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Volumn 513, Issue , 2012, Pages 297-313

Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology

Author keywords

ChIP seq; Histone modifications; Next generation sequencing; Nucleosome occupancy; RNA seq

Indexed keywords

COMPLEMENTARY DNA; DOUBLE STRANDED DNA; HISTONE; MESSENGER RNA;

EID: 84865508655     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-391938-0.00013-6     Document Type: Chapter
Times cited : (23)

References (40)
  • 1
    • 67349169780 scopus 로고    scopus 로고
    • Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8 + T cells
    • Y. Araki, Z. Wang, C. Zang, W.H. Wood 3rd, D. Schones, and K. Cui Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8 + T cells Immunity 30 2009 912 925
    • (2009) Immunity , vol.30 , pp. 912-925
    • Araki, Y.1    Wang, Z.2    Zang, C.3    Wood III, W.H.4    Schones, D.5    Cui, K.6
  • 2
    • 34249026300 scopus 로고    scopus 로고
    • High-resolution profiling of histone methylations in the human genome
    • A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, and Z. Wang High-resolution profiling of histone methylations in the human genome Cell 129 2007 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    Wang, Z.6
  • 3
    • 33646070846 scopus 로고    scopus 로고
    • A bivalent chromatin structure marks key developmental genes in embryonic stem cells
    • B.E. Bernstein, T.S. Mikkelsen, X. Xie, M. Kamal, D.J. Huebert, and J. Cuff A bivalent chromatin structure marks key developmental genes in embryonic stem cells Cell 125 2006 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    Cuff, J.6
  • 4
    • 33646882068 scopus 로고    scopus 로고
    • Polycomb complexes repress developmental regulators in murine embryonic stem cells
    • L.A. Boyer, K. Plath, J. Zeitlinger, T. Brambrink, L.A. Medeiros, and T.I. Lee Polycomb complexes repress developmental regulators in murine embryonic stem cells Nature 441 2006 349 353
    • (2006) Nature , vol.441 , pp. 349-353
    • Boyer, L.A.1    Plath, K.2    Zeitlinger, J.3    Brambrink, T.4    Medeiros, L.A.5    Lee, T.I.6
  • 5
    • 77249117360 scopus 로고    scopus 로고
    • Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq
    • I. Chepelev, G. Wei, Q. Tang, and K. Zhao Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq Nucleic Acids Research 37 2009 e106
    • (2009) Nucleic Acids Research , vol.37 , pp. 106
    • Chepelev, I.1    Wei, G.2    Tang, Q.3    Zhao, K.4
  • 7
    • 58049191558 scopus 로고    scopus 로고
    • Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation
    • K. Cui, C. Zang, T.Y. Roh, D.E. Schones, R.W. Childs, and W. Peng Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation Cell Stem Cell 4 2009 80 93
    • (2009) Cell Stem Cell , vol.4 , pp. 80-93
    • Cui, K.1    Zang, C.2    Roh, T.Y.3    Schones, D.E.4    Childs, R.W.5    Peng, W.6
  • 9
    • 79960434317 scopus 로고    scopus 로고
    • NucleR: A package for non-parametric nucleosome positioning
    • O. Flores, and M. Orozco nucleR: A package for non-parametric nucleosome positioning Bioinformatics (Oxford, England) 27 2011 2149 2150
    • (2011) Bioinformatics (Oxford, England) , vol.27 , pp. 2149-2150
    • Flores, O.1    Orozco, M.2
  • 11
    • 2942746179 scopus 로고    scopus 로고
    • Histone variants, nucleosome assembly and epigenetic inheritance
    • S. Henikoff, T. Furuyama, and K. Ahmad Histone variants, nucleosome assembly and epigenetic inheritance Trends in Genetics 20 2004 320 326
    • (2004) Trends in Genetics , vol.20 , pp. 320-326
    • Henikoff, S.1    Furuyama, T.2    Ahmad, K.3
  • 12
    • 80053501181 scopus 로고    scopus 로고
    • Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1
    • G. Hu, D.E. Schones, K. Cui, R. Ybarra, D. Northrup, and Q. Tang Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1 Genome Research 21 2011 1650 1658
    • (2011) Genome Research , vol.21 , pp. 1650-1658
    • Hu, G.1    Schones, D.E.2    Cui, K.3    Ybarra, R.4    Northrup, D.5    Tang, Q.6
  • 13
    • 80052976954 scopus 로고    scopus 로고
    • ChIP-Seq: Technical considerations for obtaining high-quality data
    • B.L. Kidder, G. Hu, and K. Zhao ChIP-Seq: Technical considerations for obtaining high-quality data Nature Immunology 12 2011 918 922
    • (2011) Nature Immunology , vol.12 , pp. 918-922
    • Kidder, B.L.1    Hu, G.2    Zhao, K.3
  • 15
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biology 10 2009 R25
    • (2009) Genome Biology , vol.10 , pp. 25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 16
    • 79551494866 scopus 로고    scopus 로고
    • Accurate quantification of transcriptome from RNA-Seq data by effective length normalization
    • S. Lee, C.H. Seo, B. Lim, J.O. Yang, J. Oh, and M. Kim Accurate quantification of transcriptome from RNA-Seq data by effective length normalization Nucleic Acids Research 39 2011 e9
    • (2011) Nucleic Acids Research , vol.39 , pp. 9
    • Lee, S.1    Seo, C.H.2    Lim, B.3    Yang, J.O.4    Oh, J.5    Kim, M.6
  • 18
    • 34547624303 scopus 로고    scopus 로고
    • Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    • T.S. Mikkelsen, M. Ku, D.B. Jaffe, B. Issac, E. Lieberman, and G. Giannoukos Genome-wide maps of chromatin state in pluripotent and lineage-committed cells Nature 448 2007 553 560
    • (2007) Nature , vol.448 , pp. 553-560
    • Mikkelsen, T.S.1    Ku, M.2    Jaffe, D.B.3    Issac, B.4    Lieberman, E.5    Giannoukos, G.6
  • 20
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • U. Nagalakshmi, Z. Wang, K. Waern, C. Shou, D. Raha, and M. Gerstein The transcriptional landscape of the yeast genome defined by RNA sequencing Science 320 2008 1344 1349
    • (2008) Science , vol.320 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6
  • 21
    • 65649126066 scopus 로고    scopus 로고
    • Transcript length bias in RNA-seq data confounds systems biology
    • A. Oshlack, and M.J. Wakefield Transcript length bias in RNA-seq data confounds systems biology Biology Direct 4 2009 14
    • (2009) Biology Direct , vol.4 , pp. 14
    • Oshlack, A.1    Wakefield, M.J.2
  • 23
    • 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
    • N.U. Rashid, P.G. Giresi, J.G. Ibrahim, W. Sun, and J.D. Lieb ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions Genome Biology 12 2011 R67
    • (2011) Genome Biology , vol.12 , pp. 67
    • Rashid, N.U.1    Giresi, P.G.2    Ibrahim, J.G.3    Sun, W.4    Lieb, J.D.5
  • 25
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
    • M.D. Robinson, D.J. McCarthy, and G.K. Smyth edgeR: A Bioconductor package for differential expression analysis of digital gene expression data Bioinformatics (Oxford, England) 26 2010 139 140
    • (2010) Bioinformatics (Oxford, England) , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 27
  • 28
    • 80054693934 scopus 로고    scopus 로고
    • Genome-wide "re"-modeling of nucleosome positions
    • R. Sadeh, and C.D. Allis Genome-wide "re"-modeling of nucleosome positions Cell 147 2011 263 266
    • (2011) Cell , vol.147 , pp. 263-266
    • Sadeh, R.1    Allis, C.D.2
  • 29
    • 39749145198 scopus 로고    scopus 로고
    • Dynamic regulation of nucleosome positioning in the human genome
    • D.E. Schones, K. Cui, S. Cuddapah, T.Y. Roh, A. Barski, and Z. Wang Dynamic regulation of nucleosome positioning in the human genome Cell 132 2008 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    Wang, Z.6
  • 30
    • 47649124124 scopus 로고    scopus 로고
    • A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
    • M. Sultan, M.H. Schulz, H. Richard, A. Magen, A. Klingenhoff, and M. Scherf A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome Science 321 2008 956 960
    • (2008) Science , vol.321 , pp. 956-960
    • Sultan, M.1    Schulz, M.H.2    Richard, H.3    Magen, A.4    Klingenhoff, A.5    Scherf, M.6
  • 32
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, and M.J. van Baren Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nature Biotechnology 28 2010 511 515
    • (2010) Nature Biotechnology , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    Van Baren, M.J.6
  • 34
    • 75249095274 scopus 로고    scopus 로고
    • DEGseq: An R package for identifying differentially expressed genes from RNA-seq data
    • L. Wang, Z. Feng, X. Wang, X. Wang, and X. Zhang DEGseq: An R package for identifying differentially expressed genes from RNA-seq data Bioinformatics (Oxford, England) 26 2010 136 138
    • (2010) Bioinformatics (Oxford, England) , vol.26 , pp. 136-138
    • Wang, L.1    Feng, Z.2    Wang, X.3    Wang, X.4    Zhang, X.5
  • 36
  • 37
    • 58149214356 scopus 로고    scopus 로고
    • Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4 + T cells
    • G. Wei, L. Wei, J. Zhu, C. Zang, J. Hu-Li, and Z. Yao Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4 + T cells Immunity 30 2009 155 167
    • (2009) Immunity , vol.30 , pp. 155-167
    • Wei, G.1    Wei, L.2    Zhu, J.3    Zang, C.4    Hu-Li, J.5    Yao, Z.6
  • 38
  • 39
    • 57449095143 scopus 로고    scopus 로고
    • Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq
    • Y. Zhang, H. Shin, J.S. Song, Y. Lei, and X.S. Liu Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq BMC Genomics 9 2008 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
  • 40
    • 79960557820 scopus 로고    scopus 로고
    • Bias detection and correction in RNA-Sequencing data
    • W. Zheng, L.M. Chung, and H. Zhao Bias detection and correction in RNA-Sequencing data BMC Bioinformatics 12 2011 290
    • (2011) BMC Bioinformatics , vol.12 , pp. 290
    • Zheng, W.1    Chung, L.M.2    Zhao, H.3


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