279
4. Buck M.J., and Lieb J.D. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83 (2004) 349-360
5. Fondell J.D., Ge H., and Roeder R.G. Ligand induction of a transcriptionally active thyroid hormone receptor coactivator complex. Proc. Natl. Acad. Sci. USA 93 (1996) 8329-8333
6. Gu W., Malik S., Ito M., Yuan C.X., Fondell J.D., Zhang X., Martinez E., Qin J., and Roeder R.G. A novel human SRB/MED-containing cofactor complex, SMCC, involved in transcription regulation. Mol. Cell 3 (1999) 97-108
7. Guglielmi B., van Berkum N.L., Klapholz B., Bijma T., Boube M., Boschiero C., Bourbon H.M., Holstege F.C., and Werner M. A high resolution protein interaction map of the yeast Mediator complex. Nucleic Acids Res. 32 (2004) 5379-5391
8. Hengartner C.J., Myer V.E., Liao S.M., Wilson C.J., Koh S.S., and Young R.A. Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin- dependent kinases. Mol. Cell 2 (1998) 43-53
9. Henry N.L., Campbell A.M., Feaver W.J., Poon D., Weil P.A., and Kornberg R.D. TFIIF-TAF-RNA polymerase II connection. Genes Dev. 8 (1994) 2868-2878
10. Hirst M., Kobor M.S., Kuriakose N., Greenblatt J., and Sadowski I. GAL4 is regulated by the RNA polymerase II holoenzyme-associated cyclin-dependent protein kinase SRB10/CDK8. Mol. Cell 3 (1999) 673-678
11. Holstege F.C., Jennings E.G., Wyrick J.J., Lee T.I., Hengartner C.J., Green M.R., Golub T.R., Lander E.S., and Young R.A. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95 (1998) 717-728
12. Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., and Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98 (2001) 4569-4574
13. Jiang Y.W., Veschambre P., Erdjument-Bromage H., Tempst P., Conaway J.W., Conaway R.C., and Kornberg R.D. Mammalian mediator of transcriptional regulation and its possible role as an end-point of signal transduction pathways. Proc. Natl. Acad. Sci. USA 95 (1998) 8538-8543
14. Kim Y.J., Bjorklund S., Li Y., Sayre M.H., and Kornberg R.D. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77 (1994) 599-608
15. Kwon J.Y., Park J.M., Gim B.S., Han S.J., Lee J., and Kim Y.J. Caenorhabditis elegans mediator complexes are required for developmental-specific transcriptional activation. Proc. Natl. Acad. Sci. USA 96 (1999) 14990-14995
16. Lee M., Chatterjee S., and Struhl K. Genetic analysis of the role of Pol II holoenzyme components in repression by the Cyc8-Tup1 corepressor in yeast. Genetics 155 (2000) 1535-1542
17. Lengronne A., Katou Y., Mori S., Yokobayashi S., Kelly G.P., Itoh T., Watanabe Y., Shirahige K., and Uhlmann F. Cohesin relocation from sites of chromosomal loading to places of convergent transcription. Nature 430 (2004) 573-578
18. Linder T., and Gustafsson C.M. The Soh1/MED31 protein is an ancient component of Schizosaccharomyces pombe and Saccharomyces cerevisiae Mediator. J. Biol. Chem. 279 (2004) 49455-49459
19. Liu Y., Kung C., Fishburn J., Ansari A.Z., Shokat K.M., and Hahn S. Two cyclin-dependent kinases promote RNA polymerase II transcription and formation of the scaffold complex. Mol. Cell. Biol. 24 (2004) 1721-1735
20. Lorch Y., Beve J., Gustafsson C.M., Myers L.C., and Kornberg R.D. Mediator-nucleosome interaction. Mol. Cell 6 (2000) 197-201
21. Lue N.F., Chasman D.I., Buchman A.R., and Kornberg R.D. Interaction of GAL4 and GAL80 gene regulatory proteins in vitro. Mol. Cell. Biol. 7 (1987) 3446-3451
22. Mittler G., Kremmer E., Timmers H.T., and Meisterernst M. Novel critical role of a human Mediator complex for basal RNA polymerase II transcription. EMBO Rep. 2 (2001) 808-813
23. Mo X., Kowenz-Leutz E., Xu H., and Leutz A. Ras induces mediator complex exchange on C/EBP beta. Mol. Cell 13 (2004) 241-250
24. Myers L.C., and Kornberg R.D. Mediator of transcriptional regulation. Annu. Rev. Biochem. 69 (2000) 729-749
25. Myers L.C., Gustafsson C.M., Bushnell D.A., Lui M., Erdjument-Bromage H., Tempst P., and Kornberg R.D. The Med proteins of yeast and their function through the RNA polymerase II carboxy-terminal domain. Genes Dev. 12 (1998) 45-54
26. Naar A.M., Beaurang P.A., Zhou S., Abraham S., Solomon W., and Tjian R. Composite co-activator ARC mediates chromatin-directed transcriptional activation. Nature 398 (1999) 828-832
27. Naar A.M., Taatjes D.J., Zhai W., Nogales E., and Tjian R. Human CRSP interacts with RNA polymerase II CTD and adopts a specific CTD-bound conformation. Genes Dev. 16 (2002) 1339-1344
28. Nonet M., Scafe C., Sexton J., and Young R. Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis. Mol. Cell. Biol. 7 (1987) 1602-1611
29. Nonet M.L., and Young R.A. Intragenic and extragenic suppressors of mutations in the heptapeptide repeat domain of Saccharomyces cerevisiae RNA polymerase II. Genetics 123 (1989) 715-724
30. O'Sullivan J.M., Tan-Wong S.M., Morillon A., Lee B., Coles J., Mellor J., and Proudfoot N.J. Gene loops juxtapose promoters and terminators in yeast. Nat. Genet. 36 (2004) 1014-1018
31. Rachez C., Lemon B.D., Suldan Z., Bromleigh V., Gamble M., Naar A.M., Erdjument-Bromage H., Tempst P., and Freedman L.P. Ligand-dependent transcription activation by nuclear receptors requires the DRIP complex. Nature 398 (1999) 824-828
32. Ryu S., and Tjian R. Purification of transcription cofactor complex CRSP. Proc. Natl. Acad. Sci. USA 96 (1999) 7137-7142
33. Samuelsen C., Baraznenok V., Spahr H., Kieselbach T., Holmberg S., and Gustafsson C.M. TRAP230 and TRAP240 Mediator subunits are functionally conserved through evolution. Proc. Natl. Acad. Sci. USA 100 (2003) 6422-6427
34. Spahr H., Khorosjutina O., Baraznenok V., Linder T., Samuelsen C.O., Hermand D., Makela T.P., Holmberg S., and Gustafsson C.M. Mediator influence Schizosaccharomyces pombe RNA polymerase II dependent transcription in vitro. J. Biol. Chem. (2003) in press
35. Sun X., Zhang Y., Cho H., Rickert P., Lees E., Lane W., and Reinberg D. NAT, a human complex containing Srb polypeptides that functions as a negative regulator of activated transcription. Mol. Cell 2 (1998) 213-222
36. Svejstrup J.Q., Li Y., Fellows J., Gnatt A., Bjorklund S., and Kornberg R.D. Evidence for a mediator cycle at the initiation of transcription. Proc. Natl. Acad. Sci. USA 94 (1997) 6075-6078
37. Takagi Y., and Kornberg R.D. Mediator as a general transcription factor. J. Biol. Chem. 281 (2005) 80-89
38. Thompson C.M., and Young R.A. General requirement for RNA polymerase II holoenzymes in vivo. Proc. Natl. Acad. Sci. USA 92 (1995) 4587-4590
39. Wang G., Balamotis M.A., Stevens J.L., Yamaguchi Y., Handa H., and Berk A.J. Mediator requirement for both recruitment and postrecruitment steps in transcription initiation. Mol. Cell 17 (2005) 683-694
40. Wery M., Shematorova E., Van Driessche B., Vandenhaute J., Thuriaux P., and Van Mullem V. Members of the SAGA and Mediator complexes are partners of the transcription elongation factor TFIIS. EMBO J. 23 (2004) 4232-4242
41. Wiren M., Silverstein R.A., Sinha I., Walfridsson J., Lee H.M., Laurenson P., Pillus L., Robyr D., Grunstein M., and Ekwall K. Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast. EMBO J. 24 (2005) 2906-2918
42. Xue Y., Haas S.A., Brino L., Gusnanto A., Reimers M., Talibi D., Vingron M., Ekwall K., and Wright A.P. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21 (2004) 25-39
43. Yudkovsky N., Ranish J.A., and Hahn S. A transcription reinitiation intermediate that is stabilized by activator. Nature 408 (2000) 225-229
44. Zaman Z., Ansari A.Z., Koh S.S., Young R., and Ptashne M. Interaction of a transcriptional repressor with the RNA polymerase II holoenzyme plays a crucial role in repression. Proc. Natl. Acad. Sci. USA 98 (2001) 2550-2554