메뉴 건너뛰기




Volumn 14, Issue 6, 2004, Pages 697-705

Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays

Author keywords

[No Author keywords available]

Indexed keywords

BINDING AFFINITY; CHROMATIN; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENOME ANALYSIS; HUMAN; IMMUNOPRECIPITATION; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN MODIFICATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW; TRANSCRIPTION INITIATION;

EID: 8644232564     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2004.09.008     Document Type: Review
Times cited : (83)

References (49)
  • 2
    • 0035945567 scopus 로고    scopus 로고
    • Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
    • V.R. Iyer, C.E. Horak, C.S. Scafe, D. Botstein, M. Snyder, and P.O. Brown Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF Nature 409 2001 533 538
    • (2001) Nature , vol.409 , pp. 533-538
    • Iyer, V.R.1    Horak, C.E.2    Scafe, C.S.3    Botstein, D.4    Snyder, M.5    Brown, P.O.6
  • 3
    • 0034934774 scopus 로고    scopus 로고
    • Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
    • J.D. Lieb, X. Liu, D. Botstein, and P.O. Brown Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association Nat Genet 28 2001 327 334
    • (2001) Nat Genet , vol.28 , pp. 327-334
    • Lieb, J.D.1    Liu, X.2    Botstein, D.3    Brown, P.O.4
  • 6
    • 0037722938 scopus 로고    scopus 로고
    • Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling
    • J. Zeitlinger, I. Simon, C.T. Harbison, N.M. Hannett, T.L. Volkert, G.R. Fink, and R.A. Young Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling Cell 113 2003 395 404 By utilizing ChIP-chip analysis, the authors show that the transcription factor Ste12p binds to and regulates expression at distinct subsets of promoters under different developmental conditions. Localization of Ste12p during mating and filamentous growth is shown to be differentially regulated by the mitogen-activated protein kinases Fus3p and Kss1p. Ste12p-binding during filamentous growth is also shown to require the transcription factor Tec1p.
    • (2003) Cell , vol.113 , pp. 395-404
    • Zeitlinger, J.1    Simon, I.2    Harbison, C.T.3    Hannett, N.M.4    Volkert, T.L.5    Fink, G.R.6    Young, R.A.7
  • 8
    • 0033607161 scopus 로고    scopus 로고
    • Effectors of a developmental mitogen-activated protein kinase cascade revealed by expression signatures of signaling mutants
    • H.D. Madhani, T. Galitski, E.S. Lander, and G.R. Fink Effectors of a developmental mitogen-activated protein kinase cascade revealed by expression signatures of signaling mutants Proc Natl Acad Sci USA 96 1999 12530 12535
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 12530-12535
    • Madhani, H.D.1    Galitski, T.2    Lander, E.S.3    Fink, G.R.4
  • 9
    • 2442606759 scopus 로고    scopus 로고
    • Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes
    • •] examine the genome-wide localization of the RNA Polymerase (Pol) III transcription machinery. These studies confirm, on a global scale, that the Pol III transcribes a large set of untranslated RNAs.
    • (2004) Mol Cell Biol , vol.24 , pp. 4118-4127
    • Moqtaderi, Z.1    Struhl, K.2
  • 12
    • 0037326054 scopus 로고    scopus 로고
    • Telomeric protein distributions and remodeling through the cell cycle in Saccharomyces cerevisiae
    • C.D. Smith, D.L. Smith, J.L. DeRisi, and E.H. Blackburn Telomeric protein distributions and remodeling through the cell cycle in Saccharomyces cerevisiae Mol Biol Cell 14 2003 556 570
    • (2003) Mol Biol Cell , vol.14 , pp. 556-570
    • Smith, C.D.1    Smith, D.L.2    Derisi, J.L.3    Blackburn, E.H.4
  • 14
    • 19344366459 scopus 로고    scopus 로고
    • Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae
    • E.F. Glynn, P.C. Megee, H. Yu, C. Mistrot, E. Unal, D.E. Koshland, J.L. DeRisi, and J.L. Gerton Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae PLoS Biol 2 2004 e259 This study reports the genome-wide distribution of cohesin, a protein complex required to maintain sister chromatid association. The majority of cohesin was bound to pericentromeric regions. Cohesin was also found along the arms of the chromosomes, mainly in intergenic regions between two convergently transcribed genes. Additionally, activating transcription of repressed genes caused the exclusion of cohesin from these loci. The results of this study reveal a strong inverse correlation between transcription and cohesin binding.
    • (2004) PLoS Biol , vol.2
    • Glynn, E.F.1    Megee, P.C.2    Yu, H.3    Mistrot, C.4    Unal, E.5    Koshland, D.E.6    Derisi, J.L.7    Gerton, J.L.8
  • 15
    • 2342501365 scopus 로고    scopus 로고
    • Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization
    • J.M. Casolari, C.R. Brown, S. Komili, J. West, H. Hieronymus, and P.A. Silver Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization Cell 117 2004 427 439 This elegant study illustrates the complexity of coordinating many cellular events over time and space. The authors map the genome-wide distribution of several components of the nuclear transport machinery and find that the majority of the karyopherins and nucleoporins are associated with highly transcribed genes. These results imply that genes undergoing a high rate of transcription are held near the nuclear pores, possibly to facilitate transport of mRNA to the cytoplasm.
    • (2004) Cell , vol.117 , pp. 427-439
    • Casolari, J.M.1    Brown, C.R.2    Komili, S.3    West, J.4    Hieronymus, H.5    Silver, P.A.6
  • 16
    • 0344022572 scopus 로고    scopus 로고
    • Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity
    • H.H. Ng, F. Robert, R.A. Young, and K. Struhl Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity Mol Cell 11 2003 709 719
    • (2003) Mol Cell , vol.11 , pp. 709-719
    • Ng, H.H.1    Robert, F.2    Young, R.A.3    Struhl, K.4
  • 17
    • 0036649756 scopus 로고    scopus 로고
    • Genome-wide binding map of the histone deacetylase Rpd3 in yeast
    • S.K. Kurdistani, D. Robyr, S. Tavazoie, and M. Grunstein Genome-wide binding map of the histone deacetylase Rpd3 in yeast Nat Genet 31 2002 248 254
    • (2002) Nat Genet , vol.31 , pp. 248-254
    • Kurdistani, S.K.1    Robyr, D.2    Tavazoie, S.3    Grunstein, M.4
  • 18
    • 6444241134 scopus 로고    scopus 로고
    • Rpd3p relocation mediates a transcriptional response to rapamycin in yeast
    • E.L. Humphrey, A.F. Shamji, B.E. Bernstein, and S.L. Schreiber Rpd3p relocation mediates a transcriptional response to rapamycin in yeast Chem Biol 11 2004 295 299 This study examines the genome-wide localization of Rpd3p occupancy before and after treatment with rapamycin. In contrast to [17], the authors find that Rpd3p binds to the promoters of rapamycin-repressible genes only after treatment, suggesting that targeted recruitment of Rpd3p is a major regulatory step in controlling gene expression.
    • (2004) Chem Biol , vol.11 , pp. 295-299
    • Humphrey, E.L.1    Shamji, A.F.2    Bernstein, B.E.3    Schreiber, S.L.4
  • 20
    • 0037123767 scopus 로고    scopus 로고
    • Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases
    • D. Robyr, Y. Suka, I. Xenarios, S.K. Kurdistani, A. Wang, N. Suka, and M. Grunstein Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases Cell 109 2002 437 446
    • (2002) Cell , vol.109 , pp. 437-446
    • Robyr, D.1    Suka, Y.2    Xenarios, I.3    Kurdistani, S.K.4    Wang, A.5    Suka, N.6    Grunstein, M.7
  • 21
    • 2942518343 scopus 로고    scopus 로고
    • Mapping global histone acetylation patterns to gene expression
    • S.K. Kurdistani, S. Tavazoie, and M. Grunstein Mapping global histone acetylation patterns to gene expression Cell 117 2004 721 733 This paper examines the acetylation pattern of 11 lysine residues in the four core histones of yeast. The authors report that distinct patterns of hyper- and hypoacetylated histones allow for the coordinate regulation of related genes.
    • (2004) Cell , vol.117 , pp. 721-733
    • Kurdistani, S.K.1    Tavazoie, S.2    Grunstein, M.3
  • 22
    • 2642570305 scopus 로고    scopus 로고
    • The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote
    • D. Schubeler, D.M. MacAlpine, D. Scalzo, C. Wirbelauer, C. Kooperberg, F. van Leeuwen, D.E. Gottschling, L.P. O'Neill, B.M. Turner, and J. Delrow The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote Genes Dev 18 2004 1263 1271 The authors map the global pattern of histone acetylation and methylation in the Drosophila genome. Hyperacetylation of histone H3 and H4 and hypermethylation of histone H3 lysines 4 and 79 are shown to occur in the same genes and are associated with transcriptionally active loci. Furthermore, the degree of modification is shown to correlate with the level of transcriptional activity. These results suggest a link between polymerase activity and histone modification.
    • (2004) Genes Dev , vol.18 , pp. 1263-1271
    • Schubeler, D.1    MacAlpine, D.M.2    Scalzo, D.3    Wirbelauer, C.4    Kooperberg, C.5    Van Leeuwen, F.6    Gottschling, D.E.7    O'Neill, L.P.8    Turner, B.M.9    Delrow, J.10
  • 23
    • 0036591875 scopus 로고    scopus 로고
    • Mechanisms of chromatin assembly and transcription
    • S. Kadam, and B.M. Emerson Mechanisms of chromatin assembly and transcription Curr Opin Cell Biol 14 2002 262 268
    • (2002) Curr Opin Cell Biol , vol.14 , pp. 262-268
    • Kadam, S.1    Emerson, B.M.2
  • 24
    • 0343924289 scopus 로고    scopus 로고
    • Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters
    • D. Kadosh, and K. Struhl Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters Cell 89 1997 365 371
    • (1997) Cell , vol.89 , pp. 365-371
    • Kadosh, D.1    Struhl, K.2
  • 25
    • 0031865050 scopus 로고    scopus 로고
    • Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo
    • D. Kadosh, and K. Struhl Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo Mol Cell Biol 18 1998 5121 5127
    • (1998) Mol Cell Biol , vol.18 , pp. 5121-5127
    • Kadosh, D.1    Struhl, K.2
  • 26
    • 0034707037 scopus 로고    scopus 로고
    • Global histone acetylation and deacetylation in yeast
    • M. Vogelauer, J. Wu, N. Suka, and M. Grunstein Global histone acetylation and deacetylation in yeast Nature 408 2000 495 498
    • (2000) Nature , vol.408 , pp. 495-498
    • Vogelauer, M.1    Wu, J.2    Suka, N.3    Grunstein, M.4
  • 27
    • 0032520953 scopus 로고    scopus 로고
    • Histone deacetylase activity of Rpd3 is important for transcriptional repression in vivo
    • D. Kadosh, and K. Struhl Histone deacetylase activity of Rpd3 is important for transcriptional repression in vivo Genes Dev 12 1998 797 805
    • (1998) Genes Dev , vol.12 , pp. 797-805
    • Kadosh, D.1    Struhl, K.2
  • 28
    • 0037382681 scopus 로고    scopus 로고
    • Collaborative spirit of histone deacetylases in regulating chromatin structure and gene expression
    • X.J. Yang, and E. Seto Collaborative spirit of histone deacetylases in regulating chromatin structure and gene expression Curr Opin Genet Dev 13 2003 143 153
    • (2003) Curr Opin Genet Dev , vol.13 , pp. 143-153
    • Yang, X.J.1    Seto, E.2
  • 29
    • 0037111879 scopus 로고    scopus 로고
    • Requirement of Hos2 histone deacetylase for gene activity in yeast
    • A. Wang, S.K. Kurdistani, and M. Grunstein Requirement of Hos2 histone deacetylase for gene activity in yeast Science 298 2002 1412 1414
    • (2002) Science , vol.298 , pp. 1412-1414
    • Wang, A.1    Kurdistani, S.K.2    Grunstein, M.3
  • 30
    • 0042736137 scopus 로고    scopus 로고
    • Epigenomic profiling using microarrays
    • B. van Steensel, and S. Henikoff Epigenomic profiling using microarrays Biotechniques 35 2003 346 350 352-354, 356-357
    • (2003) Biotechniques , vol.35 , pp. 346-350
    • Van Steensel, B.1    Henikoff, S.2
  • 31
    • 0015543341 scopus 로고
    • Reactions of nucleic acids and nucleoproteins with formaldehyde
    • M.Y. Feldman Reactions of nucleic acids and nucleoproteins with formaldehyde Prog Nucleic Acid Res Mol Biol 13 1973 1 49
    • (1973) Prog Nucleic Acid Res Mol Biol , vol.13 , pp. 1-49
    • Feldman, M.Y.1
  • 33
    • 0015748006 scopus 로고
    • The reaction of formaldehyde with deoxynucleotides and DNA in the presence of amino acids and lysine-rich histone
    • Y.A. Siomin, V.V. Simonov, and A.M. Poverenny The reaction of formaldehyde with deoxynucleotides and DNA in the presence of amino acids and lysine-rich histone Biochim Biophys Acta 331 1973 27 32
    • (1973) Biochim Biophys Acta , vol.331 , pp. 27-32
    • Siomin, Y.A.1    Simonov, V.V.2    Poverenny, A.M.3
  • 34
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • M.J. Buck, and J.D. Lieb ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments Genomics 83 2004 349 360
    • (2004) Genomics , vol.83 , pp. 349-360
    • Buck, M.J.1    Lieb, J.D.2
  • 35
    • 0001473216 scopus 로고
    • Formaldehyde-mediated DNA-protein crosslinking: A probe for in vivo chromatin structures
    • M.J. Solomon, and A. Varshavsky Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures Proc Natl Acad Sci USA 82 1985 6470 6474
    • (1985) Proc Natl Acad Sci USA , vol.82 , pp. 6470-6474
    • Solomon, M.J.1    Varshavsky, A.2
  • 36
    • 0032848160 scopus 로고    scopus 로고
    • Formaldehyde cross-linking for studying nucleosomal dynamics
    • V. Jackson Formaldehyde cross-linking for studying nucleosomal dynamics Methods 17 1999 125 139
    • (1999) Methods , vol.17 , pp. 125-139
    • Jackson, V.1
  • 37
    • 0038652118 scopus 로고    scopus 로고
    • Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin
    • P.L. Nagy, M.L. Cleary, P.O. Brown, and J.D. Lieb Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin Proc Natl Acad Sci USA 100 2003 6364 6369 This study describes a method for fractionating the yeast genome into RNA Pol II-transcribed regions and non-coding regions on the basis of differential crosslinking by formaldehyde. The authors hypothesize that the underlying mechanism involves differences in nucleosome occupancy or differences in histone modifications between coding and non-coding regions of the genome.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 6364-6369
    • Nagy, P.L.1    Cleary, M.L.2    Brown, P.O.3    Lieb, J.D.4
  • 38
    • 2942550662 scopus 로고    scopus 로고
    • Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes
    • •] each examine the detailed organization of nucleosomes at the PHO5 promoter. This study shows that the histone chaperone Asf1p facilitates the disassembly of nucleosomes at the PHO5 promoter and that disassembly is required for activation of gene expression.
    • (2004) Mol Cell , vol.14 , pp. 657-666
    • Adkins, M.W.1    Howar, S.R.2    Tyler, J.K.3
  • 39
    • 0038094502 scopus 로고    scopus 로고
    • Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter
    • •].
    • (2003) Mol Cell , vol.11 , pp. 1599-1607
    • Reinke, H.1    Horz, W.2
  • 42
    • 0027485506 scopus 로고
    • Chromatin transitions during activation and repression of galactose-regulated genes in yeast
    • G. Cavalli, and F. Thoma Chromatin transitions during activation and repression of galactose-regulated genes in yeast EMBO J 12 1993 4603 4613
    • (1993) EMBO J , vol.12 , pp. 4603-4613
    • Cavalli, G.1    Thoma, F.2
  • 43
    • 0024500464 scopus 로고
    • Upstream activation sequence-dependent alteration of chromatin structure and transcription activation of the yeast GAL1-GAL10 genes
    • M.J. Fedor, and R.D. Kornberg Upstream activation sequence-dependent alteration of chromatin structure and transcription activation of the yeast GAL1-GAL10 genes Mol Cell Biol 9 1989 1721 1732
    • (1989) Mol Cell Biol , vol.9 , pp. 1721-1732
    • Fedor, M.J.1    Kornberg, R.D.2
  • 44
    • 0031585394 scopus 로고    scopus 로고
    • Nucleosome transactions on the promoters of the yeast GAL and PHO genes
    • D. Lohr Nucleosome transactions on the promoters of the yeast GAL and PHO genes J Biol Chem 272 1997 26795 26798
    • (1997) J Biol Chem , vol.272 , pp. 26795-26798
    • Lohr, D.1
  • 45
    • 3543023310 scopus 로고    scopus 로고
    • Evidence for nucleosome depletion at active regulatory regions genome-wide
    • C.K. Lee, Y. Shibata, B. Rao, B.D. Strahl, and J.D. Lieb Evidence for nucleosome depletion at active regulatory regions genome-wide Nat Genet 36 2004 900 905 This study provides evidence that nucleosomes are depleted from the regulatory elements of actively transcribed genes throughout the yeast genome. The degree of nucleosome depletion correlates with the rate of transcription initiation at the promoter. Furthermore, altering gene expression by changing growth conditions results in increased nucleosome occupancy at repressed genes and a depletion of nucleosomes at induced genes.
    • (2004) Nat Genet , vol.36 , pp. 900-905
    • Lee, C.K.1    Shibata, Y.2    Rao, B.3    Strahl, B.D.4    Lieb, J.D.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.