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Transcriptional Regulation

Evidence for Eviction and Rapid Deposition of Histones upon Transcriptional Elongation by RNA Polymerase II

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Pages 10111-10117 | Received 01 Jun 2004, Accepted 26 Aug 2004, Published online: 27 Mar 2023

REFERENCES

  • Ahmad, K., and Henikoff S.. 2002. Histone H3 variants specify modes of chromatin assembly. Proc. Natl. Acad. Sci. USA 99:16477–16484.
  • Ahmad, K., and Henikoff S.. 2002. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell 9:1191–1200.
  • Aparicio, O. M., Geisberg J. V., and Struhl K.. 2004. Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo, p. 21.3.1–21.3.17. In Ausubel F. A., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., and Struhl K. (ed.), Current protocols in molecular biology. John Wiley & Sons, New York, N.Y.
  • Becker, P. B., and Horz W.. 2002. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71:247–273.
  • Belotserkovskaya, R., Oh S., Bondarenko V. A., Orphanides G., Studitsky V. M., and Reinberg D.. 2003. FACT facilitates transcription-dependent nucleosome alteration. Science 301:1090–1093.
  • Boeger, H., Griesenbeck J., Strattan J. S., and Kornberg R. D.. 2003. Nucleosomes unfold completely at a transcriptionally active promoter. Mol. Cell 11:1587–1598.
  • Bortvin, A., and Winston F.. 1996. Evidence that Spt6 controls chromatin structure by a direct interaction with histones. Science 272:1473–1476.
  • Cairns, B. R., Lorch Y., Li Y., Zhang M., Lacomis L., Erdjument-Bromage H., Tempst P., Du J., Laurent B., and Kornberg R. D.. 1996. RSC, an essential, abundant chromatin-remodeling complex. Cell 87:1249–1260.
  • Chang, C. H., and Luse D. S.. 1997. The H3/H4 tetramer blocks transcript elongation by RNA polymerase II in vitro. J. Biol. Chem. 272:23427–23434.
  • Cismowski, M. J., Laff G. M., Solomon M. J., and Reed S. I.. 1995. KIN28 encodes a C-terminal domain kinase that controls mRNA transcription in Saccharomyces cerevisiae but lacks cyclin-dependent kinase-activating kinase (CAK) activity. Mol. Cell. Biol. 15:2983–2992.
  • Clark, D. J., and Felsenfeld G.. 1992. A nucleosome core is transferred out of the path of a transcribing polymerase. Cell 71:11–22.
  • Damelin, M., Simon I., Moy T. I., Wilson B., Komili S., Tempst P., Roth F. P., Young R. A., Cairns B. R., and Silver P. A.. 2002. The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress. Mol. Cell 9:563–573.
  • Deckert, J., and Struhl K.. 2001. Histone acetylation at promoters is differentially affected by activators and repressors. Mol. Cell. Biol. 21:2726–2735.
  • Endoh, M., Zhu W., Hasegawa J., Watanabe H., Kim D. K., Aida M., Inukai N., Narita T., Yamada T., Furuya A., Sato H., Yamaguchi Y., Mandal S. S., Reinberg D., Wada T., and Handa H.. 2004. Human Spt6 stimulates transcription elongation by RNA polymerase II in vitro. Mol. Cell. Biol. 24:3324–3336.
  • 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.. 1998. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95:717–728.
  • Hong, L., Schroth G. P., Matthews H. R., Yau P., and Bradbury E. M.. 1993. Studies of the DNA binding properties of histone H4 amino terminus: thermal denaturation studies reveal that acetylation markedly reduces the binding constant of the H4 “tail” to DNA. J. Biol. Chem. 268:305–314.
  • Iyer, V., and Struhl K.. 1996. Absolute mRNA levels and transcriptional initiation rates in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 93:5208–5212.
  • Izban, M. G., and Luse D. S.. 1992. Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates. J. Biol. Chem. 267:13647–13655.
  • Izban, M. G., and Luse D. S.. 1991. Transcription on nucleosomal templates by RNA polymerase II in vitro: inhibition of elongation with enhancement of sequence-specific pausing. Genes Dev. 5:683–686.
  • Janicki, S. M., Tsukamoto T., Salghetti S. E., Tansey W. P., Sachidanandam R., Prasanth K. V., Ried T., Shav-Tai Y., Bertrand E., Singer R. H., and Spector D. L.. 2004. From silencing to gene expression: real-time analysis in single cells. Cell 116:683–698.
  • Kaplan, C. D., Laprade L., and Winston F.. 2003. Transcription elongation factors repress transcription initiation from cryptic sites. Science 301:1096–1099.
  • Kireeva, M. L., Walter W., Tchernajenko V., Bondarenko V., Kashlev M., and Studitsky V. M.. 2002. Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription. Mol. Cell 9:541–552.
  • Kirov, N., Tsaneva I., Einbinder E., and Tsanev R.. 1992. In vitro transcription through nucleosomes by T7 RNA polymerase. EMBO J. 11:1941–1947.
  • Kobor, M. S., Venkatasubrahmanyam S., Meneghini M. D., Gin J. W., Jennings J. L., Link A. J., Madhani H. D., and Rine J.. 2004. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A. Z into euchromatin. PLoS Biol. 2:E131.
  • 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.
  • Krogan, N. J., Keogh M. C., Datta N., Sawa C., Ryan O. W., Ding H., Haw R. A., Pootoolal J., Tong A., Canadien V., Richards D. P., Wu X., Emili A., Hughes T. R., Buratowski S., and Greenblatt J. F.. 2003. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol. Cell 12:1565–1576.
  • 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.. 2002. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomic approach. Mol. Cell. Biol. 22:6979–6992.
  • Kuras, L., and Struhl K.. 1999. Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme. Nature 399:609–612.
  • Lee, C. K., Shibata Y., Rao B., Strahl B. D., and Lieb J. D.. 2004. Evidence for nucleosome depletion at active regulatory regulation genome-wide. Nat. Genet. 36:900–905.
  • Luger, K., Mader A. W., Richmond R. K., Sargent D. F., and Richmond T. J.. 1997. Crystal structure of the nucleosome core particle at 2.8 angstrom resolution. Nature 389:251–260.
  • Malone, E. A., Clark C. D., Chiang A., and Winston F.. 1991. Mutations in SPT16/CDC68 suppress cis- and trans-acting mutations that affect promoter function in Saccharomyces cerevisiae. Mol. Cell. Biol. 11:5710–5717.
  • Martens, J. A., and Winston F.. 2003. Recent advances in understanding chromatin remodeling by Swi/Snf complexes. Curr. Opin. Genet. Dev. 13:136–142.
  • Mason, P. B., and Struhl K.. 2003. The FACT complex travels with elongating RNA polymerase II and is important for the fidelity of transcriptional initiation in vivo. Mol. Cell. Biol. 23:8323–8333.
  • McKittrick, E., Gafken P. R., Ahmad K., and Henikoff S.. 2004. Histone H3.3 is enriched in covalent modifications associated with active chromatin. Proc. Natl. Acad. Sci. USA 101:1525–1530.
  • Meneghini, M. D., Wu M., and Madhani H. D.. 2003. Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of heterochromatin. Cell 112:725–736.
  • Mizuguchi, G., Shen X., Landry J., Wu W. H., Sen S., and Wu C.. 2004. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303:343–348.
  • Narlikar, G. J., Fan H.-Y., and Kingston R. E.. 2002. Cooperation between complexes that regulate chromatin and transcription. Cell 108:475–487.
  • Ng, H. H., Ciccone D. N., Morshead K. B., Oettinger M. A., and Struhl K.. 2003. Lysine-79 of histone H3 is hypomethylated at silenced loci in yeast and mammalian cells: a potential mechanism for position-effect variegation. Proc. Natl. Acad. Sci. USA 100:1820–1825.
  • Ng, H. H., Robert F., Young R. A., and Struhl K.. 2002. Genome-wide location and regulated recruitment of the RSC nucleosome remodeling complex. Genes Dev. 16:806–819.
  • Ng, H. H., Robert F., Young R. A., and Struhl K.. 2003. Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol. Cell 11:709–719.
  • Ng, H. H., Xu R. M., Zhang Y., and Struhl K.. 2002. Ubiquitination of histone H2B by Rad6 is required for efficient Dot1-mediated methylation of histone H3-lysine 79. J. Biol. Chem. 277:34655–34657.
  • O'Neill, T. E., Smith J. G., and Bradbury E. M.. 1993. Histone octamer dissociation is not required for transcript elongation through arrays of nucleosome cores by phage T7 RNA polymerase in vitro. Proc. Natl. Acad. Sci. USA 90:6203–6207.
  • Orphanides, G., LeRoy G., Chang C. H., 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.
  • Reinke, H., and Horz W.. 2003. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol. Cell 11:1599–1607.
  • Robinson, K. M., and Schultz M. C.. 2003. Replication-independent assembly of nucleosome arrays in a novel yeast chromatin reconstitution system involves antisilencing factor Asf1p and chromodomain protein Chd1p. Mol. Cell. Biol. 23:7937–7946.
  • Saunders, A., Werner J., Andrulis E. D., Nakayama T., Hirose S., Reinberg D., and Lis J. T.. 2003. Tracking FACT and RNA polymerase II elongation complex through chromatin in vivo. Science 301:1094–1096.
  • Schroeder, S. C., Schwer B., Shuman S., and Bentley D.. 2000. Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev. 14:2435–2440.
  • Simic, R., Lindstrom D. L., Tran H. G., Roinick K. L., Costa P. J., Johnson A. D., Hartzog G. A., and Arndt K. M.. 2003. Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J. 22:1846–1856.
  • Strasser, K., Masuda S., Mason P., Pfannstiel J., Oppizzi M., Rodriguez-Navarro S., Rondon A. G., Aguilera A. A., Struhl K., Reed R., and Hurt E.. 2002. TREX is a conserved complex coupling transcription with mRNA export. Nature 417:304–307.
  • Studitsky, V. M., Clark D. J., and Felsenfeld G.. 1994. A histone octamer can step around a transcribing polymerase without leaving the template. Cell 76:371–382.
  • Studitsky, V. M., Clark D. J., and Felsenfeld G.. 1995. Overcoming a nucleosomal barrier to transcription. Cell 83:19–27.
  • Studitsky, V. M., Kassavetis G. A., Geiduschek E. P., and Felsenfeld G.. 1997. Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase. Science 278:1960–1963.
  • Tagami, H., Ray-Gallet D., Almouzni G., and Nakatani Y.. 2004. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell 116:51–61.
  • Tran, H. G., Steger D. J., Iyer V. R., and Johnson A. D.. 2000. The chromodomain protein chd1p from budding yeast is an ATP-dependent chromatin-modifying factor. EMBO J. 19:2323–2331.
  • Ura, K., Kurumizaka H., Dimitrov S., Almouzni G., and Wolffe A. P.. 1997. Histone acetylation: influence on transcription, nucleosome mobility and positioning, and linker histone-dependent transcriptional repression. EMBO J. 16:2096–2107.

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