메뉴 건너뛰기




Volumn 27, Issue 11, 2011, Pages 475-485

Genomic and chromatin signals underlying transcription start-site selection

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITE; CHROMATIN; GENE SEQUENCE; GENETIC SELECTION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; GENOMICS; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; REVIEW;

EID: 80054081798     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2011.08.001     Document Type: Review
Times cited : (55)

References (99)
  • 1
    • 0842265974 scopus 로고    scopus 로고
    • Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors
    • Kadonaga J.T. Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell 2004, 116:247-257.
    • (2004) Cell , vol.116 , pp. 247-257
    • Kadonaga, J.T.1
  • 2
  • 3
    • 33747881750 scopus 로고    scopus 로고
    • The general transcription machinery and general cofactors
    • Thomas M.C., Chiang C.-M. The general transcription machinery and general cofactors. Crit. Rev. Biochem. Mol. Biol. 2006, 41:105-178.
    • (2006) Crit. Rev. Biochem. Mol. Biol. , vol.41 , pp. 105-178
    • Thomas, M.C.1    Chiang, C.-M.2
  • 4
    • 33744805985 scopus 로고    scopus 로고
    • Genome-wide analysis of mammalian promoter architecture and evolution
    • Carninci P., et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet. 2006, 38:626-635.
    • (2006) Nat. Genet. , vol.38 , pp. 626-635
    • Carninci, P.1
  • 5
    • 33749128065 scopus 로고    scopus 로고
    • Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters
    • Ponjavic J., et al. Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters. Genome Biol. 2006, 7:R78.
    • (2006) Genome Biol. , vol.7
    • Ponjavic, J.1
  • 6
    • 32044442759 scopus 로고    scopus 로고
    • Promoter features related to tissue specificity as measured by Shannon entropy
    • Schug J., et al. Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biol. 2005, 6:R33.
    • (2005) Genome Biol. , vol.6
    • Schug, J.1
  • 7
    • 79956330964 scopus 로고    scopus 로고
    • CpG islands and the regulation of transcription
    • Deaton A.M., Bird A. CpG islands and the regulation of transcription. Genes Dev. 2011, 25:1010-1022.
    • (2011) Genes Dev. , vol.25 , pp. 1010-1022
    • Deaton, A.M.1    Bird, A.2
  • 8
  • 9
    • 31944432339 scopus 로고    scopus 로고
    • A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters
    • Saxonov S., et al. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:1412-1417.
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 1412-1417
    • Saxonov, S.1
  • 10
    • 59949103704 scopus 로고    scopus 로고
    • Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
    • Valen E., et al. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res. 2009, 19:255-265.
    • (2009) Genome Res. , vol.19 , pp. 255-265
    • Valen, E.1
  • 11
    • 79955453038 scopus 로고    scopus 로고
    • Functional relevance of CpG island length for regulation of gene expression
    • Elango N., Yi S.V. Functional relevance of CpG island length for regulation of gene expression. Genetics 2011, 187:1077-1083.
    • (2011) Genetics , vol.187 , pp. 1077-1083
    • Elango, N.1    Yi, S.V.2
  • 12
    • 47649091157 scopus 로고    scopus 로고
    • DNA methylation and structural and functional bimodality of vertebrate promoters
    • Elango N., Yi S.V. DNA methylation and structural and functional bimodality of vertebrate promoters. Mol. Biol. Evol. 2008, 25:1602-1608.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 1602-1608
    • Elango, N.1    Yi, S.V.2
  • 13
    • 79955610452 scopus 로고    scopus 로고
    • Chromatin organization in sperm may be the major functional consequence of base composition variation in the human genome
    • Vavouri T., Lehner B. Chromatin organization in sperm may be the major functional consequence of base composition variation in the human genome. PLoS Genet. 2011, 7:e1002036.
    • (2011) PLoS Genet. , vol.7
    • Vavouri, T.1    Lehner, B.2
  • 14
    • 70349312354 scopus 로고    scopus 로고
    • ChIP-seq: advantages and challenges of a maturing technology
    • Park P.J. ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. 2009, 10:669-680.
    • (2009) Nat. Rev. , vol.10 , pp. 669-680
    • Park, P.J.1
  • 15
    • 78650304236 scopus 로고    scopus 로고
    • Charting histone modifications and the functional organization of mammalian genomes
    • Zhou V., et al. Charting histone modifications and the functional organization of mammalian genomes. Nat. Rev. Genet. 2011, 12:7-18.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 7-18
    • Zhou, V.1
  • 16
    • 23644460630 scopus 로고    scopus 로고
    • Tag-based approaches for transcriptome research and genome annotation
    • Harbers M., Carninci P. Tag-based approaches for transcriptome research and genome annotation. Nat. Methods 2005, 2:495-502.
    • (2005) Nat. Methods , vol.2 , pp. 495-502
    • Harbers, M.1    Carninci, P.2
  • 17
    • 34249098071 scopus 로고    scopus 로고
    • Mammalian RNA polymerase II core promoters: insights from genome-wide studies
    • Sandelin A., et al. Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat. Rev. 2007, 8:424-436.
    • (2007) Nat. Rev. , vol.8 , pp. 424-436
    • Sandelin, A.1
  • 18
    • 20144384163 scopus 로고    scopus 로고
    • Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE
    • Zhang Z., Dietrich F.S. Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res. 2005, 33:2838-2851.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 2838-2851
    • Zhang, Z.1    Dietrich, F.S.2
  • 19
    • 70349847245 scopus 로고    scopus 로고
    • Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis
    • Yamamoto Y.Y., et al. Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis. Plant J. 2009, 60:350-362.
    • (2009) Plant J. , vol.60 , pp. 350-362
    • Yamamoto, Y.Y.1
  • 20
    • 79952257234 scopus 로고    scopus 로고
    • Nucleotide composition-linked divergence of vertebrate core promoter architecture
    • van Heeringen S.J., et al. Nucleotide composition-linked divergence of vertebrate core promoter architecture. Genome Res. 2011, 21:410-421.
    • (2011) Genome Res. , vol.21 , pp. 410-421
    • van Heeringen, S.J.1
  • 21
    • 78751595020 scopus 로고    scopus 로고
    • Polycomb preferentially targets stalled promoters of coding and noncoding transcripts
    • Enderle D., et al. Polycomb preferentially targets stalled promoters of coding and noncoding transcripts. Genome Res. 2011, 21:216-226.
    • (2011) Genome Res. , vol.21 , pp. 216-226
    • Enderle, D.1
  • 22
    • 58149179990 scopus 로고    scopus 로고
    • MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database
    • Ahsan B., et al. MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database. Nucleic Acids Res. 2009, 37:D49-D53.
    • (2009) Nucleic Acids Res. , vol.37
    • Ahsan, B.1
  • 23
    • 77954716355 scopus 로고    scopus 로고
    • A paired-end sequencing strategy to map the complex landscape of transcription initiation
    • Ni T., et al. A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat. Methods 2010, 7:521-527.
    • (2010) Nat. Methods , vol.7 , pp. 521-527
    • Ni, T.1
  • 24
    • 79551610291 scopus 로고    scopus 로고
    • Genome-wide analysis of promoter architecture in Drosophila melanogaster
    • Hoskins R.A., et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. 2011, 21:182-192.
    • (2011) Genome Res. , vol.21 , pp. 182-192
    • Hoskins, R.A.1
  • 25
    • 68049107475 scopus 로고    scopus 로고
    • Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome
    • Rach E., et al. Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. Genome Biol. 2009, 10:R73.
    • (2009) Genome Biol. , vol.10
    • Rach, E.1
  • 26
    • 33744824906 scopus 로고    scopus 로고
    • Evolutionary turnover of mammalian transcription start sites
    • Frith M.C., et al. Evolutionary turnover of mammalian transcription start sites. Genome Res. 2006, 16:713-722.
    • (2006) Genome Res. , vol.16 , pp. 713-722
    • Frith, M.C.1
  • 27
    • 77954221282 scopus 로고    scopus 로고
    • Sequence features that drive human promoter function and tissue specificity
    • Landolin J., et al. Sequence features that drive human promoter function and tissue specificity. Genome Res. 2010, 20:890.
    • (2010) Genome Res. , vol.20 , pp. 890
    • Landolin, J.1
  • 28
    • 71049155308 scopus 로고    scopus 로고
    • CpG-depleted promoters harbor tissue-specific transcription factor binding signals - implications for motif overrepresentation analyses
    • Roider H., et al. CpG-depleted promoters harbor tissue-specific transcription factor binding signals - implications for motif overrepresentation analyses. Nucleic Acids Res. 2009, 37:6305-6315.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 6305-6315
    • Roider, H.1
  • 29
    • 52949138674 scopus 로고    scopus 로고
    • On the nature of human housekeeping genes
    • Zhu J., et al. On the nature of human housekeeping genes. Trends Genet. 2008, 24:481-484.
    • (2008) Trends Genet. , vol.24 , pp. 481-484
    • Zhu, J.1
  • 30
    • 57149119464 scopus 로고    scopus 로고
    • Distinct modes of regulation by chromatin encoded through nucleosome positioning signals
    • Field Y., et al. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput. Biol. 2008, 4:e1000216.
    • (2008) PLoS Comput. Biol. , vol.4
    • Field, Y.1
  • 31
    • 47649125318 scopus 로고    scopus 로고
    • Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation
    • López-Maury L., et al. Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nat. Rev. Genet. 2008, 9:583-593.
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 583-593
    • López-Maury, L.1
  • 32
    • 33846214719 scopus 로고    scopus 로고
    • Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters
    • Yang C., et al. Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene 2007, 389:52-65.
    • (2007) Gene , vol.389 , pp. 52-65
    • Yang, C.1
  • 33
    • 0242416539 scopus 로고    scopus 로고
    • Noise in eukaryotic gene expression
    • Blake W.J., et al. Noise in eukaryotic gene expression. Nature 2003, 422:633-637.
    • (2003) Nature , vol.422 , pp. 633-637
    • Blake, W.J.1
  • 34
    • 34250785284 scopus 로고    scopus 로고
    • Genetic properties influencing the evolvability of gene expression
    • Landry C.R., et al. Genetic properties influencing the evolvability of gene expression. Science 2007, 317:118-121.
    • (2007) Science , vol.317 , pp. 118-121
    • Landry, C.R.1
  • 35
    • 2942718723 scopus 로고    scopus 로고
    • Control of stochasticity in eukaryotic gene expression
    • Raser J.M., O'Shea E.K. Control of stochasticity in eukaryotic gene expression. Science 2004, 304:1811-1814.
    • (2004) Science , vol.304 , pp. 1811-1814
    • Raser, J.M.1    O'Shea, E.K.2
  • 36
    • 77958096076 scopus 로고    scopus 로고
    • Determining the specificity of protein-DNA interactions
    • Stormo G.D., Zhao Y. Determining the specificity of protein-DNA interactions. Nat. Rev. Genet. 2010, 11:751-760.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 751-760
    • Stormo, G.D.1    Zhao, Y.2
  • 37
    • 62549128139 scopus 로고    scopus 로고
    • A census of human transcription factors: function, expression and evolution
    • Vaquerizas J.M., et al. A census of human transcription factors: function, expression and evolution. Nat. Rev. Genet. 2009, 10:252.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 252
    • Vaquerizas, J.M.1
  • 38
    • 79851485916 scopus 로고    scopus 로고
    • Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level
    • Rach E.A., et al. Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level. PLoS Genet. 2011, 7:e1001274.
    • (2011) PLoS Genet. , vol.7
    • Rach, E.A.1
  • 39
    • 77954763022 scopus 로고    scopus 로고
    • Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation
    • Goodrich J., Tjian R. Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation. Nat. Rev. Genet. 2010, 11:549-558.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 549-558
    • Goodrich, J.1    Tjian, R.2
  • 40
    • 36549013619 scopus 로고    scopus 로고
    • RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo
    • Zeitlinger J., et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat. Genet. 2007, 39:1512-1516.
    • (2007) Nat. Genet. , vol.39 , pp. 1512-1516
    • Zeitlinger, J.1
  • 41
    • 4544247852 scopus 로고    scopus 로고
    • Specialized and redundant roles of TBP and a vertebrate-specific TBP paralog in embryonic gene regulation in Xenopus
    • Jallow Z., et al. Specialized and redundant roles of TBP and a vertebrate-specific TBP paralog in embryonic gene regulation in Xenopus. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:13525-13530.
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 13525-13530
    • Jallow, Z.1
  • 42
    • 0345166849 scopus 로고    scopus 로고
    • TRF3, a TATA-box-binding protein-related factor, is vertebrate-specific and widely expressed
    • Persengiev S.P., et al. TRF3, a TATA-box-binding protein-related factor, is vertebrate-specific and widely expressed. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:14887-14891.
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 14887-14891
    • Persengiev, S.P.1
  • 43
    • 34547843539 scopus 로고    scopus 로고
    • Analysis of TATA-binding protein 2 (TBP2) and TBP expression suggests different roles for the two proteins in regulation of gene expression during oogenesis and early mouse development
    • Gazdag E., et al. Analysis of TATA-binding protein 2 (TBP2) and TBP expression suggests different roles for the two proteins in regulation of gene expression during oogenesis and early mouse development. Reproduction (Cambridge, England) 2007, 134:51-62.
    • (2007) Reproduction (Cambridge, England) , vol.134 , pp. 51-62
    • Gazdag, E.1
  • 44
    • 36249011467 scopus 로고    scopus 로고
    • Transcription of histone gene cluster by differential core-promoter factors
    • Isogai Y., et al. Transcription of histone gene cluster by differential core-promoter factors. Genes Dev. 2007, 21:2936-2949.
    • (2007) Genes Dev. , vol.21 , pp. 2936-2949
    • Isogai, Y.1
  • 45
    • 33747712023 scopus 로고    scopus 로고
    • The complexity of the mammalian transcriptome
    • Gustincich S., et al. The complexity of the mammalian transcriptome. J. Physiol. 2006, 575:321-332.
    • (2006) J. Physiol. , vol.575 , pp. 321-332
    • Gustincich, S.1
  • 46
    • 33846862405 scopus 로고    scopus 로고
    • High-throughput mapping of the chromatin structure of human promoters
    • Ozsolak F., et al. High-throughput mapping of the chromatin structure of human promoters. Nat. Biotechnol. 2007, 25:244-248.
    • (2007) Nat. Biotechnol. , vol.25 , pp. 244-248
    • Ozsolak, F.1
  • 47
    • 22744432660 scopus 로고    scopus 로고
    • Genome-scale identification of nucleosome positions in S. cerevisiae
    • Yuan G.C., et al. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 2005, 309:626-630.
    • (2005) Science , vol.309 , pp. 626-630
    • Yuan, G.C.1
  • 48
    • 43749099875 scopus 로고    scopus 로고
    • Nucleosome organization in the Drosophila genome
    • Mavrich T.N., et al. Nucleosome organization in the Drosophila genome. Nature 2008, 453:358-362.
    • (2008) Nature , vol.453 , pp. 358-362
    • Mavrich, T.N.1
  • 49
    • 61849170193 scopus 로고    scopus 로고
    • Genome-wide profiling of salt fractions maps physical properties of chromatin
    • Henikoff S., et al. Genome-wide profiling of salt fractions maps physical properties of chromatin. Genome Res. 2009, 19:460-469.
    • (2009) Genome Res. , vol.19 , pp. 460-469
    • Henikoff, S.1
  • 50
    • 34250745886 scopus 로고    scopus 로고
    • Nucleosome stability mediated by histone variants H3.3 and H2A. Z
    • Jin C., Felsenfeld G. Nucleosome stability mediated by histone variants H3.3 and H2A. Z. Genes Dev. 2007, 21:1519.
    • (2007) Genes Dev. , vol.21 , pp. 1519
    • Jin, C.1    Felsenfeld, G.2
  • 51
    • 74949110964 scopus 로고    scopus 로고
    • High-resolution nucleosome mapping reveals transcription-dependent promoter packaging
    • Weiner A., et al. High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res. 2010, 20:90.
    • (2010) Genome Res. , vol.20 , pp. 90
    • Weiner, A.1
  • 52
    • 45549093494 scopus 로고    scopus 로고
    • Promoter elements associated with RNA Pol II stalling in the Drosophila embryo
    • Hendrix D.A., et al. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:7762-7767.
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 7762-7767
    • Hendrix, D.A.1
  • 53
    • 0042329754 scopus 로고    scopus 로고
    • Structure, function and evolution of CpG island promoters
    • Antequera F. Structure, function and evolution of CpG island promoters. Cell. Mol. Life Sci. 2003, 60:1647-1658.
    • (2003) Cell. Mol. Life Sci. , vol.60 , pp. 1647-1658
    • Antequera, F.1
  • 54
    • 39749145198 scopus 로고    scopus 로고
    • Dynamic regulation of nucleosome positioning in the human genome
    • Schones D.E., et al. Dynamic regulation of nucleosome positioning in the human genome. Cell 2008, 132:887-898.
    • (2008) Cell , vol.132 , pp. 887-898
    • Schones, D.E.1
  • 55
    • 0025266610 scopus 로고
    • Alternative chromatin structure at CpG islands
    • Tazi J., Bird A. Alternative chromatin structure at CpG islands. Cell 1990, 60:909-920.
    • (1990) Cell , vol.60 , pp. 909-920
    • Tazi, J.1    Bird, A.2
  • 56
    • 43749088127 scopus 로고    scopus 로고
    • Two strategies for gene regulation by promoter nucleosomes
    • Tirosh I., Barkai N. Two strategies for gene regulation by promoter nucleosomes. Genome Res. 2008, 18:1084.
    • (2008) Genome Res. , vol.18 , pp. 1084
    • Tirosh, I.1    Barkai, N.2
  • 57
    • 68349125112 scopus 로고    scopus 로고
    • What controls nucleosome positions?
    • Segal E., Widom J. What controls nucleosome positions?. Trends Genet. 2009, 25:335-343.
    • (2009) Trends Genet. , vol.25 , pp. 335-343
    • Segal, E.1    Widom, J.2
  • 58
    • 34447098370 scopus 로고    scopus 로고
    • A chromatin landmark and transcription initiation at most promoters in human cells
    • Guenther M.G., et al. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 2007, 130:77-88.
    • (2007) Cell , vol.130 , pp. 77-88
    • Guenther, M.G.1
  • 59
    • 0033868319 scopus 로고    scopus 로고
    • Artificially recruited TATA-binding protein fails to remodel chromatin and does not activate three promoters that require chromatin remodeling
    • Ryan M.P., et al. Artificially recruited TATA-binding protein fails to remodel chromatin and does not activate three promoters that require chromatin remodeling. Mol. Cell. Biol. 2000, 20:5847.
    • (2000) Mol. Cell. Biol. , vol.20 , pp. 5847
    • Ryan, M.P.1
  • 60
    • 67649669255 scopus 로고    scopus 로고
    • A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling
    • Ramirez-Carrozzi V., et al. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 2009, 138:114-128.
    • (2009) Cell , vol.138 , pp. 114-128
    • Ramirez-Carrozzi, V.1
  • 61
    • 78149477660 scopus 로고    scopus 로고
    • Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation
    • Gilchrist D.A., et al. Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell 2010, 143:540-551.
    • (2010) Cell , vol.143 , pp. 540-551
    • Gilchrist, D.A.1
  • 62
    • 79959557189 scopus 로고    scopus 로고
    • Determinants of nucleosome organization in primary human cells
    • Valouev A., et al. Determinants of nucleosome organization in primary human cells. Nature 2011, 474:516-520.
    • (2011) Nature , vol.474 , pp. 516-520
    • Valouev, A.1
  • 63
    • 80051990662 scopus 로고    scopus 로고
    • Systematic clustering of transcription start site landscapes
    • Zhao X., et al. Systematic clustering of transcription start site landscapes. PloS ONE 2011, 10.1371/journal.pone.0023409.
    • (2011) PloS ONE
    • Zhao, X.1
  • 64
    • 34547624303 scopus 로고    scopus 로고
    • Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    • Mikkelsen T.S., et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448:553-560.
    • (2007) Nature , vol.448 , pp. 553-560
    • Mikkelsen, T.S.1
  • 65
    • 34047116826 scopus 로고    scopus 로고
    • Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
    • Weber M., et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 2007, 39:457-466.
    • (2007) Nat. Genet. , vol.39 , pp. 457-466
    • Weber, M.1
  • 66
    • 43049085949 scopus 로고    scopus 로고
    • Differential H3K4 methylation identifies developmentally poised hematopoietic genes
    • Orford K., et al. Differential H3K4 methylation identifies developmentally poised hematopoietic genes. Dev. Cell 2008, 14:798-809.
    • (2008) Dev. Cell , vol.14 , pp. 798-809
    • Orford, K.1
  • 67
    • 73349098753 scopus 로고    scopus 로고
    • The euchromatic and heterochromatic landscapes are shaped by antagonizing effects of transcription on H2A.Z. deposition
    • Hardy S., et al. The euchromatic and heterochromatic landscapes are shaped by antagonizing effects of transcription on H2A.Z. deposition. PLoS Genet. 2009, 5:e1000687.
    • (2009) PLoS Genet. , vol.5
    • Hardy, S.1
  • 68
    • 38049020974 scopus 로고    scopus 로고
    • A code for transcription initiation in mammalian genomes
    • Frith M.C., et al. A code for transcription initiation in mammalian genomes. Genome Res. 2008, 18:1-12.
    • (2008) Genome Res. , vol.18 , pp. 1-12
    • Frith, M.C.1
  • 69
    • 63849237976 scopus 로고    scopus 로고
    • A transcription factor affinity-based code for mammalian transcription initiation
    • Megraw M., et al. A transcription factor affinity-based code for mammalian transcription initiation. Genome Res. 2009, 19:644-656.
    • (2009) Genome Res. , vol.19 , pp. 644-656
    • Megraw, M.1
  • 70
    • 77649246145 scopus 로고    scopus 로고
    • Histone modification levels are predictive for gene expression
    • Karlic R., et al. Histone modification levels are predictive for gene expression. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:2926-2931.
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 2926-2931
    • Karlic, R.1
  • 71
    • 79952696158 scopus 로고    scopus 로고
    • A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets
    • Cheng C., et al. A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Genome Biol. 2011, 12:R15.
    • (2011) Genome Biol. , vol.12
    • Cheng, C.1
  • 72
    • 76249101323 scopus 로고    scopus 로고
    • PML-RARalpha/RXR alters the epigenetic landscape in acute promyelocytic leukemia
    • Martens J.H., et al. PML-RARalpha/RXR alters the epigenetic landscape in acute promyelocytic leukemia. Cancer Cell 2010, 17:173-185.
    • (2010) Cancer Cell , vol.17 , pp. 173-185
    • Martens, J.H.1
  • 73
    • 29644441714 scopus 로고    scopus 로고
    • NF-kappaB and activator protein 1 response elements and the role of histone modifications in IL-1beta-induced TGF-beta1 gene transcription
    • Lee K.Y., et al. NF-kappaB and activator protein 1 response elements and the role of histone modifications in IL-1beta-induced TGF-beta1 gene transcription. J. Immunol. 2006, 176:603-615.
    • (2006) J. Immunol. , vol.176 , pp. 603-615
    • Lee, K.Y.1
  • 74
    • 77951116072 scopus 로고    scopus 로고
    • CpG islands influence chromatin structure via the CpG-binding protein Cfp1
    • Thomson J.P., et al. CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 2010, 464:1082-1086.
    • (2010) Nature , vol.464 , pp. 1082-1086
    • Thomson, J.P.1
  • 75
    • 29244438472 scopus 로고    scopus 로고
    • CpG-binding protein (CXXC finger protein 1) is a component of the mammalian Set1 histone H3-Lys4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex
    • Lee J.-H., Skalnik D.G. CpG-binding protein (CXXC finger protein 1) is a component of the mammalian Set1 histone H3-Lys4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex. J. Biol. Chem. 2005, 280:41725-41731.
    • (2005) J. Biol. Chem. , vol.280 , pp. 41725-41731
    • Lee, J.-H.1    Skalnik, D.G.2
  • 76
    • 34848911602 scopus 로고    scopus 로고
    • Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4
    • Vermeulen M., et al. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 2007, 131:58-69.
    • (2007) Cell , vol.131 , pp. 58-69
    • Vermeulen, M.1
  • 77
    • 77951920690 scopus 로고    scopus 로고
    • C-Myc regulates transcriptional pause release
    • Rahl P.B., et al. c-Myc regulates transcriptional pause release. Cell 2010, 141:432-445.
    • (2010) Cell , vol.141 , pp. 432-445
    • Rahl, P.B.1
  • 78
    • 77950866717 scopus 로고    scopus 로고
    • Chromatin signature of embryonic pluripotency is established during genome activation
    • Vastenhouw N.L., et al. Chromatin signature of embryonic pluripotency is established during genome activation. Nature 2010, 1-7.
    • (2010) Nature , pp. 1-7
    • Vastenhouw, N.L.1
  • 79
    • 38949212693 scopus 로고    scopus 로고
    • A novel CpG island set identifies tissue-specific methylation at developmental gene loci
    • Illingworth R., et al. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 2008, 6:e22.
    • (2008) PLoS Biol. , vol.6
    • Illingworth, R.1
  • 80
    • 0036532202 scopus 로고    scopus 로고
    • Histone methylation in transcriptional control
    • Kouzarides T. Histone methylation in transcriptional control. Curr. Opin. Genet. Dev. 2002, 12:198-209.
    • (2002) Curr. Opin. Genet. Dev. , vol.12 , pp. 198-209
    • Kouzarides, T.1
  • 81
    • 0027378582 scopus 로고
    • Role for DNA methylation in genomic imprinting
    • Li E., et al. Role for DNA methylation in genomic imprinting. Nature 1993, 366:362-365.
    • (1993) Nature , vol.366 , pp. 362-365
    • Li, E.1
  • 82
    • 43749098985 scopus 로고    scopus 로고
    • DNA methylation landscapes: provocative insights from epigenomics
    • Suzuki M.M., Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet. 2008, 9:465.
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 465
    • Suzuki, M.M.1    Bird, A.2
  • 83
    • 67649648237 scopus 로고    scopus 로고
    • Control of inducible gene expression by signal-dependent transcriptional elongation
    • Hargreaves D.C., et al. Control of inducible gene expression by signal-dependent transcriptional elongation. Cell 2009, 138:129-145.
    • (2009) Cell , vol.138 , pp. 129-145
    • Hargreaves, D.C.1
  • 84
    • 74049118051 scopus 로고    scopus 로고
    • Insights into distinct regulatory modes of nucleosome positioning
    • Dai Z., et al. Insights into distinct regulatory modes of nucleosome positioning. BMC Genomics 2009, 10:602.
    • (2009) BMC Genomics , vol.10 , pp. 602
    • Dai, Z.1
  • 85
    • 0037191755 scopus 로고    scopus 로고
    • TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila
    • Hochheimer A., et al. TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila. Nature 2002, 420:439-445.
    • (2002) Nature , vol.420 , pp. 439-445
    • Hochheimer, A.1
  • 86
    • 80052458531 scopus 로고    scopus 로고
    • Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes
    • Valen E., et al. Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes. Nat. Struct. Mol. Biol. 2011, 10.1038/nsmb.2091.
    • (2011) Nat. Struct. Mol. Biol.
    • Valen, E.1
  • 87
    • 77954355150 scopus 로고    scopus 로고
    • Three key subregions contribute to the function of the downstream RNA polymerase II core promoter
    • Theisen J.W., et al. Three key subregions contribute to the function of the downstream RNA polymerase II core promoter. Mol. Cell. Biol. 2010, 30:3471-3479.
    • (2010) Mol. Cell. Biol. , vol.30 , pp. 3471-3479
    • Theisen, J.W.1
  • 88
    • 84988044467 scopus 로고    scopus 로고
    • CAGE: cap analysis of gene expression
    • Kodzius R., et al. CAGE: cap analysis of gene expression. Nat. Methods 2006, 3:211-222.
    • (2006) Nat. Methods , vol.3 , pp. 211-222
    • Kodzius, R.1
  • 89
    • 0034991911 scopus 로고    scopus 로고
    • Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites
    • Suzuki Y., et al. Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep. 2001, 2:388-393.
    • (2001) EMBO Rep. , vol.2 , pp. 388-393
    • Suzuki, Y.1
  • 90
    • 44649193565 scopus 로고    scopus 로고
    • The RNA polymerase II core promoter - the gateway to transcription
    • Juven-Gershon T., et al. The RNA polymerase II core promoter - the gateway to transcription. Curr. Opin. Cell Biol. 2008, 20:253-259.
    • (2008) Curr. Opin. Cell Biol. , vol.20 , pp. 253-259
    • Juven-Gershon, T.1
  • 91
    • 1842584947 scopus 로고    scopus 로고
    • Applied bioinformatics for the identification of regulatory elements
    • Wasserman W.W., Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet. 2004, 5:276-287.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 276-287
    • Wasserman, W.W.1    Sandelin, A.2
  • 92
    • 1842505125 scopus 로고    scopus 로고
    • Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics
    • Sandelin A., Wasserman W.W. Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J. Mol. Biol. 2004, 338:207-215.
    • (2004) J. Mol. Biol. , vol.338 , pp. 207-215
    • Sandelin, A.1    Wasserman, W.W.2
  • 93
    • 40649113925 scopus 로고    scopus 로고
    • The genome landscape of ERalpha- and ERbeta-binding DNA regions
    • Liu Y., et al. The genome landscape of ERalpha- and ERbeta-binding DNA regions. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:2604-2609.
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 2604-2609
    • Liu, Y.1
  • 94
    • 77949874234 scopus 로고    scopus 로고
    • Histone variants - ancient wrap artists of the epigenome
    • Talbert P., Henikoff S. Histone variants - ancient wrap artists of the epigenome. Nat. Rev. Mol. Cell Biol. 2010, 11:264-275.
    • (2010) Nat. Rev. Mol. Cell Biol. , vol.11 , pp. 264-275
    • Talbert, P.1    Henikoff, S.2
  • 95
    • 17044394787 scopus 로고    scopus 로고
    • Transcriptional activation triggers deposition and removal of the histone variant H3.3
    • Schwartz B.E., Ahmad K. Transcriptional activation triggers deposition and removal of the histone variant H3.3. Genes Dev. 2005, 19:804-814.
    • (2005) Genes Dev. , vol.19 , pp. 804-814
    • Schwartz, B.E.1    Ahmad, K.2
  • 96
    • 63049103410 scopus 로고    scopus 로고
    • Dynamic histone variant exchange accompanies gene induction in T cells
    • Sutcliffe E., et al. Dynamic histone variant exchange accompanies gene induction in T cells. Mol. Cell. Biol. 2009, 29:1972.
    • (2009) Mol. Cell. Biol. , vol.29 , pp. 1972
    • Sutcliffe, E.1
  • 97
    • 0035725036 scopus 로고    scopus 로고
    • H2A.Z. is required for global chromatin integrity and for recruitment of RNA polymerase II under specific conditions
    • Adam M., et al. H2A.Z. is required for global chromatin integrity and for recruitment of RNA polymerase II under specific conditions. Mol. Cell. Biol. 2001, 21:6270.
    • (2001) Mol. Cell. Biol. , vol.21 , pp. 6270
    • Adam, M.1
  • 98
    • 68149150830 scopus 로고    scopus 로고
    • H3.3/H2A.Z. double variant-containing nucleosomes mark nucleosome-free regions of active promoters and other regulatory regions
    • Jin C., et al. H3.3/H2A.Z. double variant-containing nucleosomes mark nucleosome-free regions of active promoters and other regulatory regions. Nat. Genet. 2009, 41:941-945.
    • (2009) Nat. Genet. , vol.41 , pp. 941-945
    • Jin, C.1
  • 99
    • 0020489781 scopus 로고
    • Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells
    • Ehrlich M., et al. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res. 1982, 10:2709-2721.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 2709-2721
    • Ehrlich, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.