A Novel Domain in Set2 Mediates RNA Polymerase II Interaction and Couples Histone H3 K36 Methylation with Transcript Elongation

REFERENCES

• Ahn, S. H., M. Kim, and S. Buratowski. 2004. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3′ end processing. Mol. Cell 13:67–76.
   PubMed Web of Science ®Google Scholar
• Alen, C., N. A. Kent, H. S. Jones, J. O′Sullivan, A. Aranda, and N. J. Proudfoot. 2002. A role for chromatin remodeling in transcriptional termination by RNA polymerase II. Mol. Cell 10:1441–1452.
   PubMed Web of Science ®Google Scholar
• Archambault, J., F. Lacroute, A. Ruet, and J. D. Friesen. 1992. Genetic interaction between transcription elongation factor TFIIS and RNA polymerase II. Mol. Cell. Biol. 12:4142–4152.
   PubMedGoogle Scholar
• Beisel, C., A. Imhof, J. Greene, E. Kremmer, and F. Sauer. 2002. Histone methylation by the Drosophila epigenetic transcriptional regulator Ash1. Nature 419:857–862.
   PubMed Web of Science ®Google Scholar
• Briggs, S. D., M. Bryk, B. D. Strahl, W. L. Cheung, J. K. Davie, S. Y. Dent, F. Winston, and C. D. Allis. 2001. Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes Dev. 15:3286–3295.
   PubMed Web of Science ®Google Scholar
• Byrd, K. N., and A. Shearn. 2003. ASH1, a Drosophila trithorax group protein, is required for methylation of lysine 4 residues on histone H3. Proc. Natl. Acad. Sci. USA 100:11535–11540.
   PubMedGoogle Scholar
• Edmondson, D. G., M. M. Smith, and S. Y. Roth. 1996. Repression domain of the yeast global repressor Tup1 interacts directly with histones H3 and H4. Genes Dev. 10:1247–1259.
   PubMed Web of Science ®Google Scholar
• Exinger, F., and F. Lacroute. 1992. 6-Azauracil inhibition of GTP biosynthesis in Saccharomyces cerevisiae. Curr. Genet. 22:9–11.
   PubMedGoogle Scholar
• Gelbart, M. E., T. Rechsteiner, T. J. Richmond, and T. Tsukiyama. 2001. Interactions of Isw2 chromatin remodeling complex with nucleosomal arrays: analyses using recombinant yeast histones and immobilized templates. Mol. Cell. Biol. 21:2098–2106.
   PubMed Web of Science ®Google Scholar
• Gerber, M., and A. Shilatifard. 2003. Transcriptional elongation by RNA polymerase II and histone methylation. J. Biol. Chem. 278:26303–26306.
   PubMed Web of Science ®Google Scholar
• Hampsey, M., and D. Reinberg. 2003. Tails of intrigue: phosphorylation of RNA polymerase II mediates histone methylation. Cell 113:429–432.
   PubMed Web of Science ®Google Scholar
• Henry, K. W., A. Wyce, W. S. Lo, L. J. Duggan, N. C. Emre, C. F. Kao, L. Pillus, A. Shilatifard, M. A. Osley, and S. L. Berger. 2003. Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev. 17:2648–2663.
   PubMed Web of Science ®Google Scholar
• Hsu, J. Y., Z. W. Sun, X. Li, M. Reuben, K. Tatchell, D. K. Bishop, J. M. Grushcow, C. J. Brame, J. A. Caldwell, D. F. Hunt, R. Lin, M. M. Smith, and C. D. Allis. 2000. Mitotic phosphorylation of histone H3 is governed by Ipl1/aurora kinase and Glc7/PP1 phosphatase in budding yeast and nematodes. Cell 102:279–291.
   PubMed Web of Science ®Google Scholar
• Hyle, J. W., R. J. Shaw, and D. Reines. 2003. Functional distinctions between IMP dehydrogenase genes in providing mycophenolate resistance and guanine prototrophy to yeast. J. Biol. Chem. 278:28470–28478.
   PubMed Web of Science ®Google Scholar
• Jackson, R. C., G. Weber, and H. P. Morris. 1975. IMP dehydrogenase, an enzyme linked with proliferation and malignancy. Nature 256:331–333.
   PubMed Web of Science ®Google Scholar
• Jones, J. C., H. P. Phatnani, T. A. Haystead, J. A. MacDonald, S. M. Alam, and A. L. Greenleaf. 2004. C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats. J. Biol. Chem. 279:24957–24964.
   PubMed Web of Science ®Google Scholar
• Komarnitsky, P., E. J. Cho, and S. Buratowski. 2000. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14:2452–2460.
   PubMed Web of Science ®Google Scholar
• Krogan, N. J., J. Dover, A. Wood, J. Schneider, J. Heidt, M. A. Boateng, K. Dean, O. W. Ryan, A. Golshani, M. Johnston, J. F. Greenblatt, and A. Shilatifard. 2003. The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. Mol. Cell 11:721–729.
   PubMed Web of Science ®Google Scholar
• Krogan, N. J., M. Kim, A. Tong, A. Golshani, G. Cagney, V. Canadien, D. P. Richards, B. K. Beattie, A. Emili, C. Boone, A. Shilatifard, S. Buratowski, and J. Greenblatt. 2003. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol. Cell. Biol. 23:4207–4218.
   PubMed Web of Science ®Google Scholar
• Landry, J., A. Sutton, T. Hesman, J. Min, R. M. Xu, M. Johnston, and R. Sternglanz. 2003. Set2-catalyzed methylation of histone H3 represses basal expression of GAL4 in Saccharomyces cerevisiae. Mol. Cell. Biol. 23:5972–5978.
   PubMedGoogle Scholar
• Li, B., L. Howe, S. Anderson, J. R. Yates III, and J. L. Workman. 2003. The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II. J. Biol. Chem. 278:8897–8903.
   PubMed Web of Science ®Google Scholar
• Li, J., D. Moazed, and S. P. Gygi. 2002. Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation. J. Biol. Chem. 277:49383–49388.
   PubMedGoogle Scholar
• Mandal, S. S., H. Cho, S. Kim, K. Cabane, and D. Reinberg. 2002. FCP1, a phosphatase specific for the heptapeptide repeat of the largest subunit of RNA polymerase II, stimulates transcription elongation. Mol. Cell. Biol. 22:7543–7552.
   PubMed Web of Science ®Google Scholar
• Morillon, A., N. Karabetsou, J. O'Sullivan, N. Kent, N. Proudfoot, and J. Mellor. 2003. Isw1 chromatin remodeling ATPase coordinates transcription elongation and termination by RNA polymerase II. Cell 115:425–435.
   PubMed Web of Science ®Google Scholar
• Morillon, A., J. O′Sullivan, A. Azad, N. Proudfoot, and J. Mellor. 2003. Regulation of elongating RNA polymerase II by forkhead transcription factors in yeast. Science 300:492–495.
   PubMedGoogle Scholar
• Morris, D. P., J. M. Lee, D. E. Sterner, W. J. Brickey, and A. L. Greenleaf. 1997. Assaying CTD kinases in vitro and phosphorylation-modulated properties of RNA polymerase II in vivo. Methods 12:264–275.
   PubMedGoogle Scholar
• Morris, D. P., H. P. Phatnani, and A. L. Greenleaf. 1999. Phospho-carboxyl-terminal domain binding and the role of a prolyl isomerase in pre-mRNA 3′-end formation. J. Biol. Chem. 274:31583–31587.
   PubMed Web of Science ®Google Scholar
• Mueller, C. L., S. E. Porter, M. G. Hoffman, and J. A. Jaehning. 2004. The Paf1 complex has functions independent of actively transcribing RNA polymerase II. Mol. Cell 14:447–456.
   PubMed Web of Science ®Google Scholar
• Ng, H. H., F. Robert, R. A. Young, and K. Struhl. 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.
   PubMed Web of Science ®Google Scholar
• Orphanides, G., W. H. Wu, W. S. Lane, M. Hampsey, and D. Reinberg. 1999. The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins. Nature 400:284–288.
   PubMed Web of Science ®Google Scholar
• Phatnani, H. P., J. C. Jones, and A. L. Greenleaf. 2004. Expanding the functional repertoire of CTD kinase I and RNA polymerase II: novel phosphoCTD-associating proteins in the yeast proteome. Biochemistry 43:15702–15719.
   PubMed Web of Science ®Google Scholar
• Riles, L., R. J. Shaw, M. Johnston, and D. Reines. 2004. Large-scale screening of yeast mutants for sensitivity to the IMP dehydrogenase inhibitor 6-azauracil. Yeast 21:241–248.
   PubMedGoogle Scholar
• Schaft, D., A. Roguev, K. M. Kotovic, A. Shevchenko, M. Sarov, A. Shevchenko, K. M. Neugebauer, and A. F. Stewart. 2003. The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation. Nucleic Acids Res. 31:2475–2482.
   PubMed Web of Science ®Google Scholar
• Schroeder, S. C., B. Schwer, S. Shuman, and D. Bentley. 2000. Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev. 14:2435–2440.
   PubMed Web of Science ®Google Scholar
• Shaw, R. J., J. L. Wilson, K. T. Smith, and D. Reines. 2001. Regulation of an IMP dehydrogenase gene and its overexpression in drug-sensitive transcription elongation mutants of yeast. J. Biol. Chem. 276:32905–32916.
   PubMedGoogle Scholar
• Shilatifard, A. 2004. Transcriptional elongation control by RNA polymerase II: a new frontier. Biochim. Biophys. Acta 1677:79–86.
   PubMedGoogle Scholar
• Sims, R. J., III, R. Belotserkovskaya, and D. Reinberg. 2004. Elongation by RNA polymerase II: the short and long of it. Genes Dev. 18:2437–2468.
   PubMed Web of Science ®Google Scholar
• Smith, J. S., C. B. Brachmann, I. Celic, M. A. Kenna, S. Muhammad, V. J. Starai, J. L. Avalos, J. C. Escalante-Semerena, C. Grubmeyer, C. Wolberger, and J. D. Boeke. 2000. A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family. Proc. Natl. Acad. Sci. USA 97:6658–6663.
   PubMed Web of Science ®Google Scholar
• Strahl, B. D., P. A. Grant, S. D. Briggs, Z. W. Sun, J. R. Bone, J. A. Caldwell, S. Mollah, R. G. Cook, J. Shabanowitz, D. F. Hunt, and C. D. Allis. 2002. Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol. Cell. Biol. 22:1298–1306.
   PubMed Web of Science ®Google Scholar
• Woodage, T., M. A. Basrai, A. D. Baxevanis, P. Hieter, and F. S. Collins. 1997. Characterization of the CHD family of proteins. Proc. Natl. Acad. Sci. USA 94:11472–11477.
   PubMed Web of Science ®Google Scholar
• Wu, X., A. Rossettini, and S. D. Hanes. 2003. The ESS1 prolyl isomerase and its suppressor BYE1 interact with RNA pol II to inhibit transcription elongation in Saccharomyces cerevisiae. Genetics 165:1687–1702.
   PubMedGoogle Scholar
• Xiao, T., H. Hall, K. O. Kizer, Y. Shibata, M. C. Hall, C. H. Borchers, and B. D. Strahl. 2003. Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev. 17:654–663.
   PubMed Web of Science ®Google Scholar
• Xiao, T., C. F. Kao, N. J. Krogan, Z. W. Sun, J. Greenblatt, M. A. Osley, and B. D. Strahl. 2005. Histone H2B ubiquitylation is associated with elongating RNA polymerase II. Mol. Cell. Biol. 25:637–651.
   PubMed Web of Science ®Google Scholar
• Zhang, W., J. R. Bone, D. G. Edmondson, B. M. Turner, and S. Y. Roth. 1998. Essential and redundant functions of histone acetylation revealed by mutation of target lysines and loss of the Gcn5p acetyltransferase. EMBO J. 17:3155–3167.
   PubMed Web of Science ®Google Scholar