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Volumn , Issue , 2011, Pages 235-254

Transcriptional Initiation: Frequency, Bursting, and Transcription Factories

Author keywords

Green fluorescent protein; RNA FISH; RNA polymerase; Single molecule analysis; Transcription

Indexed keywords


EID: 84875622004     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527639991.ch10     Document Type: Chapter
Times cited : (5)

References (78)
  • 1
    • 0141733014 scopus 로고
    • A mammalian system for the incorporation of cytidine triphosphate into ribonucleic acid
    • Weiss, S.B. and Gladstone, L. (1959) A mammalian system for the incorporation of cytidine triphosphate into ribonucleic acid. J AmChemSoc, 81, 4118-4119.
    • (1959) J AmChemSoc , vol.81 , pp. 4118-4119
    • Weiss, S.B.1    Gladstone, L.2
  • 2
    • 0016412414 scopus 로고
    • Eukaryotic nuclear RNA polymerases
    • Chambon, P. (1975) Eukaryotic nuclear RNA polymerases. Ann Rev Biochem, 44, 613-638.
    • (1975) Ann Rev Biochem , vol.44 , pp. 613-638
    • Chambon, P.1
  • 3
    • 0032808150 scopus 로고    scopus 로고
    • Quantitation of RNA polymerase II and its transcription factors in an HeLa cell: little soluble holoenzyme but significant amounts of polymerases attached to the nuclear substructure
    • Kimura, H., Tao, Y., Roeder, R.G., and Cook, P.R. (1999) Quantitation of RNA polymerase II and its transcription factors in an HeLa cell: little soluble holoenzyme but significant amounts of polymerases attached to the nuclear substructure. Mol Cell Biol, 19, 5383-5392.
    • (1999) Mol Cell Biol , vol.19 , pp. 5383-5392
    • Kimura, H.1    Tao, Y.2    Roeder, R.G.3    Cook, P.R.4
  • 5
    • 33745499068 scopus 로고    scopus 로고
    • Structural biology of RNA polymerase III: subcomplex C17/25 x-ray structure and 11 subunit enzyme model
    • Jasiak, A.J., Armache, K.-J., Martens, B., Jansen, R.-P., and Cramer, P. (2006) Structural biology of RNA polymerase III: subcomplex C17/25 x-ray structure and 11 subunit enzyme model. Mol Cell, 23, 71-81.
    • (2006) Mol Cell , vol.23 , pp. 71-81
    • Jasiak, A.J.1    Armache, K.-J.2    Martens, B.3    Jansen, R.-P.4    Cramer, P.5
  • 7
    • 1942535198 scopus 로고    scopus 로고
    • RNA polymerase II structure: from core to functional complexes
    • Cramer, P. (2004) RNA polymerase II structure: from core to functional complexes. Curr Opin Genet Dev, 14, 218-226.
    • (2004) Curr Opin Genet Dev , vol.14 , pp. 218-226
    • Cramer, P.1
  • 8
    • 0019788189 scopus 로고
    • Transcription of mouse rRNA genes by RNA polymerase I: in vitro and in vivo initiation and processing sites
    • Miller, K.G. and Sollner-Webb, B. (1981) Transcription of mouse rRNA genes by RNA polymerase I: in vitro and in vivo initiation and processing sites. Cell, 27, 165-174.
    • (1981) Cell , vol.27 , pp. 165-174
    • Miller, K.G.1    Sollner-Webb, B.2
  • 11
    • 77952988986 scopus 로고    scopus 로고
    • Defining the RNA polymerase III transcriptome: genome-wide localization of the RNA polymerase III transcription machinery in human cells
    • Canella, D., Praz, V., Reina, J.H., Cousin, P., and Hernandez, N. (2010) Defining the RNA polymerase III transcriptome: genome-wide localization of the RNA polymerase III transcription machinery in human cells. Genome Res, 20, 710-721.
    • (2010) Genome Res , vol.20 , pp. 710-721
    • Canella, D.1    Praz, V.2    Reina, J.H.3    Cousin, P.4    Hernandez, N.5
  • 14
    • 0025309216 scopus 로고
    • RNA polymerase B (II) and general transcription factors
    • Sawadogo, M. and Sentenac, A. (1990) RNA polymerase B (II) and general transcription factors. Ann Rev Biochem, 59, 711-754.
    • (1990) Ann Rev Biochem , vol.59 , pp. 711-754
    • Sawadogo, M.1    Sentenac, A.2
  • 15
    • 0034507632 scopus 로고    scopus 로고
    • Transcription of eukaryotic proteincoding genes
    • Lee, T.I. and Young, R.A. (2000) Transcription of eukaryotic proteincoding genes. Ann Rev Genet, 34, 77-137.
    • (2000) Ann Rev Genet , vol.34 , pp. 77-137
    • Lee, T.I.1    Young, R.A.2
  • 18
    • 0031813779 scopus 로고    scopus 로고
    • Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei
    • Jackson, D.A., Iborra, F.J., Manders, E. M.M., and Cook, P.R. (1998) Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei. Mol Biol Cell, 9, 1523-1536.
    • (1998) Mol Biol Cell , vol.9 , pp. 1523-1536
    • Jackson, D.A.1    Iborra, F.J.2    Manders, E.M.M.3    Cook, P.R.4
  • 19
    • 0014530533 scopus 로고
    • Enzymatic and chromosomal characterization of HeLa variants
    • Bottomley, R.H., Trainer, A.L., and Griffin, M.J. (1969) Enzymatic and chromosomal characterization of HeLa variants. J Cell Biol, 41, 806-815.
    • (1969) J Cell Biol , vol.41 , pp. 806-815
    • Bottomley, R.H.1    Trainer, A.L.2    Griffin, M.J.3
  • 20
    • 0000672061 scopus 로고
    • Morphological studies of transcription
    • Miller, O.L. Jr and Bakken, A.H. (1972) Morphological studies of transcription. Eur J Endocrinol, 71, S155-S177.
    • (1972) Eur J Endocrinol , vol.71
    • Miller O.L.Jr1    Bakken, A.H.2
  • 21
  • 22
    • 0037177855 scopus 로고    scopus 로고
    • Transcript abundance in yeast varies over six orders of magnitude
    • Holland, M.J. (2002) Transcript abundance in yeast varies over six orders of magnitude. J Biol Chem, 277, 14363-14366.
    • (2002) J Biol Chem , vol.277 , pp. 14363-14366
    • Holland, M.J.1
  • 24
    • 33845669025 scopus 로고    scopus 로고
    • Many expressed genes in bacteria and yeast are transcribed only once per cell cycle
    • Bon, M., McGowan, S.J., and Cook, P.R. (2006) Many expressed genes in bacteria and yeast are transcribed only once per cell cycle. FASEB J, 20, 1721-1723.
    • (2006) FASEB J , vol.20 , pp. 1721-1723
    • Bon, M.1    McGowan, S.J.2    Cook, P.R.3
  • 25
    • 57149101122 scopus 로고    scopus 로고
    • Single-RNA counting reveals alternative modes of gene expression in yeast
    • Zenklusen, D., Larson, D.R., and Singer, R.H. (2008) Single-RNA counting reveals alternative modes of gene expression in yeast. Nat Struct Mol Biol, 15, 1263-1271.
    • (2008) Nat Struct Mol Biol , vol.15 , pp. 1263-1271
    • Zenklusen, D.1    Larson, D.R.2    Singer, R.H.3
  • 26
    • 0024323320 scopus 로고
    • Transcription mapping of the Escherichia coli chromosome by electron microscopy
    • French, S.L. and Miller, O.L. Jr. (1989) Transcription mapping of the Escherichia coli chromosome by electron microscopy. J Bacteriol, 171, 4207-4216.
    • (1989) J Bacteriol , vol.171 , pp. 4207-4216
    • French, S.L.1    Miller, O.L.Jr.2
  • 27
    • 0014960630 scopus 로고
    • Visualization of bacterial genes in action
    • Miller, O.L. Jr, Hamkalo, B.A., and Thomas, C.A. Jr. (1970) Visualization of bacterial genes in action. Science, 169, 392-395.
    • (1970) Science , vol.169 , pp. 392-395
    • Miller O.L.Jr Hamkalo, B.A.1    Thomas, C.A.Jr.2
  • 29
    • 33645771210 scopus 로고    scopus 로고
    • Insights into transcriptional regulation and s competition from an equilibrium model of RNA polymerase binding to DNA
    • Grigorova, I.L., Phleger, N.J., Mutalik, V. K., and Gross, C.A. (2006) Insights into transcriptional regulation and s competition from an equilibrium model of RNA polymerase binding to DNA. Proc Natl Acad Sci, 103, 5332-5337.
    • (2006) Proc Natl Acad Sci , vol.103 , pp. 5332-5337
    • Grigorova, I.L.1    Phleger, N.J.2    Mutalik, V.K.3    Gross, C.A.4
  • 30
    • 0000640710 scopus 로고    scopus 로고
    • Modulation of chemical composition and other parameters of the cell by growth rate
    • coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd edn (ed. F. Neidhardt), American Society for Microbiology
    • Bremer, H. and Dennis, P. (1996) Modulation of chemical composition and other parameters of the cell by growth rate, in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd edn (ed. F. Neidhardt), American Society for Microbiology, pp. 1553-1569.
    • (1996) Escherichia , pp. 1553-1569
    • Bremer, H.1    Dennis, P.2
  • 31
    • 0842285841 scopus 로고    scopus 로고
    • Summing up the noise in gene networks
    • Paulsson, J. (2004) Summing up the noise in gene networks. Nature, 427, 415-418.
    • (2004) Nature , vol.427 , pp. 415-418
    • Paulsson, J.1
  • 32
    • 0037119587 scopus 로고    scopus 로고
    • Stochastic gene expression in a single cell
    • Elowitz, M.B., Levine, A.J., Siggia, E.D., and Swain, P.S. (2002) Stochastic gene expression in a single cell. Science, 297, 1183-1186.
    • (2002) Science , vol.297 , pp. 1183-1186
    • Elowitz, M.B.1    Levine, A.J.2    Siggia, E.D.3    Swain, P.S.4
  • 35
    • 0032562720 scopus 로고    scopus 로고
    • Visualization of single RNA transcripts in situ
    • Femino, A.M., Fay, F.S., Fogarty, K., and Singer, R.H. (1998) Visualization of single RNA transcripts in situ. Science, 280, 585-590.
    • (1998) Science , vol.280 , pp. 585-590
    • Femino, A.M.1    Fay, F.S.2    Fogarty, K.3    Singer, R.H.4
  • 36
    • 25844433114 scopus 로고    scopus 로고
    • Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels
    • Bengtsson, M., Sta°hlberg, A., Rorsman, P., and Kubista, M. (2005) Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels. Genome Res, 15, 1388-1392.
    • (2005) Genome Res , vol.15 , pp. 1388-1392
    • Bengtsson, M.1    Sta°hlberg, A.2    Rorsman, P.3    Kubista, M.4
  • 37
    • 71649113974 scopus 로고    scopus 로고
    • Visualization of individual scr mRNAs during Drosophila embryogenesis yields evidence for transcriptional bursting
    • Paré, A., Lemons, D., Kosman, D., Beaver, W., Freund, Y., and McGinnis, W. (2009) Visualization of individual scr mRNAs during Drosophila embryogenesis yields evidence for transcriptional bursting. Curr Biol, 19, 2037-2042.
    • (2009) Curr Biol , vol.19 , pp. 2037-2042
    • Paré, A.1    Lemons, D.2    Kosman, D.3    Beaver, W.4    Freund, Y.5    McGinnis, W.6
  • 38
    • 2942718723 scopus 로고    scopus 로고
    • Control of stochasticity in eukaryotic gene expression
    • Raser, J.M. and O'Shea, E.K. (2004) Control of stochasticity in eukaryotic gene expression. Science, 304, 1811-1814.
    • (2004) Science , vol.304 , pp. 1811-1814
    • Raser, J.M.1    O'Shea, E.K.2
  • 39
    • 38349185928 scopus 로고    scopus 로고
    • Effects of molecular memory and bursting on fluctuations in gene expression
    • Pedraza, J.M. and Paulsson, J. (2008) Effects of molecular memory and bursting on fluctuations in gene expression. Science, 319, 339-343.
    • (2008) Science , vol.319 , pp. 339-343
    • Pedraza, J.M.1    Paulsson, J.2
  • 41
    • 28944434119 scopus 로고    scopus 로고
    • Real-time kinetics of gene activity in individual bacteria
    • Golding, I., Paulsson, J., Zawilski, S.M., and Cox, E.C. (2005) Real-time kinetics of gene activity in individual bacteria. Cell, 123, 1025-1036.
    • (2005) Cell , vol.123 , pp. 1025-1036
    • Golding, I.1    Paulsson, J.2    Zawilski, S.M.3    Cox, E.C.4
  • 42
    • 0014290634 scopus 로고
    • Periodicity of RNA polymerase initiations -a new regulatory feature of transcription
    • Baker, R.F. and Yanofsky, C. (1968) Periodicity of RNA polymerase initiations -a new regulatory feature of transcription. Proc Natl Acad Sci USA, 60, 313.
    • (1968) Proc Natl Acad Sci USA , vol.60 , pp. 313
    • Baker, R.F.1    Yanofsky, C.2
  • 43
    • 0014289998 scopus 로고
    • On the initiation of transcription of the tryptophan operon in Escherichia coli
    • Imamoto, F. (1968) On the initiation of transcription of the tryptophan operon in Escherichia coli. Proc Natl Acad Sci, 60, 305-312.
    • (1968) Proc Natl Acad Sci , vol.60 , pp. 305-312
    • Imamoto, F.1
  • 44
    • 33646591544 scopus 로고    scopus 로고
    • Transcriptional pulsing of a developmental gene
    • Chubb, J.R., Trcek, T., Shenoy, S.M., and Singer, R.H. (2006) Transcriptional pulsing of a developmental gene. Curr Biol, 16, 1018-1025.
    • (2006) Curr Biol , vol.16 , pp. 1018-1025
    • Chubb, J.R.1    Trcek, T.2    Shenoy, S.M.3    Singer, R.H.4
  • 45
    • 33645033645 scopus 로고    scopus 로고
    • Probing gene expression in live cells, one protein molecule at a time
    • Yu, J., Xiao, J., Ren, X., Lao, K., and Xie, X.S. (2006) Probing gene expression in live cells, one protein molecule at a time. Science, 311, 1600-1603.
    • (2006) Science , vol.311 , pp. 1600-1603
    • Yu, J.1    Xiao, J.2    Ren, X.3    Lao, K.4    Xie, X.S.5
  • 46
    • 54249083606 scopus 로고    scopus 로고
    • A stochastic single-molecule event triggers phenotype switching of a bacterial cell
    • Choi, P.J., Cai, L., Frieda, K., and Xie, X. S. (2008) A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science, 322, 442-446.
    • (2008) Science , vol.322 , pp. 442-446
    • Choi, P.J.1    Cai, L.2    Frieda, K.3    Xie, X.S.4
  • 48
    • 37349099448 scopus 로고    scopus 로고
    • Intranuclear distribution and local dynamics of RNA polymerase II during transcription activation
    • Yao, J., Ardehali, M.B., Fecko, C.J., Webb, W.W., and Lis, J.T. (2007) Intranuclear distribution and local dynamics of RNA polymerase II during transcription activation. Mol Cell, 28, 978-990.
    • (2007) Mol Cell , vol.28 , pp. 978-990
    • Yao, J.1    Ardehali, M.B.2    Fecko, C.J.3    Webb, W.W.4    Lis, J.T.5
  • 49
    • 0025007114 scopus 로고
    • Quantitative-analysis of the glucocorticoid receptor-DNA interaction at the mouse mammary-tumor virus glucocorticoid response element
    • Erlmann, T., Eriksson, P., and Wrange, O. (1990) Quantitative-analysis of the glucocorticoid receptor-DNA interaction at the mouse mammary-tumor virus glucocorticoid response element. J Biol Chem, 265, 17222-17229.
    • (1990) J Biol Chem , vol.265 , pp. 17222-17229
    • Erlmann, T.1    Eriksson, P.2    Wrange, O.3
  • 50
    • 0343415609 scopus 로고    scopus 로고
    • The glucocorticoid receptor: rapid exchange with regulatory sites in living cells
    • McNally, J.G., Muller, W.G., Walker, D., Wolford, R., and Hager, G.L. (2000) The glucocorticoid receptor: rapid exchange with regulatory sites in living cells. Science, 287, 1262-1265.
    • (2000) Science , vol.287 , pp. 1262-1265
    • McNally, J.G.1    Muller, W.G.2    Walker, D.3    Wolford, R.4    Hager, G.L.5
  • 51
    • 3042760021 scopus 로고    scopus 로고
    • Global nature of dynamic protein-chromatin interactions in vivo: threedimensional genome scanning and dynamic interaction networks of chromatin proteins
    • Phair, R.D., Scaffidi, P., Elbi, C., Vecerova, J., Dey, A., Ozato, K., Brown, D.T., Hager, G., Bustin, M., and Misteli, T. (2004) Global nature of dynamic protein-chromatin interactions in vivo: threedimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol Cell Biol, 24, 6393-6402.
    • (2004) Mol Cell Biol , vol.24 , pp. 6393-6402
    • Phair, R.D.1    Scaffidi, P.2    Elbi, C.3    Vecerova, J.4    Dey, A.5    Ozato, K.6    Brown, D.T.7    Hager, G.8    Bustin, M.9    Misteli, T.10
  • 53
    • 33748304273 scopus 로고    scopus 로고
    • Dynamics of heat shock factor association with native gene loci in living cells
    • Yao, J., Munson, K.M., Webb, W.W., and Lis, J.T. (2006) Dynamics of heat shock factor association with native gene loci in living cells. Nature, 442, 1050-1053.
    • (2006) Nature , vol.442 , pp. 1050-1053
    • Yao, J.1    Munson, K.M.2    Webb, W.W.3    Lis, J.T.4
  • 54
    • 0036151490 scopus 로고    scopus 로고
    • TBP dynamics in living human cells: constitutive association of TBP with mitotic chromosomes
    • Chen, D., Hinkley, C.S., Henry, R.W., and Huang, S. (2002) TBP dynamics in living human cells: constitutive association of TBP with mitotic chromosomes. Mol Biol Cell, 13, 276-284.
    • (2002) Mol Biol Cell , vol.13 , pp. 276-284
    • Chen, D.1    Hinkley, C.S.2    Henry, R.W.3    Huang, S.4
  • 58
    • 34249932435 scopus 로고    scopus 로고
    • Probing transcription factor dynamics at the single-molecule level in a living cell
    • Elf, J., Li, G.-W., and Xie, X.S. (2007) Probing transcription factor dynamics at the single-molecule level in a living cell. Science, 316, 1191-1194.
    • (2007) Science , vol.316 , pp. 1191-1194
    • Elf, J.1    Li, G.-W.2    Xie, X.S.3
  • 59
    • 70249121045 scopus 로고    scopus 로고
    • The logic of chromatin architecture and remodelling at promoters
    • Cairns, B.R. (2009) The logic of chromatin architecture and remodelling at promoters. Nature, 461, 193-198.
    • (2009) Nature , vol.461 , pp. 193-198
    • Cairns, B.R.1
  • 61
    • 70450222694 scopus 로고    scopus 로고
    • A model for all genomes: the role of transcription factories
    • Cook, P.R. (2010) A model for all genomes: the role of transcription factories. J Mol Biol, 395, 1-10.
    • (2010) J Mol Biol , vol.395 , pp. 1-10
    • Cook, P.R.1
  • 62
    • 0033546210 scopus 로고    scopus 로고
    • The organization of replication and transcription
    • Cook, P.R. (1999) The organization of replication and transcription. Science, 284, 1790-1795.
    • (1999) Science , vol.284 , pp. 1790-1795
    • Cook, P.R.1
  • 64
    • 33750212321 scopus 로고    scopus 로고
    • Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation captureon-chip (4C)
    • Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B., and de Laat, W. (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation captureon-chip (4C). Nat Genet, 38, 1348.
    • (2006) Nat Genet , vol.38 , pp. 1348
    • Simonis, M.1    Klous, P.2    Splinter, E.3    Moshkin, Y.4    Willemsen, R.5    de Wit, E.6    van Steensel, B.7    de Laat, W.8
  • 66
    • 0033561153 scopus 로고    scopus 로고
    • Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III
    • Pombo, A., Jackson, D.A., Hollinshead, M., Wang, Z., Roeder, R.G., and Cook, P.R. (1999) Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J, 18, 2241-2253.
    • (1999) EMBO J , vol.18 , pp. 2241-2253
    • Pombo, A.1    Jackson, D.A.2    Hollinshead, M.3    Wang, Z.4    Roeder, R.G.5    Cook, P.R.6
  • 67
    • 62549158168 scopus 로고    scopus 로고
    • Replication timing and epigenetic reprogramming of gene expression: a two-way relationship?
    • Gondor, A. and Ohlsson, R. (2009) Replication timing and epigenetic reprogramming of gene expression: a two-way relationship?. Nat Rev in Genetics, 10, 269-276.
    • (2009) Nat Rev in Genetics , vol.10 , pp. 269-276
    • Gondor, A.1    Ohlsson, R.2
  • 68
    • 53249124651 scopus 로고    scopus 로고
    • FISH-eyed and genome-wide views on the spatial organisation of gene expression
    • Simonis, M. and de Laat, W. (2008) FISH-eyed and genome-wide views on the spatial organisation of gene expression. Biochim Biophys Acta, 1783, 2052-2060.
    • (2008) Biochim Biophys Acta , vol.1783 , pp. 2052-2060
    • Simonis, M.1    de Laat, W.2
  • 72
    • 44149106396 scopus 로고    scopus 로고
    • Similar active genes cluster in specialized transcription factories
    • Xu, M. and Cook, P.R. (2008) Similar active genes cluster in specialized transcription factories. J Cell Biol, 181, 615-623.
    • (2008) J Cell Biol , vol.181 , pp. 615-623
    • Xu, M.1    Cook, P.R.2
  • 73
  • 74
    • 34249307315 scopus 로고    scopus 로고
    • Nuclear organization of the genome and the potential for gene regulation
    • Fraser, P. and Bickmore, W. (2007) Nuclear organization of the genome and the potential for gene regulation. Nature, 447, 413-417.
    • (2007) Nature , vol.447 , pp. 413-417
    • Fraser, P.1    Bickmore, W.2
  • 75
    • 0032490917 scopus 로고    scopus 로고
    • Perinuclear localization of chromatin facilitates transcriptional silencing
    • Andrulis, E.D., Neiman, A.M., Zappulla, D.C., and Sternglanz, R. (1998) Perinuclear localization of chromatin facilitates transcriptional silencing. Nature, 394, 592-595.
    • (1998) Nature , vol.394 , pp. 592-595
    • Andrulis, E.D.1    Neiman, A.M.2    Zappulla, D.C.3    Sternglanz, R.4


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