A human RNA polymerase II complex containing factors that modify chromatin structure

Molecular and Cellular Biology

Volumn 18, Issue 9, 1998, Pages 5355-5363

  Cho, Helen ^a   Orphanides, George ^a   Sun, Xiaoqing ^a   Yang, Xiang Jiao ^b   Ogryzko, Vasily ^b   Lees, Emma ^c   Nakatani, Yoshihiro ^b   Reinberg, Danny ^a  

^a RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

^b EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^c MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE;

AFFINITY CHROMATOGRAPHY; ARTICLE; CHROMATIN STRUCTURE; ENZYME ACTIVITY; HELA CELL; HUMAN; HUMAN CELL; IMMUNOBLOTTING; IMMUNOPRECIPITATION; PHENOTYPE; PRIORITY JOURNAL; PROTEIN INTERACTION; TRANSCRIPTION REGULATION; YEAST;

EID: 0031841947     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.18.9.5355     Document Type: Article

References (82)

1. Alland, L., R. Muhle, H. Hou, J. Potes, L. Chin, N. Schreiber-Agus, and R. DePinho. 1997. Role for N-CoR and histone deacetylase in Sin3-mediated transcriptional repression. Nature (London) 387:49-55.
2. Allison, L., J. Wong, V. Fitzpatrick, M. Moyle, and J. Ingles. 1988. The C-terminal domain of the largest subunit of RNA polymerase II of Saccharomyces cerevisiae, Drosophila melanogaster, and mammals: a conserved structure with an essential function. Mol. Cell. Biol. 8:321-329.
3. Bannister, A., and T. Kouzarides. 1996. The CBP-co-activator is a histone acetyltransferase. Nature (London) 384:641-643.
4. Brownell, J., J. Zhou, T. Ranalli, R. Kobayashi, D. Edmond son, S. Roth, and D. Allis. 1996. Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84:843-851.
5. Cairns, B., Y. Lorch, M. Zhang, L. Lacomis, H. Erdjument-Bromage, P. Tempst, J. Du, B. Laurent, and R. Kornberg. 1996. RSC, an essential, abundant chromatin-remodelling complex. Cell 87:1249-1260.
6. Candau, R., P. Moore, L. Wang, N. Barlev, C. Ying, C. Rosen, and S. Berger. 1996. Identification of human proteins functionally conserved with the yeast putative adaptors ADA2 and GCN5. Mol. Cell. Biol. 16:593-602.
7. Carlson, M. 1997. Genetics of transcriptional regulation in yeast: connections to the RNA polymerase II CTD. Annu. Rev. Cell Dev. Biol. 13:1-23.
8. Chang, M., and J. Jaehning. 1997. A multiplicity of mediators: alternative forms of transcription complexes communicate with transcriptional regulators. Nucleic Acids Res. 25:4861-4865.
9. Chao, D., E. Gadbois, P. Murray, S. Anderson, M. Sonu. J. Parvin, and R. Young. 1996. A mammalian SRB protein associated with an RNA polymerase II holoenzyme. Nature (London) 380:82-85.
10. Chestnut, J., J. Stephens, and M. Dahmus. 1992. The interaction of RNA polymerase II with the adenovirus-2 major late promoter is precluded by phosphorylation of the C-terminal domain of subunit IIa. J. Biol. Chem. 267:10500-10506.
11. Cho, H., E. Maldonado, and D. Reinberg. 1997. Affinity purification of a human RNA polymerase II complex using monoclonal antibodies against transcription factor IIF. J. Biol. Chem. 272:11495-11502.
12. Cujec, T. P., H. Cho, E. Maldonado, J. Meyer, D. Reinberg, and B. M. Peterlin. 1997. The human immunodeficiency virus transactivator Tat interacts with the RNA polymerase II holoenzyme. Mol. Cell. Biol. 17:1817-1823.
13. Currie, R. 1998. NF-Y is associated with the histone acetyltransferases GCN5 and P/CAF. J. Biol. Chem. 273:1430-1434.
14. Dahmus, M. 1996. Reversible phosphorylation of the C-terminal domain of RNA polymerase II. J. Biol. Chem. 271: 19009-19012.
15. Flanagan, P., R. kelleher, M. Sayre, H. Tshochner, and R. Kornberg. 1991. A mediator required for activation of RNA polymerase II transcription in vitro. Nature (London) 350:436-438.
16. Gaudreau, L., A. Schmid, D. Blaschke, M. Ptashne, and W. Horz. 1997. RNA polymerase II holoenzyme recruitment is sufficient to remodel chromatin at the yeast PHO5 promoter. Cell 89:55-62.
17. Grant, P., L. Duggan, J. Cote, S. Roberts, J. Brownell, R. Candau, R. Ohba, T. Owen-Hughes, D. Allis, F. Winston, S. Berger, and J. Workman. 1997. Yeast Gcn5 functions in two multiprotein complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 11:1640-1650.
18. Grunstein, M. 1997. Histone acetylation in chromatin structure and transcription. Nature (London) 389:349-352.
19. Gustafsson, C., L. Myers, Y. Li, M. Redd, M. Lui, H. Erdjument-Bromage, P. Tempst, and R. Kornberg. 1997. Identification of Rox3 as a component of mediator and RNA polymerase II holoenzyme. J. Biol. Chem. 272:48-50.
20. Hampsey, M. 1998. Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol. Mol. Biol. Rev. 62:465-503.
21. Hassig, C., T. Fleischer, A. Billin, S. Schreiber, and D. Ayer. 1997. Histone deacetylase activity is required for full transcriptional repression by mSin3A. Cell 89:341-347.
22. Hebbes, T., A. Clayton, A. Thorne, and C. Crane-Robinson. 1994. A direct link between core histone acetylation and transcriptionally active chromatin. EMBO J. 7:1395-1402.
23. Heinzel, T., R. Lavinsky, T. Mullen, M. Soderstrom, C. Laherty, J. Torchia, W.-M. Yang, G. Brard, S. Ngo, J. Davie, E. Seto, R. Eisenman, D. Rose, C. Glass, and M. Rosenfeld. 1997. A complex containing N-CoR, mSin3A and histone deacetylase mediates transcriptional repression. Nature (London) 387:43-48.
24. Ito, T., M. Bulger, M. Pazin, R. Kobayashi, and J. Kadonaga. 1997. ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90:145-155.
25. Janknecht, R., and T. Hunter, 1996. Transcription. A growing coactivator network. Nature (London) 383:22-23.
26. Kadosh, D., and K. Struhl. 1997. Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor Rpd3 histone deacetylase to target promoters. Cell 89:365-371.
27. Kelleher, R., P. Flanagan, and R. Kornberg. 1990. A novel mediator between activator proteins and the RNA polymerase II transcription apparatus. Cell 61:1209-1215.
28. Kelleher, R., P. Flanagan, D. Chasman, A. Ponticelli, K. Struhl, and R. Kornberg. 1992. Yeast and human TFIIDs are interchangeable for the response to acidic transcriptional activators in vitro. Genes Dev. 6:296-304.
29. Kim, Y., S. Bjorklund, Y. Li, M. Sayre, and R. Kornberg. 1994. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77:599-608.
30. Kingston, R., C. Bunker, and A. Imbalzano. 1996. Repression and activation by multiprotein complexes that alter chromatin structure. Genes Dev. 10:905-920.
31. Koleske, A., and R. Young. 1994, An RNA polymerase II holoenzyme responsive to activators. Nature (London) 368:466-469.
32. Kornberg, R. 1977. Structure of chromatin. Annu. Rev. Biochem. 46:931-954.
33. Kuchin, S., P. Yeghiayan, and M. Carlson. 1995. Cyclin-dependent protein kinase and cyclin homologs SSN3 and SSN8 contribute to transcriptional control in yeast. Proc. Natl. Acad. Sci. USA 92:4006-4010.
34. Kwon, H., A. Imbalzano, P. Khavari, R. Kingston, and M. Green. 1994. Nucleosome disruption and enhancement of activator binding by a human SWI/SNF complex. Nature (London) 370:477-481.
35. Lai, J.-S., and W. Herr. 1992. Ethidium bromide provides a simple tool for identifying genuine DNA-independent protein associations. Proc. Natl. Acad. Sci. USA 89:6958-6962.
36. Lee, Y. C., S. Min, B. S. Gim, and Y.-J. Kim. 1997. A transcriptional mediator protein that is required for activation of many RNA polymerase II promoters and is conserved from yeast to humans. Mol. Cell. Biol. 17:4622-4632.
37. Li, Y., S. Bjorklund, Y. Jiang, Y.-J. Kim, W. Lane. D. Stillman, and R. Kornberg. 1995. Yeast global transcriptional regulators Sin4 and Rgr1 are components of mediator complex/RNA polymerase II holoenzyme. Proc. Natl. Acad. Sci. USA 92:10864-10868.
38. Liao, S., D. Zhang, D. Jefferey, A. Koleske, C. Thompson, D. Chao, M. Viljoen, H. van Vuure, and R. Young. 1995. A kinase-cyclin pair in the RNA polymerase II holoenzyme. Nature (London) 374:193-196.
39. Lu, H., O. Flores, R. Weinman, and D. Reinberg. 1991. The nonphosphorylated form of RNA polymerase II preferentially associates with the preinitiation complex. Proc. Natl. Acad. Sci. USA 88:10004-10008.
40. Maldonado, E., R. Shiekhattar, M. Sheldon, H. Cho, R. Drapkin, P. Rickert, E. Lees, C. Anderson, S. Linn, and D. Reinberg. 1996. A human RNA polymerase II complex associated with SRB and DNA-repair proteins. Nature (London) 381:86-89.
41. Maldonado, E., R. Drapkin, and D. Reinberg. 1996. Purification of human RNA polymerase II and general transcription factors. Methods Enzymol. 174:72-100.
42. Marcus, G., N. Silverman, S. Berger, J. Horiuchi, and L. Guarente. 1994. Functional similarities and physical association between Gcn5 and Ada2putative transcriptional adaptors. EMBO J. 13:4807-4815.
43. McCracken, S., N. Fong, K. Yankulov, S. Ballantyne, G. Pan, J. Greenblatt, S. Patterson, M. Wickens, and D. Bentley. 1997. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature (London) 385:357-361.
44. II250 subunit of TFIID has histone acetyltransferase activity. Cell 87:1261-1270.
45. Myers, L., C. Gustafsson, D. Bushnell, M. Lui, H. Erdjument-Bromage, P. Tempst, and R. Kornberg. 1998. The Med proteins of yeast and their function through the RNA polymerase II carboxy-terminal domain. Genes Dev. 12:45-54.
46. Nagy, L., H.-Y. Kao, D. Chakravarti, R. Lin, C. Hassig, D. Ayer, S. Schreiber, and R. Evans. 1997. Nuclear receptor repression is mediated by a complex containing SMRT, mSin3A, and histone deacetylase. Cell 89:373-380.
47. Nakajima, T., C. Uchida, S. Anderson, J. Parvin, and M. Montminy. 1997. Analysis of a cAMP-responsive activator reveals a two-component mechanism for transcription induction via signal-dependent factors. Genes Dev. 11:738-747.
48. Nakajima, T., C. Uchida, S. Anderson, C.-G. Lee, J. Hurwitz, J. Parvin, and M. Montminy. 1997. RNA helicase A mediates association of CBP with RNA polymerase II. Cell 90:1107-1112.
49. Neigeborn, L., and M. Carlson. 1984. Genes affecting the regulation of SUC2 gene expression by glucose repression in Saccharomyces cerevisiae. Genetics 108:845-858.
50. Neish, A., S. Anderson, B. S. W. Wei, and J. Parvin. 1998. Factors associated with the mammalian RNA polymerase II holoenzyme. Nucleic Acids Res. 26:847-853.
51. Neugebauer, K., and M. Roth. 1997. Transcription units as RNA processing units. Genes Dev. 11:3279-3285.
52. Nonet, M., and R. Young. 1989. Intragenic and extragenic suppressors of mutations in the heptapeptide repeat domain of Saccharomyces cerevisiae RNA polymerase II. Genetics 123:715-724.
53. O'Brien, T., S. Hardin, A. Greenleaf, and J. Lis. 1994. Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation. Nature (London) 370:75-77.
54. Ogryzko, V., L. Schiltz, V. Russanova, B. Howard, and Y. Nakatani. 1996. The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell 87:953-959.
55. Orphanides, G., T. Lagrange, and D. Reinberg. 1996. The general transcription factors of RNA polymerase II. Genes Dev. 10:2657-2683.
56. Orphanides, G., G. LeRoy, C. Chang, D. Luse, and D. Reinberg. 1998. FACT, a factor that facilitates transcript elongation through nucleosomes. Cell 92:105-116.
57. Pan, G., T. Aso, and J. Greenblatt. 1997. Interaction of elongation factors TFIIS and Elongin A with a human RNA polymerase II holoenzyme capable of promoter-specific initiation and responsive to transcriptional activators. J. Biol. Chem. 272:24563-24571.
58. Payne, J., P. Laybourn, and M. Dahmus. 1989. The transition of RNA polymerase II from initiation to elongation is associated with phosphoryla tion of the carboxyl-terminal domain of subunit IIa. J. Biol. Chem. 264: 19621-19629.
59. Peterson, C., and J. Tamkun. 1995. The SWI-SNF complex: a chromatin remodeling machine? Trends Biochem. Sci. 20:143-146.
60. Reifsnyder, C., J. Lowell, A. Clarke, and L. Pillus. 1996. Yeast SAS silencing genes and human genes associated with AML and HIV-1 Tat interactions are homologous with acetyltransferases. Nat. Genet. 14:42-49.
61. Rickert, P., W. Seghezzi, F. Shanahan, H. Cho, and E. Lees. 1996. Cyclin C/CDK8 is a novel CTD kinase associated with RNA polymerase II. Oncogene 12:2631-2640.
62. Sawadogo, M., and R. Roeder. 1985. Factors involved in specific transcription by human RNA polymerase II: analysis by a rapid and quantitative in vitro assay. Proc. Natl. Acad. Sci. USA 82:4394-4398.
63. Scully, R., S. Anderson, D. Chao, W. Wanjiang, Y. Liyan, R. Young, D. Livingston, and J. Parvin. 1997. BRCA1 is a component of the RNA polymerase II holoenzyme. Proc. Natl. Acad. Sci. USA 94:5605-5610.
64. Shi, X., M. Chang, A. Wolf, C. Chang, A. Frazer-Abel, P. Wade, Z. Burton, and J. Jaehning. 1997. Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex from the Srbp-containing holoenzyme. Mol. Cell. Biol. 17:1160-1169.
65. Shikama, N., J. Lyon, and N. LaThangue. 1997. The p300/CBP family: integrating signals with transcription factors and chromatin. Trends Cell Biol. 7:232-236.
66. Shuman, S. 1997. Origins of mRNA identity: capping enzymes bind to the phosphorylated C-terminal domain of the RNA polymerase II. Proc. Natl. Acad. Sci. USA 94:12758-12760.
67. Song, W., I. Treich, N. Qian, S. Kuchin, and M. Carlson. 1996. SSN genes that affect transcriptional repression in Saccharomyces cerevisiae encode SIN4, ROX3, and SRB proteins associated with RNA polymerase II. Mol. Cell. Biol. 16:115-120.
68. Sqvestrup, J., Y. Li, J. Fellows, A. Gnatt, S. Bjorklund, and R. Kornberg. 1997. Evidence for a mediator cycle at the initiation of transcription. Proc. Natl. Acad. Sci. USA 94:6075-6078.
69. Sun, X., Y. Zhang, H. Cho, P. Rickert, E. Lees, W. Lane, and D. Reinberg. NAT, a human complex Srb polypeptides that functions as a negative regulator of activated transcription. Mol. Cell, in press.
70. Sune, C., T. Hayashi, Y. Liu, W. Lane, R. Young, and M. Garcia-Blanco. 1997. CA150, a nuclear protein associated with the RNA polymerase II holoenzyme, is involved in Tat-activated human immunodeficiency virus type 1 transcription. Mol. Cell. Biol. 17:6029-6039.
71. Tsukiyama, T., and C. Wu. 1995. Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell 83:1011-1020.
72. Tsukiyama, T., and C. Wu. 1997. Chromatin remodelling and transcription. Curr. Opin. Genet. Dev. 7:182-191.
73. van Gool, A., E. Citterio, S. Rademakers, R. Os, W. Vermeulen, A. Constantinou, J.-M. Egly, D. Bootsma, and H. Hoejmakers. 1997. The Cockayne syndrome B protein, involved in transcription-coupled DNA repair, resides in an RNA polymerase II-containing complex. EMBO J. 16:5955-5965.
74. Varga-Weisz, P., M. Wilm, E. Bonte, K. Dumas, M. Mann, and P. Becker. 1997. Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature (London) 388:598-602.
75. Wade, P., D. Pruss, and A. Wolffe. 1997. Histone acetylation: chromatin in action. Trends Biochem. Sci. 22:128-132.
76. Wang, W., J. Cote, Y. Xue, P. Khavari, S. Biggar, C. Muchardt, G. Kalpana, S. Goff, M. Yaniv, J. Workman, and G. Crabtree. 1996. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. EMBO J. 15:5370-5382.
77. Wilson, C., D. Chao, A. Imbalzano, G. Schnitzler, R. Kingston, and R. Young. 1996. RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodelling. Cell 84:235-244.
78. Workman, J., S. Abmayr, W. Cromlish, and R. Roeder. 1988. Transcriptional regulation by the immediate early promoter of pseudorabies virus during in vitro nucleosome assembly. Cell 55:211-219.
79. Yang, X.-J., V. Ogryzko, J. Nishikawa, B. Howard, and Y. Nakatani. 1996. A p300/CBP-associated factor that competes with the adenoviral oncoprotein E1A. Nature (London) 382:319-324.
80. Young, R. 1991. RNA polymerase II. Annu. Rev. Biochem. 60:689-715.
81. Zehring, W., J. Lee, J. Weeks, R. Jokerst, and A. Greenleaf. 1988. The C-terminal repeat domain of RNA polymerase II largest subunit is essential in vivo but is not required for accurate transcription in vitro. Proc. Natl. Acad. Sci. USA 85:3698-3702.
82. Zhang, Y., R. Iratni, H. Erdjument-Bromage, P. Tempst, and D. Reinberg. 1997. Histone deacetylases and SAP18, a novel polypeptide, are components of a human Sin3 complex. Cell 89:357-364.