Drosophila Paf1 Modulates Chromatin Structure at Actively Transcribed Genes

REFERENCES

• Adelman, K., M. T. Marr, J. Werner, A. Saunders, Z. Ni, E. D. Andrulis, and J. T. Lis. 2005. Efficient release from promoter-proximal stall sites requires transcript cleavage factor TFIIS. Mol. Cell 17:103–112.
   PubMed Web of Science ®Google Scholar
• Andrulis, E. D., E. Guzman, P. Doring, J. Werner, and J. T. Lis. 2000. High-resolution localization of Drosophila Spt5 and Spt6 at heat shock genes in vivo: roles in promoter proximal pausing and transcription elongation. Genes Dev. 14:2635–2649.
   PubMed Web of Science ®Google Scholar
• Andrulis, E. D., J. Werner, A. Nazarian, H. Erdjument-Bromage, P. Tempst, and J. T. Lis. 2002. The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila. Nature 420:837–841.
   PubMedGoogle Scholar
• Belotserkovskaya, R., A. Saunders, J. T. Lis, and D. Reinberg. 2004. Transcription through chromatin: understanding a complex FACT. Biochim. Biophys. Acta 1677:87–99.
   PubMedGoogle Scholar
• Betz, J. L., M. Chang, T. M. Washburn, S. E. Porter, C. L. Mueller, and J. A. Jaehning. 2002. Phenotypic analysis of Paf1/RNA polymerase II complex mutations reveals connections to cell cycle regulation, protein synthesis, and lipid and nucleic acid metabolism. Mol. Genet. Genomics 268:272–285.
   PubMed Web of Science ®Google Scholar
• Boehm, A. K., A. Saunders, J. Werner, and J. T. Lis. 2003. Transcription factor and polymerase recruitment, modification, and movement on dhsp70 in vivo in the minutes following heat shock. Mol. Cell. Biol. 23:7628–7637.
   PubMed Web of Science ®Google Scholar
• Canaani, E., T. Nakamura, T. Rozovskaia, S. T. Smith, T. Mori, C. M. Croce, and A. Mazo. 2004. ALL-1/MLL1, a homologue of Drosophila TRITHORAX, modifies chromatin and is directly involved in infant acute leukaemia. Br. J. Cancer 90:756–760.
   PubMedGoogle Scholar
• Chang, M., D. French-Cornay, H. Y. Fan, H. Klein, C. L. Denis, and J. A. Jaehning. 1999. A complex containing RNA polymerase II, Paf1p, Cdc73p, Hpr1p, and Ccr4p plays a role in protein kinase C signaling. Mol. Cell. Biol. 19:1056–1067.
   PubMedGoogle Scholar
• Costa, P. J., and K. M. Arndt. 2000. Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae Rtf1 protein in transcription elongation. Genetics 156:535–547.
   PubMed Web of Science ®Google Scholar
• Costlow, N., and J. T. Lis. 1984. High-resolution mapping of DNase I-hypersensitive sites of Drosophila heat shock genes in Drosophila melanogaster and Saccharomyces cerevisiae. Mol. Cell. Biol. 4:1853–1863.
   PubMed Web of Science ®Google Scholar
• Formosa, T., S. Ruone, M. D. Adams, A. E. Olsen, P. Eriksson, Y. Yu, A. R. Rhoades, P. D. Kaufman, and D. J. Stillman. 2002. Defects in SPT16 or POB3 (yFACT) in Saccharomyces cerevisiae cause dependence on the Hir/Hpc pathway: polymerase passage may degrade chromatin structure. Genetics 162:1557–1571.
   PubMedGoogle 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
• Hartzog, G. A. 2003. Transcription elongation by RNA polymerase II. Curr. Opin. Genet. Dev. 13:119–126.
   PubMedGoogle Scholar
• Izban, M. G., and D. S. Luse. 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.
   PubMed Web of Science ®Google Scholar
• Izban, M. G., and D. S. Luse. 1991. Transcription on nucleosomal templates by RNA polymerase II in vitro: inhibition of elongation with enhancement of sequence-specific pausing. Genes Dev. 5:683–696.
   PubMed Web of Science ®Google Scholar
• Jensen, T. H., K. Dower, D. Libri, and M. Rosbash. 2003. Early formation of mRNP: license for export or quality control? Mol. Cell 11:1129–1138.
   PubMed Web of Science ®Google Scholar
• Kaplan, C. D., M. J. Holland, and F. Winston. 2005. Interaction between transcription elongation factors and mRNA 3′-end formation at the Saccharomyces cerevisiae GAL10-GAL7 locus. J. Biol. Chem. 280:913–922.
   PubMedGoogle Scholar
• Kaplan, C. D., L. Laprade, and F. Winston. 2003. Transcription elongation factors repress transcription initiation from cryptic sites. Science 301:1096–1099.
   PubMed Web of Science ®Google Scholar
• Kim, M., S. H. Ahn, N. J. Krogan, J. F. Greenblatt, and S. Buratowski. 2004. Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes. EMBO J. 23:354–364.
   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, S. H. Ahn, G. Zhong, M. S. Kobor, G. Cagney, A. Emili, A. Shilatifard, S. Buratowski, and J. F. Greenblatt. 2002. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol. Cell. Biol. 22:6979–6992.
   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
• Libri, D., K. Dower, J. Boulay, R. Thomsen, M. Rosbash, and T. H. Jensen. 2002. Interactions between mRNA export commitment, 3′-end quality control, and nuclear degradation. Mol. Cell. Biol. 22:8254–8266.
   PubMed Web of Science ®Google Scholar
• Lis, J. 1998. Promoter-associated pausing in promoter architecture and postinitiation transcriptional regulation. Cold Spring Harbor Symp. Quant. Biol. 63:347–356.
   PubMedGoogle Scholar
• Lis, J. T., P. Mason, J. Peng, D. H. Price, and J. Werner. 2000. P-TEFb kinase recruitment and function at heat shock loci. Genes Dev. 14:792–803.
   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., S. Dole, and K. Struhl. 2003. The Rtf1 component of the Paf1 transcriptional elongation complex is required for ubiquitination of histone H2B. J. Biol. Chem. 278:33625–33628.
   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
• Ni, Z., B. E. Schwartz, J. Werner, J. R. Suarez, and J. T. Lis. 2004. Coordination of transcription, RNA processing, and surveillance by P-TEFb kinase on heat shock genes. Mol. Cell 13:55–65.
   PubMed Web of Science ®Google Scholar
• Orphanides, G., G. LeRoy, C. H. Chang, D. S. Luse, and D. Reinberg. 1998. FACT, a factor that facilitates transcript elongation through nucleosomes. Cell 92:105–116.
   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
• Pokholok, D. K., N. M. Hannett, and R. A. Young. 2002. Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Mol. Cell 9:799–809.
   PubMed Web of Science ®Google Scholar
• Porter, S. E., K. L. Penheiter, and J. A. Jaehning. 2005. Separation of the Saccharomyces cerevisiae Paf1 complex from RNA polymerase II results in changes in its subnuclear localization. Eukaryot. Cell 4:209–220.
   PubMedGoogle Scholar
• Rondon, A. G., M. Gallardo, M. Garcia-Rubio, and A. Aguilera. 2004. Molecular evidence indicating that the yeast PAF complex is required for transcription elongation. EMBO Rep. 5:47–53.
   PubMed Web of Science ®Google Scholar
• Rozenblatt-Rosen, O., C. M. Hughes, S. J. Nannepaga, K. S. Shanmugam, T. D. Copeland, T. Guszczynski, J. H. Resau, and M. Meyerson. 2005. The parafibromin tumor suppressor protein is part of a human Paf1 complex. Mol. Cell. Biol. 25:612–620.
   PubMed Web of Science ®Google Scholar
• Santos-Rosa, H., R. Schneider, A. J. Bannister, J. Sherriff, B. E. Bernstein, N. C. Emre, S. L. Schreiber, J. Mellor, and T. Kouzarides. 2002. Active genes are tri-methylated at K4 of histone H3. Nature 419:407–411.
   PubMed Web of Science ®Google Scholar
• Saunders, A., J. Werner, E. D. Andrulis, T. Nakayama, S. Hirose, D. Reinberg, and J. T. Lis. 2003. Tracking FACT and the RNA polymerase II elongation complex through chromatin in vivo. Science 301:1094–1096.
   PubMed Web of Science ®Google Scholar
• Schneider, R., A. J. Bannister, F. A. Myers, A. W. Thorne, C. Crane-Robinson, and T. Kouzarides. 2004. Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nat. Cell Biol. 6:73–77.
   PubMed Web of Science ®Google Scholar
• Schubeler, D., D. M. MacAlpine, D. Scalzo, C. Wirbelauer, C. Kooperberg, F. van Leeuwen, D. E. Gottschling, L. P. O'Neill, B. M. Turner, J. Delrow, S. P. Bell, and M. Groudine. 2004. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 18:1263–1271.
   PubMed Web of Science ®Google Scholar
• Shanower, G. A., M. Muller, J. L. Blanton, V. Honti, H. Gyurkovics, and P. Schedl. 2005. Characterization of the grappa gene, the Drosophila histone H3 lysine 79 methyltransferase. Genetics 169:173–184.
   PubMed Web of Science ®Google Scholar
• Shi, X., M. Chang, A. J. Wolf, C. H. Chang, A. A. Frazer-Abel, P. A. Wade, Z. F. Burton, and J. A. Jaehning. 1997. Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme. Mol. Cell. Biol. 17:1160–1169.
   PubMed Web of Science ®Google Scholar
• Shi, X., A. Finkelstein, A. J. Wolf, P. A. Wade, Z. F. Burton, and J. A. Jaehning. 1996. Paf1p, an RNA polymerase II-associated factor in Saccharomyces cerevisiae, may have both positive and negative roles in transcription. Mol. Cell. Biol. 16:669–676.
   PubMedGoogle Scholar
• Shilatifard, A. 2004. Transcriptional elongation control by RNA polymerase II: a new frontier. Biochim. Biophys. Acta 1677:79–86.
   PubMedGoogle Scholar
• Simic, R., D. L. Lindstrom, H. G. Tran, K. L. Roinick, P. J. Costa, A. D. Johnson, G. A. Hartzog, and K. M. Arndt. 2003. Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J. 22:1846–1856.
   PubMed Web of Science ®Google Scholar
• Sims, R. J., III, S. S. Mandal, and D. Reinberg. 2004. Recent highlights of RNA-polymerase-II-mediated transcription. Curr. Opin. Cell Biol. 16:263–271.
   PubMed Web of Science ®Google Scholar
• Smith, S. T., S. Petruk, Y. Sedkov, E. Cho, S. Tillib, E. Canaani, and A. Mazo. 2004. Modulation of heat shock gene expression by the TAC1 chromatin-modifying complex. Nat. Cell Biol. 6:162–167.
   PubMed Web of Science ®Google Scholar
• Solomon, M. J., P. L. Larsen, and A. Varshavsky. 1988. Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 53:937–947.
   PubMed Web of Science ®Google Scholar
• Squazzo, S. L., P. J. Costa, D. L. Lindstrom, K. E. Kumer, R. Simic, J. L. Jennings, A. J. Link, K. M. Arndt, and G. A. Hartzog. 2002. The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO J. 21:1764–1774.
   PubMed Web of Science ®Google Scholar
• Sun, Z. W., and C. D. Allis. 2002. Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418:104–108.
   PubMed Web of Science ®Google Scholar
• Wood, A., J. Schneider, J. Dover, M. Johnston, and A. Shilatifard. 2003. The Paf1 complex is essential for histone monoubiquitination by the Rad6-Bre1 complex, which signals for histone methylation by COMPASS and Dot1p. J. Biol. Chem. 278:34739–34742.
   PubMed Web of Science ®Google Scholar
• Wu, C. 1980. The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 286:854–860.
   PubMed Web of Science ®Google Scholar
• Wu, C. 1984. Two protein-binding sites in chromatin implicated in the activation of heat-shock genes. Nature 309:229–234.
   PubMed Web of Science ®Google Scholar
• Wu, C. H., Y. Yamaguchi, L. R. Benjamin, M. Horvat-Gordon, J. Washinsky, E. Enerly, J. Larsson, A. Lambertsson, H. Handa, and D. Gilmour. 2003. NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila. Genes Dev. 17:1402–1414.
   PubMed Web of Science ®Google Scholar
• Xiao, T., C. F. Kao, N. J. Krogan, Z. W. Sun, J. F. 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
• Yart, A., M. Gstaiger, C. Wirbelauer, M. Pecnik, D. Anastasiou, D. Hess, and W. Krek. 2005. The HRPT2 tumor suppressor gene product parafibromin associates with human PAF1 and RNA polymerase II. Mol. Cell. Biol. 25:5052–5060.
   PubMed Web of Science ®Google Scholar
• Zhu, B., S. S. Mandal, A. D. Pham, Y. Zheng, H. Erdjument-Bromage, S. K. Batra, P. Tempst, and D. Reinberg. 2005. The human PAF complex coordinates transcription with events downstream of RNA synthesis. Genes Dev. 19:1668–1673.
   PubMed Web of Science ®Google Scholar
• Zorio, D. A., and D. L. Bentley. 2004. The link between mRNA processing and transcription: communication works both ways. Exp. Cell Res. 296:91–97.
   PubMedGoogle Scholar