A Chromatin Landmark and Transcription Initiation at
Most Promoters in Human Cells
Data
Figures
Supplemental Information
Acknowledgements
References
|
References
Abeyta, M. J., Clark, A. T., Rodriguez, R. T., Bodnar, M. S., Pera, R. A., and Firpo, M. T. (2004). Unique gene expression signatures of independently-derived human embryonic stem cell lines. Hum Mol Genet 13, 601-608.
Azuara, V., Perry, P., Sauer, S., Spivakov, M., Jorgensen, H. F., John, R. M., Gouti, M., Casanova, M., Warnes, G., Merkenschlager, M., and Fisher, A. G. (2006). Chromatin signatures of pluripotent cell lines. Nat Cell Biol.
Bannister, A. J., Schneider, R., Myers, F. A., Thorne, A. W., Crane-Robinson, C., and Kouzarides, T. (2005). Spatial distribution of di- and tri-methyl lysine 36 of histone H3 at active genes. J Biol Chem 280, 17732-17736.
Bernstein, B. E., Humphrey, E. L., Erlich, R. L., Schneider, R., Bouman, P., Liu, J. S., Kouzarides, T., and Schreiber, S. L. (2002). Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A 99, 8695-8700.
Bernstein, B. E., Kamal, M., Lindblad-Toh, K., Bekiranov, S., Bailey, D. K., Huebert, D. J., McMahon, S., Karlsson, E. K., Kulbokas, E. J., 3rd, Gingeras, T. R., et al. (2005). Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120, 169-181.
Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006). A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315-326.
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.
Brandenberger, R., Khrebtukova, I., Thies, R. S., Miura, T., Jingli, C., Puri, R., Vasicek, T., Lebkowski, J., and Rao, M. (2004a). MPSS profiling of human embryonic stem cells. BMC Dev Biol 4, 10.
Brandenberger, R., Wei, H., Zhang, S., Lei, S., Murage, J., Fisk, G. J., Li, Y., Xu, C., Fang, R., Guegler, K., et al. (2004b). Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. Nat Biotechnol 22, 707-716.
Brinkman, A. B., Roelofsen, T., Pennings, S. W., Martens, J. H., Jenuwein, T., and Stunnenberg, H. G. (2006). Histone modification patterns associated with the human X chromosome. EMBO Rep 7, 628-634.
Buhler, M., Verdel, A., and Moazed, D. (2006). Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing. Cell 125, 873-886.
Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H., Helt, G., et al. (2005). Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308, 1149-1154.
Conaway, J. W., Shilatifard, A., Dvir, A., and Conaway, R. C. (2000). Control of elongation by Pol II. Trends Biochem Sci 25, 375-380.
Dvir, A. (2002). Promoter escape by Pol II. Biochim Biophys Acta 1577, 208-223.
Farh, K. K., Grimson, A., Jan, C., Lewis, B. P., Johnston, W. K., Lim, L. P., Burge, C. B., and Bartel, D. P. (2005). The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science 310, 1817-1821.
Hughes, C. M., Rozenblatt-Rosen, O., Milne, T. A., Copeland, T. D., Levine, S. S., Lee, J. C., Hayes, D. N., Shanmugam, K. S., Bhattacharjee, A., Biondi, C. A., et al. (2004). Menin associates with a trithorax family histone methyltransferase complex and with the hoxc8 locus. Mol Cell 13, 587-597.
Jenuwein, T., and Allis, C. D. (2001). Translating the histone code. Science 293, 1074-1080.
Kato, H., Goto, D. B., Martienssen, R. A., Urano, T., Furukawa, K., and Murakami, Y. (2005). Pol II is required for RNAi-dependent heterochromatin assembly. Science 309, 467-469.
Kim, T. H., Barrera, L. O., Zheng, M., Qu, C., Singer, M. A., Richmond, T. A., Wu, Y., Green, R. D., and Ren, B. (2005). A high-resolution map of active promoters in the human genome. Nature 436, 876-880.
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. (2003a). The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: 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., et al. (2003b). Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by Pol II. Mol Cell Biol 23, 4207-4218.
Krumm, A., Meulia, T., and Groudine, M. (1993). Common mechanisms for the control of eukaryotic transcriptional elongation. Bioessays 15, 659-665.
Kuras, L., and Struhl, K. (1999). Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme. Nature 399, 609-613.
Laribee, R. N., Krogan, N. J., Xiao, T., Shibata, Y., Hughes, T. R., Greenblatt, J. F., and Strahl, B. D. (2005). BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex. Curr Biol 15, 1487-1493.
Laspia, M. F., Wendel, P., and Mathews, M. B. (1993). HIV-1 Tat overcomes inefficient transcriptional elongation in vitro. J Mol Biol 232, 732-746.
Law, A., Hirayoshi, K., O'Brien, T., and Lis, J. T. (1998). Direct cloning of DNA that interacts in vivo with a specific protein: application to Pol II and sites of pausing in Drosophila. Nucleic Acids Res 26, 919-924.
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. (2006). Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301-313.
Li, B., Howe, L., Anderson, S., Yates, J. R., 3rd, and Workman, J. L. (2003). The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of Pol II. J Biol Chem 278, 8897-8903.
Li, J., Moazed, D., and Gygi, S. P. (2002). Association of the histone methyltransferase Set2 with Pol II plays a role in transcription elongation. J Biol Chem 277, 49383-49388.
Liang, G., Lin, J. C., Wei, V., Yoo, C., Cheng, J. C., Nguyen, C. T., Weisenberger, D. J., Egger, G., Takai, D., Gonzales, F. A., and Jones, P. A. (2004). Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome. Proc Natl Acad Sci U S A 101, 7357-7362.
Lis, J. (1998). Promoter-associated pausing in promoter architecture and postinitiation transcriptional regulation. Cold Spring Harb Symp Quant Biol 63, 347-356.
Lomvardas, S., Barnea, G., Pisapia, D. J., Mendelsohn, M., Kirkland, J., and Axel, R. (2006). Interchromosomal interactions and olfactory receptor choice. Cell 126, 403-413.
Mayhall, E. A., Paffett-Lugassy, N., and Zon, L. I. (2004). The clinical potential of stem cells. Curr Opin Cell Biol 16, 713-720.
Meshorer, E., and Misteli, T. (2006). Chromatin in pluripotent embryonic stem cells and differentiation. Nat Rev Mol Cell Biol 7, 540-546.
Meshorer, E., Yellajoshula, D., George, E., Scambler, P. J., Brown, D. T., and Misteli, T. (2006). Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev Cell 10, 105-116.
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 U S A 98, 12902-12907.
Morillon, A., Karabetsou, N., Nair, A., and Mellor, J. (2005). Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription. Mol Cell 18, 723-734.
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.
Parada, C. A., and Roeder, R. G. (1999). A novel Pol II-containing complex potentiates Tat-enhanced HIV-1 transcription. Embo J 18, 3688-3701.
Pera, M. F., and Trounson, A. O. (2004). Human embryonic stem cells: prospects for development. Development 131, 5515-5525.
Pokholok, D. K., Harbison, C. T., Levine, S., Cole, M., Hannett, N. M., Lee, T. I., Bell, G. W., Walker, K., Rolfe, P. A., Herbolsheimer, E., et al. (2005). Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517-527.
Ptashne, M. (1986). A Genetic Switch (Cambridge, Massachusetts, Cell Press and Blackwell Sci Pubs).
Radonjic, M., Andrau, J. C., Lijnzaad, P., Kemmeren, P., Kockelkorn, T. T., van Leenen, D., van Berkum, N. L., and Holstege, F. C. (2005). Genome-wide analyses reveal Pol II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit. Mol Cell 18, 171-183.
Roh, T. Y., Cuddapah, S., Cui, K., and Zhao, K. (2006). The genomic landscape of histone modifications in human T cells. Proc Natl Acad Sci U S A 103, 15782-15787.
Santos-Rosa, H., Schneider, R., Bannister, A. J., Sherriff, J., Bernstein, B. E., Emre, N. C., Schreiber, S. L., Mellor, J., and Kouzarides, T. (2002). Active genes are tri-methylated at K4 of histone H3. Nature 419, 407-411.
Sato, N., Sanjuan, I. M., Heke, M., Uchida, M., Naef, F., and Brivanlou, A. H. (2003). Molecular signature of human embryonic stem cells and its comparison with the mouse. Dev Biol 260, 404-413.
Saunders, A., Core, L. J., and Lis, J. T. (2006). Breaking barriers to transcription elongation. Nat Rev Mol Cell Biol 7, 557-567.
Schneider, R., Bannister, A. J., Myers, F. A., Thorne, A. W., Crane-Robinson, C., and Kouzarides, T. (2004). Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nat Cell Biol 6, 73-77.
Schubeler, D., MacAlpine, D. M., Scalzo, D., Wirbelauer, C., Kooperberg, C., van Leeuwen, F., Gottschling, D. E., O'Neill, L. P., Turner, B. M., Delrow, J., et al. (2004). The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev 18, 1263-1271.
Sims, R. J., 3rd, Belotserkovskaya, R., and Reinberg, D. (2004). Elongation by Pol II: the short and long of it. Genes Dev 18, 2437-2468.
Soutoglou, E., and Talianidis, I. (2002). Coordination of PIC assembly and chromatin remodeling during differentiation-induced gene activation. Science 295, 1901-1904.
Sterner, D. E., and Berger, S. L. (2000). Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev 64, 435-459.
Strahl, B. D., and Allis, C. D. (2000). The language of covalent histone modifications. Nature 403, 41-45.
Strahl, B. D., Grant, P. A., Briggs, S. D., Sun, Z. W., Bone, J. R., Caldwell, J. A., Mollah, S., Cook, R. G., Shabanowitz, J., Hunt, D. F., and Allis, C. D. (2002). Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol Cell Biol 22, 1298-1306.
Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., et al. (2004). A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101, 6062-6067.
Tenney, K., and Shilatifard, A. (2005). A COMPASS in the voyage of defining the role of trithorax/MLL-containing complexes: linking leukemogensis to covalent modifications of chromatin. J Cell Biochem 95, 429-436.
Turner, B. M. (2002). Cellular memory and the histone code. Cell 111, 285-291.
Wei, C. L., Miura, T., Robson, P., Lim, S. K., Xu, X. Q., Lee, M. Y., Gupta, S., Stanton, L., Luo, Y., Schmitt, J., et al. (2005). Transcriptome profiling of human and murine ESCs identifies divergent paths required to maintain the stem cell state. Stem Cells 23, 166-185.
Wei, P., Garber, M. E., Fang, S. M., Fischer, W. H., and Jones, K. A. (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, 451-462.
Xiao, T., Hall, H., Kizer, K. O., Shibata, Y., Hall, M. C., Borchers, C. H., and Strahl, B. D. (2003). Phosphorylation of Pol II CTD regulates H3 methylation in yeast. Genes Dev 17, 654-663.
|
