c-Myc Regulates Transcriptional Pause Release

Cell - Tập 141 - Trang 432-445 - 2010
Peter B. Rahl1, Charles Y. Lin1,2, Amy C. Seila3, Ryan A. Flynn3, Scott McCuine1, Christopher B. Burge2, Phillip A. Sharp2,3, Richard A. Young1,2
1Whitehead Institute for Biomedical Research, Cambridge, MA 02142 USA
2Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
3Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA

Tài liệu tham khảo

Adelman, 2006, Drosophila Paf1 modulates chromatin structure at actively transcribed genes, Mol. Cell. Biol., 26, 250, 10.1128/MCB.26.1.250-260.2006 Ahn, 2004, Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3′ end processing, Mol. Cell, 13, 67, 10.1016/S1097-2765(03)00492-1 Andrulis, 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, 10.1101/gad.844200 Barboric, 2001, NF-kappaB binds P-TEFb to stimulate transcriptional elongation by RNA polymerase II, Mol. Cell, 8, 327, 10.1016/S1097-2765(01)00314-8 Bentley, 1986, A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells, Nature, 321, 702, 10.1038/321702a0 Beroukhim, 2010, The landscape of somatic copy-number alteration across human cancers, Nature, 463, 899, 10.1038/nature08822 Cartwright, 2005, LIF/STAT3 controls ES cell self-renewal and pluripotency by a Myc-dependent mechanism, Development, 132, 885, 10.1242/dev.01670 Chao, 2001, Flavopiridol inactivates P-TEFb and blocks most RNA polymerase II transcription in vivo, J. Biol. Chem., 276, 31793, 10.1074/jbc.M102306200 Chao, 2000, Flavopiridol inhibits P-TEFb and blocks HIV-1 replication, J. Biol. Chem., 275, 28345, 10.1074/jbc.C000446200 Chen, 2008, Integration of external signaling pathways with the core transcriptional network in embryonic stem cells, Cell, 133, 1106, 10.1016/j.cell.2008.04.043 Cheng, 2007, Properties of RNA polymerase II elongation complexes before and after the P-TEFb-mediated transition into productive elongation, J. Biol. Chem., 282, 21901, 10.1074/jbc.M702936200 Core, 2008, Transcription regulation through promoter-proximal pausing of RNA polymerase II, Science, 319, 1791, 10.1126/science.1150843 Core, 2008, Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters, Science, 322, 1845, 10.1126/science.1162228 Eberhardy, 2001, c-Myc mediates activation of the cad promoter via a post-RNA polymerase II recruitment mechanism, J. Biol. Chem., 276, 48562, 10.1074/jbc.M109014200 Eberhardy, 2002, Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter, J. Biol. Chem., 277, 40156, 10.1074/jbc.M207441200 Eilers, 2008, Myc's broad reach, Genes Dev., 22, 2755, 10.1101/gad.1712408 Espinosa, 2003, p53 functions through stress- and promoter-specific recruitment of transcription initiation components before and after DNA damage, Mol. Cell, 12, 1015, 10.1016/S1097-2765(03)00359-9 Fuda, 2009, Defining mechanisms that regulate RNA polymerase II transcription in vivo, Nature, 461, 186, 10.1038/nature08449 Gargano, 2007, P-TEFb is a crucial co-factor for Myc transactivation, Cell Cycle, 6, 2031, 10.4161/cc.6.16.4554 Gilchrist, 2008, Genes Dev., 22, 1921, 10.1101/gad.1643208 Gilmour, 1986, RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells, Mol. Cell. Biol., 6, 3984, 10.1128/MCB.6.11.3984 Glover-Cutter, 2008, RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes, Nat. Struct. Mol. Biol., 15, 71, 10.1038/nsmb1352 Guenther, 2007, A chromatin landmark and transcription initiation at most promoters in human cells, Cell, 130, 77, 10.1016/j.cell.2007.05.042 Hall, 2009, Oct4 and LIF/Stat3 additively induce Kruppel factors to sustain embryonic stem cell self-renewal, Cell Stem Cell, 5, 597, 10.1016/j.stem.2009.11.003 Hammoudeh, 2009, Multiple independent binding sites for small-molecule inhibitors on the oncoprotein c-Myc, J. Am. Chem. Soc., 131, 7390, 10.1021/ja900616b Hanyu-Nakamura, 2008, Drosophila Pgc protein inhibits P-TEFb recruitment to chromatin in primordial germ cells, Nature, 451, 730, 10.1038/nature06498 Hochheimer, 2003, Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression, Genes Dev., 17, 1309, 10.1101/gad.1099903 Kanazawa, 2003, c-Myc recruits P-TEFb for transcription, cellular proliferation and apoptosis, Oncogene, 22, 5707, 10.1038/sj.onc.1206800 Kidder, 2008, Stat3 and c-Myc genome-wide promoter occupancy in embryonic stem cells, PLoS ONE, 3, e3932, 10.1371/journal.pone.0003932 Kim, 2008, An extended transcriptional network for pluripotency of embryonic stem cells, Cell, 132, 1049, 10.1016/j.cell.2008.02.039 Kim, 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, 10.1074/jbc.M010908200 Komarnitsky, 2000, Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription, Genes Dev., 14, 2452, 10.1101/gad.824700 Krogan, 2003, The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation, Mol. Cell, 11, 721, 10.1016/S1097-2765(03)00091-1 Lis, 2000, P-TEFb kinase recruitment and function at heat shock loci, Genes Dev., 14, 792 Mandal, 2004, Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II, Proc. Natl. Acad. Sci. USA, 101, 7572, 10.1073/pnas.0401493101 Margaritis, 2008, Poised RNA polymerase II gives pause for thought, Cell, 133, 581, 10.1016/j.cell.2008.04.027 Marshall, 1995, Purification of P-TEFb, a transcription factor required for the transition into productive elongation, J. Biol. Chem., 270, 12335, 10.1074/jbc.270.21.12335 Marshall, 1996, Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase, J. Biol. Chem., 271, 27176, 10.1074/jbc.271.43.27176 Marson, 2008, Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells, Cell, 134, 521, 10.1016/j.cell.2008.07.020 Matoba, 2006, Dissecting Oct3/4-regulated gene networks in embryonic stem cells by expression profiling, PLoS ONE, 1, e26, 10.1371/journal.pone.0000026 McCracken, 1997, 5′-Capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II, Genes Dev., 11, 3306, 10.1101/gad.11.24.3306 McCracken, 1997, The C-terminal domain of RNA polymerase II couples mRNA processing to transcription, Nature, 385, 357, 10.1038/385357a0 Meyer, 2008, Reflecting on 25 years with MYC, Nat. Rev. Cancer, 8, 976, 10.1038/nrc2231 Mikkelsen, 2007, Genome-wide maps of chromatin state in pluripotent and lineage-committed cells, Nature, 448, 553, 10.1038/nature06008 Moore, 2009, Pre-mRNA processing reaches back to transcription and ahead to translation, Cell, 136, 688, 10.1016/j.cell.2009.02.001 Muse, 2007, RNA polymerase is poised for activation across the genome, Nat. Genet., 39, 1507, 10.1038/ng.2007.21 Ni, 2004, Coordination of transcription, RNA processing, and surveillance by P-TEFb kinase on heat shock genes, Mol. Cell, 13, 55, 10.1016/S1097-2765(03)00526-4 Ni, 2008, P-TEFb is critical for the maturation of RNA polymerase II into productive elongation in vivo, Mol. Cell. Biol., 28, 1161, 10.1128/MCB.01859-07 Niwa, 2000, Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells, Nat. Genet., 24, 372, 10.1038/74199 O'Brien, 1991, RNA polymerase II pauses at the 5′ end of the transcriptionally induced Drosophila hsp70 gene, Mol. Cell. Biol., 11, 5285, 10.1128/MCB.11.10.5285 Peterlin, 2006, Controlling the elongation phase of transcription with P-TEFb, Mol. Cell, 23, 297, 10.1016/j.molcel.2006.06.014 Pokholok, 2002, Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo, Mol. Cell, 9, 799, 10.1016/S1097-2765(02)00502-6 Pokholok, 2005, Genome-wide map of nucleosome acetylation and methylation in yeast, Cell, 122, 517, 10.1016/j.cell.2005.06.026 Price, 2008, Poised polymerases: On your mark…get set…go!, Mol. Cell, 30, 7, 10.1016/j.molcel.2008.03.001 Ptashne, 1997, Transcriptional activation by recruitment, Nature, 386, 569, 10.1038/386569a0 Reppas, 2006, The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting, Mol. Cell, 24, 747, 10.1016/j.molcel.2006.10.030 Roeder, 2005, Transcriptional regulation and the role of diverse coactivators in animal cells, FEBS Lett., 579, 909, 10.1016/j.febslet.2004.12.007 Rougvie, 1988, The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged, Cell, 54, 795, 10.1016/S0092-8674(88)91087-2 Saunders, 2006, Breaking barriers to transcription elongation, Nat. Rev. Mol. Cell Biol., 7, 557, 10.1038/nrm1981 Sawado, 2003, The beta -globin locus control region (LCR) functions primarily by enhancing the transition from transcription initiation to elongation, Genes Dev., 17, 1009, 10.1101/gad.1072303 Seila, 2008, Divergent transcription from active promoters, Science, 322, 1849, 10.1126/science.1162253 Seydoux, 1997, Transcriptionally repressed germ cells lack a subpopulation of phosphorylated RNA polymerase II in early embryos of Caenorhabditis elegans and Drosophila melanogaster, Development, 124, 2191, 10.1242/dev.124.11.2191 Sharova, 2009, Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells, DNA Res., 16, 45, 10.1093/dnares/dsn030 Takahashi, 2006, Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors, Cell, 126, 663, 10.1016/j.cell.2006.07.024 Takahashi, 2007, Induction of pluripotent stem cells from adult human fibroblasts by defined factors, Cell, 131, 861, 10.1016/j.cell.2007.11.019 Wade, 2008, The transition from transcriptional initiation to elongation, Curr. Opin. Genet. Dev., 18, 130, 10.1016/j.gde.2007.12.008 Wada, 1998, DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs, Genes Dev., 12, 343, 10.1101/gad.12.3.343 Wada, 1998, Evidence that P-TEFb alleviates the negative effect of DSIF on RNA polymerase II-dependent transcription in vitro, EMBO J., 17, 7395, 10.1093/emboj/17.24.7395 Wang, 2007, Improved low molecular weight Myc-Max inhibitors, Mol. Cancer Ther., 6, 2399, 10.1158/1535-7163.MCT-07-0005 Wei, 1998, A novel CDK9-associated C-type cyclin interacts directly with HIV-1 Tat and mediates its high-affinity, loop-specific binding to TAR RNA, Cell, 92, 451, 10.1016/S0092-8674(00)80939-3 Wen, 1999, Transcription elongation factor hSPT5 stimulates mRNA capping, Genes Dev., 13, 1774, 10.1101/gad.13.14.1774 Wu, 2003, NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila, Genes Dev., 17, 1402, 10.1101/gad.1091403 Yamada, 2006, P-TEFb-mediated phosphorylation of hSpt5 C-terminal repeats is critical for processive transcription elongation, Mol. Cell, 21, 227, 10.1016/j.molcel.2005.11.024 Yamaguchi, 1999, NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation, Cell, 97, 41, 10.1016/S0092-8674(00)80713-8 Yin, 2003, Low molecular weight inhibitors of Myc-Max interaction and function, Oncogene, 22, 6151, 10.1038/sj.onc.1206641 Zeitlinger, 2007, RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo, Nat. Genet., 39, 1512, 10.1038/ng.2007.26 Zhang, 2003, A model of repression: CTD analogs and PIE-1 inhibit transcriptional elongation by P-TEFb, Genes Dev., 17, 748, 10.1101/gad.1068203 Zhou, 2006, Tax interacts with P-TEFb in a novel manner to stimulate human T-lymphotropic virus type 1 transcription, J. Virol., 80, 4781, 10.1128/JVI.80.10.4781-4791.2006 Zhu, 2005, The human PAF complex coordinates transcription with events downstream of RNA synthesis, Genes Dev., 19, 1668, 10.1101/gad.1292105 Adelman, K., Wei, W., Ardehali, M.B., Werner, J., Zhu, B., Reinberg, D., and Lis, J.T. (2006). Drosophila Paf1 modulates chromatin structure at actively transcribed genes. Mol. Cell. Biol. 26, 250–260. Arabi, A., Wu, S., Ridderstrale, K., Bierhoff, H., Shiue, C., Fatyol, K., Fahlen, S., Hydbring, P., Soderberg, O., Grummt, I., et al. (2005). c-Myc associates with ribosomal DNA and activates RNA polymerase I transcription. Nat. Cell Biol. 7, 303–310. Bilodeau, S., Kagey, M.H., Frampton, G.M., Rahl, P.B., and Young, R.A. (2009). SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev. 23, 2484–2489. Boyer, L.A., Lee, T.I., Cole, M.F., Johnstone, S.E., Levine, S.S., Zucker, J.P., Guenther, M.G., Kumar, R.M., Murray, H.L., Jenner, R.G., et al. (2005). Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956. Chen, X., Xu, H., Yuan, P., Fang, F., Huss, M., Vega, V.B., Wong, E., Orlov, Y.L., Zhang, W., Jiang, J., et al. (2008). Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106–111117. Fang, Z.H., Dong, C.L., Chen, Z., Zhou, B., Liu, N., Lan, H.F., Liang, L., Liao, W.B., Zhang, L., and Han, Z.C. (2008). Transcriptional regulation of survivin by c-Myc in BCR/ABL-transformed cells: implications in anti-leukemic strategy. J. Cell. Mol. Med. 13, 2039–2052. Faumont, N., Durand-Panteix, S., Schlee, M., Gromminger, S., Schuhmacher, M., Holzel, M., Laux, G., Mailhammer, R., Rosenwald, A., Staudt, L.M., et al. (2009). c-Myc and Rel/NF-kappaB are the two master transcriptional systems activated in the latency III program of Epstein-Barr virus-immortalized B cells. J. Virol. 83, 5014–5027. Follis, A.V., Hammoudeh, D.I., Wang, H., Prochownik, E.V., and Metallo, S.J. (2008). Structural rationale for the coupled binding and unfolding of the c-Myc oncoprotein by small molecules. Chem. Biol. 15, 1149–1155. Guenther, M.G., Lawton, L.N., Rozovskaia, T., Frampton, G.M., Levine, S.S., Volkert, T.L., Croce, C.M., Nakamura, T., Canaani, E., and Young, R.A. (2008). Aberrant chromatin at genes encoding stem cell regulators in human mixed-lineage leukemia. Genes Dev. 22, 3403–3408. Hailesellasse Sene, K., Porter, C.J., Palidwor, G., Perez-Iratxeta, C., Muro, E.M., Campbell, P.A., Rudnicki, M.A., and Andrade-Navarro, M.A. (2007). Gene function in early mouse embryonic stem cell differentiation. BMC Genomics 8, 85. Hammoudeh, D.I., Follis, A.V., Prochownik, E.V., and Metallo, S.J. (2009). Multiple independent binding sites for small-molecule inhibitors on the oncoprotein c-Myc. J. Am. Chem. Soc. 131, 7390–7401. Khanna, A., Bockelman, C., Hemmes, A., Junttila, M.R., Wiksten, J.P., Lundin, M., Junnila, S., Murphy, D.J., Evan, G.I., Haglund, C., et al. (2009). MYC-dependent regulation and prognostic role of CIP2A in gastric cancer. J. Natl. Cancer Inst. 101, 793–805. Kim, J., Chu, J., Shen, X., Wang, J., and Orkin, S.H. (2008). An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132, 1049–1061. Krogan, N.J., Dover, J., Wood, A., Schneider, J., Heidt, J., Boateng, M.A., Dean, K., Ryan, O.W., Golshani, A., Johnston, M., et al. (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. Lee, T.I., Jenner, R.G., Boyer, L.A., Guenther, M.G., Levine, S.S., Kumar, R.M., Chevalier, B., Johnstone, S.E., Cole, M.F., Isono, K., et al. (2006a). Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301–313. Lee, T.I., Johnstone, S.E., and Young, R.A. (2006b). Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat. Protoc. 1, 729–748. Lee, W.H., Liu, F.H., Lin, J.Y., Huang, S.Y., Lin, H., Liao, W.J., and Huang, H.M. (2009). JAK pathway induction of c-Myc critical to IL-5 stimulation of cellproliferation and inhibition of apoptosis. J. Cell. Biochem. 106, 929–936. Marson, A., Levine, S.S., Cole, M.F., Frampton, G.M., Brambrink, T., Johnstone, S., Guenther, M.G., Johnston, W.K., Wernig, M., Newman, J., et al. (2008). Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonicstem cells. Cell 134, 521–533. Matoba, R., Niwa, H., Masui, S., Ohtsuka, S., Carter, M.G., Sharov, A.A., and Ko, M.S. (2006). Dissecting Oct3/4-regulated gene networks in embryonic stemcells by expression profiling. PLoS ONE 1, e26. Niwa, H., Miyazaki, J., and Smith, A.G. (2000). Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of EScells. Nat. Genet. 24, 372–376. Peng, J., Zhu, Y., Milton, J.T., and Price, D.H. (1998). Identification of multiple cyclin subunits of human P-TEFb. Genes Dev. 12, 755–762. 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. Sampson, V.B., Rong, N.H., Han, J., Yang, Q., Aris, V., Soteropoulos, P., Petrelli, N.J., Dunn, S.P., and Krueger, L.J. (2007). MicroRNA let-7a downregulates MYC and reverts MYC-induced growth in Burkitt lymphoma cells. Cancer Res. 67, 9762–9770. Saunders, A., Core, L.J., and Lis, J.T. (2006). Breaking barriers to transcription elongation. Nat. Rev. Mol. Cell Biol. 7, 557–567. Stock, J.K., Giadrossi, S., Casanova, M., Brookes, E., Vidal, M., Koseki, H., Brockdorff, N., Fisher, A.G., and Pombo, A. (2007). Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nat. Cell Biol. 9, 1428–1435. Wada, T., Takagi, T., Yamaguchi, Y., Ferdous, A., Imai, T., Hirose, S., Sugimoto, S., Yano, K., Hartzog, G.A., Winston, F., et al. (1998). DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev. 12, 343–356. Wang, H., Hammoudeh, D.I., Follis, A.V., Reese, B.E., Lazo, J.S., Metallo, S.J., and Prochownik, E.V. (2007). Improved low molecular weight Myc-Max inhibitors. Mol. Cancer Ther. 6, 2399–2408. Yamada, T., Yamaguchi, Y., Inukai, N., Okamoto, S., Mura, T., and Handa, H. (2006). P-TEFb-mediated phosphorylation of hSpt5C-terminal repeats is critical for processive transcription elongation. Mol. Cell 21, 227–237. Zhu, B., Mandal, S.S., Pham, A.D., Zheng, Y., Erdjument-Bromage, H., Batra, S.K., Tempst, P., and Reinberg, D. (2005). The human PAF complex coordinates transcription with events downstream of RNA synthesis. Genes Dev. 19, 1668–1673.