Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation (original) (raw)

• Lemon, B. & Tjian, R. Orchestrated response: a symphony of transcription factors for gene control. Genes Dev. 14, 2551–2569 (2000).
  Article CAS Google Scholar
• Maniatis, T. & Reed, R. An extensive network of coupling among gene expression machines. Nature 416, 499–506 (2002).
  Article CAS Google Scholar
• Orphanides, G. & Reinberg, D. A unified theory of gene expression. Cell 108, 439–451 (2002).
  Article CAS Google Scholar
• McNally, J. G., Muller, W. G., Walker, D., Wolford, R. & Hager, G. L. The glucocorticoid receptor: rapid exchange with regulatory sites in living cells. Science 287, 1262–1265 (2000).
  Article CAS Google Scholar
• Robinett, C. C. et al. In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition. J. Cell Biol. 135, 1685–1700 (1996).
  Article CAS Google Scholar
• Tumbar, T., Sudlow, G. & Belmont, A. S. Large-scale chromatin unfolding and remodeling induced by VP16 acidic activation domain. J. Cell Biol. 145, 1341–1354 (1999).
  Article CAS Google Scholar
• Yao, J., Munson, K. M., Webb, W. W. & Lis, J. T. Dynamics of heat shock factor association with native gene loci in living cells. Nature 442, 1050–1053 (2006).
  Article CAS Google Scholar
• Janicki, S. M. et al. From silencing to gene expression: real-time analysis in single cells. Cell 116, 683–698 (2004).
  Article CAS Google Scholar
• Ben-Ari, Y. et al. The life of an mRNA in space and time. J. Cell Sci. 123, 1761–1774 (2010).
  Article CAS Google Scholar
• Probst, A. V., Dunleavy, E. & Almouzni, G. Epigenetic inheritance during the cell cycle. Nat. Rev. Mol. Cell Biol. 10, 192–206 (2009).
  Article CAS Google Scholar
• Sarge, K. D. & Park-Sarge, O. K. Gene bookmarking: keeping the pages open. Trends Biochem. Sci. 30, 605–610 (2005).
  Article CAS Google Scholar
• Sarge, K. D. & Park-Sarge, O. K. Mitotic bookmarking of formerly active genes: keeping epigenetic memories from fading. Cell Cycle 8, 818–823 (2009).
  Article CAS Google Scholar
• Zaidi, S. K. et al. Mitotic bookmarking of genes: a novel dimension to epigenetic control. Nat. Rev. Genet. 11, 583–589 (2010).
  Article CAS Google Scholar
• Rafalska-Metcalf, I. U., Powers, S. L., Joo, L. M., LeRoy, G. & Janicki, S. M. Single cell analysis of transcriptional activation dynamics. PLoS One 5, e10272 (2010).
  Article Google Scholar
• Metivier, R. et al. Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115, 751–763 (2003).
  Article CAS Google Scholar
• Darzacq, X. et al. In vivo dynamics of RNA polymerase II transcription. Nat. Struct. Mol. Biol. 14, 796–806 (2007).
  Article CAS Google Scholar
• Kumaran, R. I. & Spector, D. L. A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence. J. Cell Biol. 180, 51–65 (2008).
  Article CAS Google Scholar
• Prasanth, K. V., Sacco-Bubulya, P. A., Prasanth, S. G. & Spector, D. L. Sequential entry of components of the gene expression machinery into daughter nuclei. Mol. Biol. Cell 14, 1043–1057 (2003).
  Article CAS Google Scholar
• Pines, J. & Rieder, C. L. Re-staging mitosis: a contemporary view of mitotic progression. Nat. Cell Biol. 3, E3–E6 (2001).
  Article CAS Google Scholar
• Shav-Tal, Y. et al. Dynamics of single mRNPs in nuclei of living cells. Science 304, 1797–1800 (2004).
  Article CAS Google Scholar
• Yang, Z., He, N. & Zhou, Q. Brd4 recruits P-TEFb to chromosomes at late mitosis to promote G1 gene expression and cell cycle progression. Mol. Cell Biol. 28, 967–976 (2008).
  Article CAS Google Scholar
• Valls, E., Sanchez-Molina, S. & Martinez-Balbas, M. A. Role of histone modifications in marking and activating genes through mitosis. J. Biol. Chem. 280, 42592–42600 (2005).
  Article CAS Google Scholar
• Prescott, D. M. & Bender, M. A. Synthesis of RNA and protein during mitosis in mammalian tissue culture cells. Exp. Cell Res. 26, 260–268 (1962).
  Article Google Scholar
• Muramoto, T., Muller, I., Thomas, G., Melvin, A. & Chubb, J. R. Methylation of H3K4 is required for inheritance of active transcriptional states. Curr. Biol. 20, 397–406 (2010).
  Article CAS Google Scholar
• Dey, A., Nishiyama, A., Karpova, T., McNally, J. & Ozato, K. Brd4 marks select genes on mitotic chromatin and directs postmitotic transcription. Mol. Biol. Cell 20, 4899–4909 (2009).
  Article CAS Google Scholar
• Jeppesen, P. Histone acetylation: a possible mechanism for the inheritance of cell memory at mitosis. Bioessays 19, 67–74 (1997).
  Article CAS Google Scholar
• Zippo, A. et al. Histone crosstalk between H3S10ph and H4K16ac generates a histone code that mediates transcription elongation. Cell 138, 1122–1136 (2009).
  Article CAS Google Scholar
• MacDonald, V. E. & Howe, L. J. Histone acetylation: where to go and how to get there. Epigenetics 4, 139–143 (2009).
  Article CAS Google Scholar
• Edmunds, J. W., Mahadevan, L. C. & Clayton, A. L. Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation. EMBO J. 27, 406–420 (2008).
  Article CAS Google Scholar
• LeRoy, G., Rickards, B. & Flint, S. J. The double bromodomain proteins Brd2 and Brd3 couple histone acetylation to transcription. Mol. Cell 30, 51–60 (2008).
  Article CAS Google Scholar
• Kouskouti, A. & Talianidis, I. Histone modifications defining active genes persist after transcriptional and mitotic inactivation. EMBO J. 24, 347–357 (2005).
  Article CAS Google Scholar
• Liu, Y. et al. Structural basis and binding properties of the second bromodomain of Brd4 with acetylated histone tails. Biochemistry 47, 6403–6417 (2008).
  Article CAS Google Scholar
• Yang, Z. et al. Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4. Mol. Cell 19, 535–545 (2005).
  Article CAS Google Scholar
• Jang, M. K. et al. The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription. Mol. Cell 19, 523–534 (2005).
  Article CAS Google Scholar
• Masotti, A. et al. Comparison of different commercially available cationic liposome-DNA lipoplexes: Parameters influencing toxicity and transfection efficiency. Colloids Surf. B Biointerfaces 68, 136–144 (2009).
  Article CAS Google Scholar
• Andrews, J. M., Newbound, G. C. & Lairmore, M. D. Transcriptional modulation of viral reporter gene constructs following induction of the cellular stress response. Nucleic Acids Res. 25, 1082–1084 (1997).
  Article CAS Google Scholar
• Ip, J. Y. et al. Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Res. 21, 390–401 (2011).
  Article CAS Google Scholar
• Filippakopoulos, P. et al. Selective inhibition of BET bromodomains. Nature 468, 1067–1073 (2010).
  Article CAS Google Scholar
• Dey, A., Chitsaz, F., Abbasi, A., Misteli, T. & Ozato, K. The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis. Proc. Natl Acad. Sci. USA 100, 8758–8763 (2003).
  Article CAS Google Scholar
• Larsen, A. & Weintraub, H. An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chick globin chromatin. Cell 29, 609–622 (1982).
  Article CAS Google Scholar
• Michelotti, E. F., Sanford, S. & Levens, D. Marking of active genes on mitotic chromosomes. Nature 388, 895–899 (1997).
  Article CAS Google Scholar
• Marushige, K. Activation of chromatin by acetylation of histone side chains. Proc. Natl Acad. Sci. USA 73, 3937–3941 (1976).
  Article CAS Google Scholar
• Eskeland, R., Freyer, E., Leeb, M., Wutz, A. & Bickmore, W. A. Histone acetylation and the maintenance of chromatin compaction by polycomb repressive complexes. Cold Spring Harb. Symp. Quant. Biol. 75, 71–78 (2010).
  Article CAS Google Scholar
• Eskeland, R. et al. Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination. Mol. Cell 38, 452–464 (2010).
  Article CAS Google Scholar
• Mochizuki, K. et al. The bromodomain protein Brd4 stimulates G1 gene transcription and promotes progression to S phase. J. Biol. Chem. 283, 9040–9048 (2008).
  Article CAS Google Scholar
• Blobel, G. A. et al. A reconfigured pattern of MLL occupancy within mitotic chromatin promotes rapid transcriptional reactivation following mitotic exit. Mol. Cell 36, 970–983 (2009).
  Article CAS Google Scholar
• Kanno, T. et al. Selective recognition of acetylated histones by bromodomain proteins visualized in living cells. Mol. Cell 13, 33–43 (2004).
  Article CAS Google Scholar
• Umehara, T. et al. Structural basis for acetylated histone H4 recognition by the human BRD2 bromodomain. J. Biol. Chem. 285, 7610–7618 (2010).
  Article CAS Google Scholar
• Umehara, T. et al. Structural implications for K5/K12-di-acetylated histone H4 recognition by the second bromodomain of BRD2. FEBS Lett. 584, 3901–3908 (2010).
  Article CAS Google Scholar
• Bisgrove, D. A., Mahmoudi, T., Henklein, P. & Verdin, E. Conserved P-TEFb-interacting domain of BRD4 inhibits HIV transcription. Proc. Natl Acad. Sci. USA 104, 13690–13695 (2007).
  Article CAS Google Scholar
• Wu, S. Y. & Chiang, C. M. The double bromodomain-containing chromatin adaptor Brd4 and transcriptional regulation. J. Biol. Chem. 282, 13141–13145 (2007).
  Article CAS Google Scholar
• Chen, Y. C., Kappel, C., Beaudouin, J., Eils, R. & Spector, D. L. Live cell dynamics of promyelocytic leukemia nuclear bodies upon entry into and exit from mitosis. Mol. Biol. Cell 19, 3147–3162 (2008).
  Article CAS Google Scholar
• Linkert, M. et al. Metadata matters: access to image data in the real world. J. Cell Biol. 189, 777–782 (2010).
  Article CAS Google Scholar
• Mao, Y. S. et al. Essential and unique roles of PIP5K-γ and −α in Fcγ receptor-mediated phagocytosis. J. Cell Biol. 184, 281–296 (2009).
  Article CAS Google Scholar
• Steger, D. J. et al. DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells. Mol. Cell Biol. 28, 2825–2839 (2008).
  Article CAS Google Scholar