Hahn, S., Buratowski, S., Sharp, P., and Guarente, L. (1989). Yeast TATA-binding protein TFIID binds to TATA elements with both consensus and nonconsensus DNA sequences. Proc. Natl. Acad. Sci. USA 86, 5718-5722.

Hamspey, M. (1998). Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol. And Mol. Biol. Rev. 465-503.

Hampsey, M., and Reinberg, D. (2003). Tails of intrigue: phosphorylation of RNA polymerase II mediates histone methylation. Cell 113, 429-432.

Han, M., and Grunstein, M. (1988). Nucleosome loss activates yeast downstream promoters in vivo. Cell 55, 1137-1145. Han, M., Kim, U.J., Kayne, P., and Grunstein, M. (1988). Depletion of histone H4 and nucleosomes activates the PH05 gene in Saccharomyces cerevisiae EMBO J. 7, 2221-2228. Han, S.J., Lee, Y.C., Gim, B.S., Ryu, G-H., Park, S.J., Lane, W.S., and Kim, Y-J. (1999). Activator specific requirement of yeast mediator proteins for RNA polymerase II transcriptional activation. Mol. Cell. Biol. 19, 979-988.

Hartzog, G.A., Wada, T., Handa, H., and Winston, F. (1998). Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev. 12, 357-369.

Hekmatpanah, D.S., and Young, R.A. (1991). Mutations in a conserved region of RNA polyermase II influence the accuracy of mRNA start site selection. Mol. Cell. Biol. 11, 5781-5791. Hengartner, C.J., Thompson, C.M., Zhang, J., Chao, D.M., Liao, S.M., Koleske, A.J., Okamura, S„ and Young, R.A. (1995). Association of an activator with an RNA polyemrae II holenzyme. Genes Dev. 9, 897-910.

Ho, C.K., Schwer, B., and Shuman S. (1998). Genetic, physical, and functional interactions between the triphosphatase and guanylyltransferase components of the yeast mRNA capping apparatus. Mol. Cell. Biol. 18, 5189-5198. Ho, C.K., and Shuman, S. (1999). Distinct roles for CTD Ser-2 and Ser-5 phosphorylation in the recruitment and allosteric activation of mammalian mRNA capping enzyme. Mol. Cell 3, 405-411.

Holstege, F.C.P., Jennings, E.J., Wyrick, J.J., Lee, T.I., Hengartner, C.J., Green, M.R., Golub, T.R., Lander, E.S., and Young, R.A. (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717-728.

Ivanov, D., Kwak, Y.T., Guo, J., and Gaynor, R.B. (2000). Domains in the SPT5 protein that modulate its transcriptional regulatory properties. Mol. Cell. Biol. 20, 2970-2983. Jenuwein, R., and Allis, C.D. (2001). Translating the histone code. Science 293, 1074-1080.

Kang, J.S., Kim, S.H., Hwang, M.S., Han, S.J., Lee, Y.C., and Kim, Y.J. (2001). The structural and functional organization of the yeast mediator complex. J. Biol.Chem. 276, 42003-42010. Keller, W., and Minvielle-Sebastia, L. (1997). A comparison of mammalian and yeast pre-mRNA 3'-end processing. Curr. Opin. Cell Biol. 9, 329-336.

Kelley, D.E., Stokes, D.G., and Perry, R.P. (1999). CHD1 Interacts with SSRP1 and depends on both its chromodomain and its ATPase/helicase-like domain for proper association with chromatin. Chromosoma 108, 10-25.

Kettenberger, H., Armache, K-J., and Cramer, P. (2004). Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol. Cell 16, 955-965. Kim, J.L., Nikolov, D.B., and Burley, S.K. (1993a). Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365, 520-527.

Kim, Y„ Geiger, J H., Hahn, S„ and Sigler, P.B. (1993b). Crystal structure of a yeast TBP/TATA-box complex. Nature 365, 512-520.

Kim, Y.J., Bjorklund, S., Li, S., Sayre, M.H., and Kornberg, R D. (1994). A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77, 599-608.

Kim, J.B., and Sharp, P.A. (2001). Positive transcription elongation factor B phosphorylates hSPT5 and RNA polymerase II carboxyl-terminal domain independently of cyclin-dependent kinase-activating kinase. J. Biol. Chem. 276, 12317-12323. Kim, M., Ahn, S. H., Krogan, N. J., Greenblatt, J. F., Buratowski, S. (2004) Transitions in RNA polymerase II elongation complexes at the 3' ends of genes. EMBO J. 23, 354-364. Kireeva, M.L., Komissarova, N., Waugh, D.S., and Kashlev, M. (2000). The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex. J. Biol. Chem. 275, 6530-6536. Koch, C., Wollmann, P., Dahl, M., and Lottspeich, F. (1999). A role for Ctr9p and Paflp in the regulation of G1 cyclin expression in yeast. Nucleic Acids Res. 27, 2126-2134. Koh, S.S., Ansari, A.Z., Ptashne, M., and Young, R.A. (1998). An activator target in the RNA polymerase II holoenzyme. Mol. Cell 895-904.

Komarnitsky, P., Cho, E.J., and Buratowski, S. (2000). Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14, 2452-2460.

Kornberg, R.D., and Lorch, Y. (1991). Irresistible force meets immovable object: Transcription and the nucleosome. Cell 67, 833-836.

Krogan, N.J., and Greenblatt, J.F. (2001). Characterization of a six-subunit holo-elongator required for the regulated expression of a group of genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 21, 8203-8212.

Krogan, N.J., Dover, J., Khorrami, S., Greenblatt, J.F., Schneider, J, Johnston, M„ and Shilatifard (2002a). COMPASS, a histone H3 (lysine 4) methyltransferase required for telomeric silencing of gene expression. J. Biol. Chem., 277, 10753-10755. Krogan, N.J., Kim, M., Ahn, S.H., Zhong, G., Kobor, M.S., Cagney, G., Emili, A., Shilatifard, A., Buratowski, S., and Greenblatt, J.F. (2002b). RNA polymerase II elongation factors of S. cerevisiae: a targeted proteomics approach. Mol. Cell. Biol. 22, 6979-6992.

Krogan, N.J., Dover, J., Wood, A., Schneider, J., Heidt, J., Boateng, M.A., Dean, K., Ryan, O.W., Golshani, A., Johnston, M., Greenblat, J.F., and Shilatifard, A. (2003a). The Pafl complex is required for histone H3 methylation by COMPASS and Dotlp: linking transcriptional elongation to histone methylation. Mol. Cell 11, 721-729.

Krogan, N.J., Kim, M., Tong, A., Golshani, A., Cagney, G., Canadien, V., Richards, D.P., Beattie, B.K., Emili, A., Boone, C., Shilatifard, A., Buratowski, S., and Greenblatt J.F. (2003b). Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol. Cell. Biol. 23, 4207-4218.

Kulish, D., and Struhl, K. (2001). TFIIS enhances transcriptional elongation through an artificial arrest site in vivo. Mol. Cell. Biol. 21, 4162-4168.

Kumar, K.P, Akoulitchev S., and Reinberg, D. (1998). Promoter-proximal stalling results from the inability to recruit transcription factor IIH to the transcription complex and is a regulated event. Proc. Natl. Acad. Sci. USA 95, 9767-9772. Lachner, M., O'Sullivan, R.J., and Jenuwein, T. (2003). An epigenetic road map for histone lysine methylation. J. Cell. Sci. 116, 2117-2124.

Lagrange, T., Kapanidis, A.N., Tang, H., Reinberg, D., and Ebright, R.H. (1998). New core promoter element in RNA polymerase Il-dependent transcription: Sequence-specific DNA binding by transcription factor IIB. Genes Dev. 12, 34-44. Laybourn, P.J., and Dahmus, M.E. (1989). Transcription -dependent structural changes in the C-terminal doman of mammalian RNA polymerase subunit Ila/o J. Biol. Chem. 264, 6693-6698.

Laybourn, P.J., and Dahmus, M.E. (1990). Phosphorylation of RNA polymerase IIA occurs subsequent to interaction with the promoter and before the initiation of transcription. J. Biol. Chem. 265, 13165-13173.

Lee, C.L., and Kim, Y.J. (1998). Requirement for a functional interaction between Mediator components Med6 and Srb4 in RNA polymerase II transcription. Mol. Cell Biol. 18, 5364-5370. Lee, I.L., and Young, R.A. (2000). Transcription of eukaryotic protein-coding genes. Annu. Rev. Genet. 34, 77-137. Lewis, J.D., Gunderson, S.I., and Mattaj, I.W. (1995). The influence of 5'-end and 3'-end structures on pre-messenger-RNA metabolism. J. Cell Sci. 19, 13-19.

Li, B., Howe, L., Anderson, S., Yates, J.R. Ill, and Workman, J.L.

(2003). The Ser 2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II. J. Biol. Chem. 278, 897-8903.

Li, Y„ Bjorklund, S., Hiang, Y.W., Kim, Y.J., Lane, W.S., Stillman, D.J., and Kornberg, R.D. (1995). Yeast global transcriptional regulators Sin4 and Rgrl are components of mediator complex/RNA polymerase II holoenzyme. Proc. Natl. Acad. Sci. USA 92, 10864-10868.

Licatalosi, D.D., Geiger, G., Minet, M., Schroeder, S., Cilli, K., McNeil, J.B., and Bentley, D.L. (2002). Functional interaction of yeast pre-mRNA 3' end processing factors with RNA polymerase II. Mol. Cell 9, 1101-1111.

Licht, C.L., Stevnsner, T., and Bohr, V.A. (2003). Cockayne syndrome group B cellular and biochemical functions. Am. J. Hum. Genet. 73, 1217-1239.

Lindstrom, D.L., Squazzo, S.L., Muster, N., Burckin, T.A., Wachter, K.C., Emigh, C.A., McCleeiy, J.A., Yates, J.R. Ill, and Hartzog, G.A. (2003). Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Mol. Cell. Biol. 23, 1368-1378. Liu, H.Y., Badarinarayana, V., Audino, D.C., Rappsilber, J., Mann, M., and Denis, C.L. (1998). The NOT proteins are part of the CCR4 transcriptional complex and affect gene expression both positively and negatively. EMBO J. 17, 1096-1106 Lorch, Y., Beve, J., Gustafsson, C.M., Myers, L.C., and Kornberg, R.D. (2000). Mediator-nucleosome interaction. Mol. Cell 6, 197-201.

Lu, H., Flores, O., Weinmann R., and Reinberg, D. (1991). The nonphosphoryylated form of RNA polymerase II preferentially associates with the preinitiation complex. Proc. Natl. Acad. Sci. USA 88, 10004-10008.

Malik, S., and Roeder, R.G. (2000). Transcriptional regulation through mediator-like coactivators in yeast and metazoan cells. TIBS 25, 277-283.

Maniatis, T., and Reed, R. (2002). An extensive network of coupling among gene expression machines. Nature 416, 499-506. McCracken, S., Fong, N., Yankulov, K., Ballantyne, S., Pan, G.H., Greenblatt, J., Patterson, S.D., Wickens, M., and Bentley, D.L. (1997a). The C-terminal domain of RNA polymerase II couples messenger RNA processing to transcription. Nature 385, 357-361.

McCracken, S., Fong, N., Rosonina, R., Yankulov, K., Brothers, G., Siderovski, D., Hessel, A., Foster, S., Shuman, S., and Bentley, D.L. (1997b). 5'-capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II. Genes Dev. 11, 3306-3318. McKine, K., Moore, P.A., Hull, M.W., and Woychik, N.A. (1995). Six human RNA polymerase subunits functionally substitute for their yeast counterparts. Mol. Cell. Biol. 15, 6895-6900. Miller, T., Williams, K., Johnstone, R.W., and Shilatifard, A. (2000). Identification, cloning, expression, and biochemical characterization of the testis-specific RNA polymerase II

elongation factor ELL3 J. Biol. Chem. 275, 32052-32056. Miller, T., Krogan, N.J., Dover, J., Erdjument-Bromage, H., Tempst, P., Johnston, M., Greenblatt, J.F., and Shilatifard, A.

(2001). COMPASS: a complex of proteins associated with a trithorax-related SET domain protein. Proc. Natl. Acad. Sci. 98, 12902-12907.

Moteki, S., and Price, D. (2002). Functional coupling of capping and transcription of mRNA. Mol. Cell 10, 599-609. Mueller, C.L., and Jaehning, J.A. (2002). Ctr9, Rtfl, and Leol are components of the Pafl/RNApolymerase II complex. Mol. Cell. Biol. 22, 1971-1980.

Mueller, C.L., Porter, S.E., Hoffman, M.G., and Jaehning, J.A. (2004). The Pafl complex has functions independent of actively transcribing RNA polymerase II. Mol. Cell 14, 447-456. Myer, V.E., and Young, R.A. (1998). RNA polymerase II holoenzymes and subcomplexes. J. Biol. Chem. 273, 27757-27760.

Myers, L.C., Leuther, K., Bushnell, D.A., Gustafsson, C. M., and Kornberg, R.D. (1997). Yeast RNA polymerase II transcription reconstituted with purified proteins. Methods in Enzymol. 12, 212-216.

Myers, L.C., Gustafsson, C.M., Bushnell, D.A., Lui, M., Erdjument-Bromage, H., Tempst, P. and Kornberg, R.D. (1998). The Med proteins of yeast and their function through the RNA polymerse II carboxy-terminal domain. Genes Dev. 12, 45-54. Myers, L.C., Gustafsson, C.M., Hayashibara, K.C., Brown, P.O., and Kornberg, R.D. (1999). Mediator protein mutations that selectively abolish activated transcription. Proc. Natl. Acad. Sci. USA 96, 67-72.

Myers, L.C., Lacomis, L., Erdjument-Bromage, H., and Tempst, P. (2002). The yeast capping enzyme represses RNA polymerase II transcription. Mol. Cell 10, 883-894.

Nagy, P.L., Griesenbeck, J., Kornberg, R.D., and Cleary, M.L.

(2002). A trithorax-group complex purified from Saccharomyces cerevisiae is required for methylation of histone H3. Proc. Natl. Acad. Sci. USA 99, 90-94.

Natori, S., Takeuchi, K., Takahashi, K., and Mizuno, D. (1973). DNA dependent RNA polymerase from Ehrlich ascites tumor cells. II. Factors stimulating the activity of RNA polymerase II. J. Biochem. (Tokyo) 73, 879-888.

Ng, H.H., Robert, F„ Young, R.A., and Strahl, K. (2003). Targeted recruitment of Setl histone methylase by elongating pol II provides a localized mark and memory of recent transcriptional activity. Mol. Cell. 11, 709-719.

Noma, K., and Grewal, S.I. (2002). Histone H3 lysine 4 methylation is mediated by Setl and promotes maintenance of active chromatin states in fission yeast. Proc. Natl. Acad. Sci. USA 99, 16438-16445.

Nonet, M., Sweetser, D., and Young, R.A. (1987). Functional redundancy and structural polymorphism in the large subunit of RNA polymerase II. Cell 50, 909-915.

Nonet, M.L., and Young, R.A. (1989). Intragenic and extragenic suppressors of mutations in the heptapeptide repeat domain of Saccharomyces cerevisiae RNA polymerase II. Genetics 123, 715-724.

O'Brien, T., Hardin, S., Greenleaf, A., and Lis, J.T. (1994) Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation. Nature 370, 75-77. Orphanides, G., Lagrange, T., and Reinberg, D. (1996). The general transcription factors of RNA polymerase II. Genes Dev. 10, 2657-2683.

Orphanides, G., LeRoy, G., Chang, C.J., Luse, D.S., and Reinberg, D. (1998). FACT, a factor that facilitates transcript elongation through nucleosomes. Cell 92, 105-116. Orphanides, G., Wu, W.H., Lane, W.S., Hampsey, M., and Reinberg, D. (1999). The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins. Nature 400, 284-288.

Orphanides, G., and Reinberg, D. (2002). A unified theory of gene expression. Cell 108, 439-451.

Otero, G„ Fellows, J., Li, Y., de Bizemont, T., Dirac, A.M.G., Gustafsson, C.M., Erdjument-Bromage, H., Tempst, P., and Svejstrup, J.Q. (1999). Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. Mol. Cell 3, 109-118.

Pal, M., and Luse, D.S. (2002). Strong natural pausing by RNA polymerase II within 10 bases of transcription start may result in repeated slippage and reextension of the nascent RNA. Mol. Cell. Biol. 22, 30-40.

Pal, M., and Luse, D.S. (2003). The initiation-elongation transition: Lateral mobility of RNA in RNA polymerase II complexes is greatly reduced at +8/+9 and absent by +23. Proc. Natl. Acad. Sci. USA 100, 5700-5705.

Peterson, C.L., and Tamkun, J.W. (1995). The SWI-SNF complex: a chromatin remodeling machine? Trends Biochem. Sci. 20, 143-146.

Pokholok, D.K., Hannett, N.M., and Young, R.A. (2002).

Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Mol. Cell 9, 799-809.

Poon, D., and Weil, P.A. (1993). Immunopurification of yeast

TATA-binding protein and associated factors: presence of transcription factor IIB transcription activity. J. Biol. Chem. 268,

0 0

Post a comment