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Volumn 9, Issue 9, 2013, Pages

Regulation of the Boundaries of Accessible Chromatin

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HISTONE;

EID: 84884691455     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003778     Document Type: Article
Times cited : (14)

References (44)
  • 1
    • 38649099445 scopus 로고    scopus 로고
    • High-resolution mapping and characterization of open chromatin across the genome
    • Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, et al. (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132: 311-322.
    • (2008) Cell , vol.132 , pp. 311-322
    • Boyle, A.P.1    Davis, S.2    Shulha, H.P.3    Meltzer, P.4    Margulies, E.H.5
  • 2
    • 80053539409 scopus 로고    scopus 로고
    • Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
    • Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, et al. (2011) Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res 21: 1757-1767.
    • (2011) Genome Res , vol.21 , pp. 1757-1767
    • Song, L.1    Zhang, Z.2    Grasfeder, L.L.3    Boyle, A.P.4    Giresi, P.G.5
  • 4
    • 63849308888 scopus 로고    scopus 로고
    • Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
    • Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, et al. (2009) Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 6: 283-289.
    • (2009) Nat Methods , vol.6 , pp. 283-289
    • Hesselberth, J.R.1    Chen, X.2    Zhang, Z.3    Sabo, P.J.4    Sandstrom, R.5
  • 5
    • 73249131172 scopus 로고    scopus 로고
    • A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae
    • Berchowitz LE, Hanlon SE, Lieb JD, Copenhaver GP, (2009) A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae. Genome Res 19: 2245-2257.
    • (2009) Genome Res , vol.19 , pp. 2245-2257
    • Berchowitz, L.E.1    Hanlon, S.E.2    Lieb, J.D.3    Copenhaver, G.P.4
  • 6
    • 70350669746 scopus 로고    scopus 로고
    • Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells
    • Audit B, Zaghloul L, Vaillant C, Chevereau G, d'Aubenton-Carafa Y, et al. (2009) Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells. Nucl Acids Res 37: 6064-6075.
    • (2009) Nucl Acids Res , vol.37 , pp. 6064-6075
    • Audit, B.1    Zaghloul, L.2    Vaillant, C.3    Chevereau, G.4    d'Aubenton-Carafa, Y.5
  • 7
    • 0035839136 scopus 로고    scopus 로고
    • Translating the histone code
    • Jenuwein T, Allison CD, (2001) Translating the histone code. Science 293: 1074-1080.
    • (2001) Science , vol.293 , pp. 1074-1080
    • Jenuwein, T.1    Allison, C.D.2
  • 8
    • 33847076849 scopus 로고    scopus 로고
    • Chromatin modifications and their function
    • Kouzarides T, (2007) Chromatin modifications and their function. Cell 128: 693-705.
    • (2007) Cell , vol.128 , pp. 693-705
    • Kouzarides, T.1
  • 9
    • 34249026300 scopus 로고    scopus 로고
    • High-resolution profiling of histone methylations in the human genome
    • Barski A, Cuddapah S, Cui K, Roh T-Y, Schones DE, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
    • (2007) Cell , vol.129 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3    Roh, T.-Y.4    Schones, D.E.5
  • 10
    • 46249112085 scopus 로고    scopus 로고
    • Combinatorial patterns of histone acetylations and methylations in the human genome
    • Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, et al. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40: 897-903.
    • (2008) Nat Genet , vol.40 , pp. 897-903
    • Wang, Z.1    Zang, C.2    Rosenfeld, J.A.3    Schones, D.E.4    Barski, A.5
  • 11
    • 33646070846 scopus 로고    scopus 로고
    • A bivalent chromatin structure marks key developmental genes in embryonic stem cells
    • Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, et al. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315-326.
    • (2006) Cell , vol.125 , pp. 315-326
    • Bernstein, B.E.1    Mikkelsen, T.S.2    Xie, X.3    Kamal, M.4    Huebert, D.J.5
  • 12
    • 65549104157 scopus 로고    scopus 로고
    • Histone modifications at human enhancers reflect global cell-type-specific gene expression
    • Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108-112.
    • (2009) Nature , vol.459 , pp. 108-112
    • Heintzman, N.D.1    Hon, G.C.2    Hawkins, R.D.3    Kheradpour, P.4    Stark, A.5
  • 13
    • 78650758676 scopus 로고    scopus 로고
    • Histone H3K27ac separates active from poised enhancers and predicts developmental state
    • Creyghtona MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, et al. (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci 107: 21931-21936.
    • (2010) Proc Natl Acad Sci , vol.107 , pp. 21931-21936
    • Creyghtona, M.P.1    Cheng, A.W.2    Welstead, G.G.3    Kooistra, T.4    Carey, B.W.5
  • 14
    • 80051564877 scopus 로고    scopus 로고
    • Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions
    • Zentner GE, Tesar PJ, Scacheri1 PC, (2011) Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res 21: 1273-1283.
    • (2011) Genome Res , vol.21 , pp. 1273-1283
    • Zentner, G.E.1    Tesar, P.J.2    Scacheri1, P.C.3
  • 15
    • 84861429489 scopus 로고    scopus 로고
    • Cell-type-specific control of enhancer activity by H3K9 trimethylation
    • Zhu Y, Essen Dv, Saccan S, (2012) Cell-type-specific control of enhancer activity by H3K9 trimethylation. Mol Cell 46: 408-423.
    • (2012) Mol Cell , vol.46 , pp. 408-423
    • Zhu, Y.1    Essen, D.v.2    Saccan, S.3
  • 16
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473: 43-49.
    • (2011) Nature , vol.473 , pp. 43-49
    • Ernst, J.1    Kheradpour, P.2    Mikkelsen, T.S.3    Shoresh, N.4    Ward, L.D.5
  • 17
    • 30044449116 scopus 로고    scopus 로고
    • Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)
    • Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, et al. (2006) Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res 16: 123-131.
    • (2006) Genome Res , vol.16 , pp. 123-131
    • Crawford, G.E.1    Holt, I.E.2    Whittle, J.3    Webb, B.D.4    Tai, D.5
  • 18
    • 33745416080 scopus 로고    scopus 로고
    • Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays
    • Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, et al. (2006) Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods 3: 511-518.
    • (2006) Nat Methods , vol.3 , pp. 511-518
    • Sabo, P.J.1    Kuehn, M.S.2    Thurman, R.3    Johnson, B.E.4    Johnson, E.M.5
  • 19
    • 34250369627 scopus 로고    scopus 로고
    • FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
    • Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD, (2007) FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res 17: 877-885.
    • (2007) Genome Res , vol.17 , pp. 877-885
    • Giresi, P.G.1    Kim, J.2    McDaniell, R.M.3    Iyer, V.R.4    Lieb, J.D.5
  • 20
    • 0037177625 scopus 로고    scopus 로고
    • Genetic dissection of transcriptional regulation in budding yeast
    • Brem RB, Yvert G, Clinton R, Kruglyak L, (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
    • (2002) Science , vol.296 , pp. 752-755
    • Brem, R.B.1    Yvert, G.2    Clinton, R.3    Kruglyak, L.4
  • 21
    • 13444306165 scopus 로고    scopus 로고
    • The landscape of genetic complexity across 5,700 gene expression traits in yeast
    • Brem RB, Kruglyak L, (2005) The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci 102: 1572-1577.
    • (2005) Proc Natl Acad Sci , vol.102 , pp. 1572-1577
    • Brem, R.B.1    Kruglyak, L.2
  • 22
    • 23644434284 scopus 로고    scopus 로고
    • Genetic interactions between polymorphisms that affect gene expression in yeast
    • Brem RB, Storey JD, Whittle J, Kruglyak L, (2005) Genetic interactions between polymorphisms that affect gene expression in yeast. Nature 436: 701-703.
    • (2005) Nature , vol.436 , pp. 701-703
    • Brem, R.B.1    Storey, J.D.2    Whittle, J.3    Kruglyak, L.4
  • 24
    • 79959557189 scopus 로고    scopus 로고
    • Determinants of nucleosome organization in primary human cells
    • Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, et al. (2011) Determinants of nucleosome organization in primary human cells. Nature 474: 516-520.
    • (2011) Nature , vol.474 , pp. 516-520
    • Valouev, A.1    Johnson, S.M.2    Boyd, S.D.3    Smith, C.L.4    Fire, A.Z.5
  • 25
    • 84874764357 scopus 로고    scopus 로고
    • Genetic landscape of open chromatin in yeast
    • Lee K, Kim SC, Jung I, Kim K, Seo J, et al. (2013) Genetic landscape of open chromatin in yeast. PLoS Genet 9: e1003229.
    • (2013) PLoS Genet , vol.9
    • Lee, K.1    Kim, S.C.2    Jung, I.3    Kim, K.4    Seo, J.5
  • 27
    • 39749145198 scopus 로고    scopus 로고
    • Dynamic regulation of nucleosome positioning in the human genome
    • Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, et al. (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-898.
    • (2008) Cell , vol.132 , pp. 887-898
    • Schones, D.E.1    Cui, K.2    Cuddapah, S.3    Roh, T.Y.4    Barski, A.5
  • 28
    • 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, Zang C, Wei G, Cui K, Peng W, et al. (2009) H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat Genet 41: 941-945.
    • (2009) Nat Genet , vol.41 , pp. 941-945
    • Jin, C.1    Zang, C.2    Wei, G.3    Cui, K.4    Peng, W.5
  • 29
    • 79952762476 scopus 로고    scopus 로고
    • Histone H4 Lys 20 monomethylation by histone methylase SET8 mediates Wnt target gene activation
    • Li Z, Nie F, Wang S, Li L, (2010) Histone H4 Lys 20 monomethylation by histone methylase SET8 mediates Wnt target gene activation. Proc Natl Acad Sci 108: 3116-3123.
    • (2010) Proc Natl Acad Sci , vol.108 , pp. 3116-3123
    • Li, Z.1    Nie, F.2    Wang, S.3    Li, L.4
  • 30
    • 73449092184 scopus 로고    scopus 로고
    • Discovery and annotation of functional chromatin signatures in the human genome
    • Hon G, Wang W, Ren B, (2009) Discovery and annotation of functional chromatin signatures in the human genome. PLoS Comput Biol 5: e1000566.
    • (2009) PLoS Comput Biol , vol.5
    • Hon, G.1    Wang, W.2    Ren, B.3
  • 31
    • 2642570305 scopus 로고    scopus 로고
    • The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote
    • Schübeler D, MacAlpine DM, Scalzo D, Wirbelauer C, Kooperberg C, 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.
    • (2004) Genes Dev , vol.18 , pp. 1263-1271
    • Schübeler, D.1    MacAlpine, D.M.2    Scalzo, D.3    Wirbelauer, C.4    Kooperberg, C.5
  • 32
    • 17444375685 scopus 로고    scopus 로고
    • hDOT1L links histone methylation to leukemogenesis
    • Okada Y, Feng Q, Lin Y, Jiang Q, Li Y, et al. (2005) hDOT1L links histone methylation to leukemogenesis. Cell 121: 167-178.
    • (2005) Cell , vol.121 , pp. 167-178
    • Okada, Y.1    Feng, Q.2    Lin, Y.3    Jiang, Q.4    Li, Y.5
  • 33
    • 61349098460 scopus 로고    scopus 로고
    • Differential chromatin marking of introns and expressed exons by H3K36me3
    • Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, et al. (2009) Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 41: 376-381.
    • (2009) Nat Genet , vol.41 , pp. 376-381
    • Kolasinska-Zwierz, P.1    Down, T.2    Latorre, I.3    Liu, T.4    Liu, X.S.5
  • 34
    • 80053217575 scopus 로고    scopus 로고
    • ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity
    • Young MD, Willson TA, Wakefield MJ, Trounson E, Hilton DJ, et al. (2011) ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity. Nucleic Acids Res 39: 7415-7427.
    • (2011) Nucleic Acids Res , vol.39 , pp. 7415-7427
    • Young, M.D.1    Willson, T.A.2    Wakefield, M.J.3    Trounson, E.4    Hilton, D.J.5
  • 35
    • 0034601464 scopus 로고    scopus 로고
    • A chromatin remodelling complex involved in transcription and DNA processing
    • Shen X, Mizuguchi G, Hamiche A, Wu C, (2000) A chromatin remodelling complex involved in transcription and DNA processing. Nature 406: 541-544.
    • (2000) Nature , vol.406 , pp. 541-544
    • Shen, X.1    Mizuguchi, G.2    Hamiche, A.3    Wu, C.4
  • 36
    • 54949147307 scopus 로고    scopus 로고
    • F-Seq: a feature density estimator for high-throughput sequence tags
    • Boyle AP, Guinney J, Crawford GE, Furey TS, (2008) F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 24: 2537-2538.
    • (2008) Bioinformatics , vol.24 , pp. 2537-2538
    • Boyle, A.P.1    Guinney, J.2    Crawford, G.E.3    Furey, T.S.4
  • 37
    • 79960614727 scopus 로고    scopus 로고
    • ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
    • Rashid NU, Giresi PG, Ibrahim JG, Sun W, Lieb JD, (2011) ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome Biol 12: R67.
    • (2011) Genome Biol , vol.12
    • Rashid, N.U.1    Giresi, P.G.2    Ibrahim, J.G.3    Sun, W.4    Lieb, J.D.5
  • 38
    • 57449095143 scopus 로고    scopus 로고
    • Identifying positioned nucleosomes with epigenetic marks in human from ChIP-seq
    • Zhang Y, Shin H, Song JS, Lei Y, Liu XS, (2008) Identifying positioned nucleosomes with epigenetic marks in human from ChIP-seq. BMC Genomics 9: 537.
    • (2008) BMC Genomics , vol.9 , pp. 537
    • Zhang, Y.1    Shin, H.2    Song, J.S.3    Lei, Y.4    Liu, X.S.5
  • 39
    • 43349089437 scopus 로고    scopus 로고
    • GeneTrack-a genomic data processing and visualization framework
    • Albert I, Wachi S, Jiang C, Pugh BF, (2008) GeneTrack-a genomic data processing and visualization framework. Bioinformatics 24: 1305-1306.
    • (2008) Bioinformatics , vol.24 , pp. 1305-1306
    • Albert, I.1    Wachi, S.2    Jiang, C.3    Pugh, B.F.4
  • 40
    • 46449112319 scopus 로고    scopus 로고
    • A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
    • Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, et al. (2008) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 18: 1073-1083.
    • (2008) Genome Res , vol.18 , pp. 1073-1083
    • Mavrich, T.N.1    Ioshikhes, I.P.2    Venters, B.J.3    Jiang, C.4    Tomsho, L.P.5
  • 41
    • 77952567987 scopus 로고    scopus 로고
    • Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    • Heinz S, Benner C, Spann N, Bertolino E, Lin YC, et al. (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38: 576-589.
    • (2010) Mol Cell , vol.38 , pp. 576-589
    • Heinz, S.1    Benner, C.2    Spann, N.3    Bertolino, E.4    Lin, Y.C.5
  • 42
    • 33749037129 scopus 로고    scopus 로고
    • Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification
    • Lee S-I, Pe'er D, Dudley AM, Church GM, Koller D, (2006) Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc Natl Acad Sci 103: 14062-14067.
    • (2006) Proc Natl Acad Sci , vol.103 , pp. 14062-14067
    • Lee, S.-I.1    Pe'er, D.2    Dudley, A.M.3    Church, G.M.4    Koller, D.5
  • 43
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc Ser B 57: 289-300.
    • (1995) J Roy Statist Soc Ser B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 44
    • 60549117986 scopus 로고    scopus 로고
    • Two distinct modes of nucleosome modulation associated with different degrees of dependence of nucleosome positioning on the underlying DNA sequence
    • Dai Z, Dai X, Xiang Q, Feng J, Wang J, et al. (2009) Two distinct modes of nucleosome modulation associated with different degrees of dependence of nucleosome positioning on the underlying DNA sequence. BMC Genomics 10: 15.
    • (2009) BMC Genomics , vol.10 , pp. 15
    • Dai, Z.1    Dai, X.2    Xiang, Q.3    Feng, J.4    Wang, J.5


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