메뉴 건너뛰기




Volumn 103, Issue 2-3, 2014, Pages 222-228

H3K4me2 reliably defines transcription factor binding regions in different cells

Author keywords

ChIP seq; H3K4me2; Histone modification; Transcription factor binding regions

Indexed keywords

HISTONE; HISTONE H2AZ; HISTONE H3K27AC; HISTONE H3K27ME3; HISTONE H3K36ME3; HISTONE H3K4ME1; HISTONE H3K4ME2; HISTONE H3K9ME3; HISTONE H4K20ME1; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

EID: 84898021970     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2014.02.002     Document Type: Article
Times cited : (73)

References (45)
  • 1
    • 79959359483 scopus 로고    scopus 로고
    • Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4
    • Zhou X., O'Shea E.K. Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4. Mol. Cell 2011, 42:826-836.
    • (2011) Mol. Cell , vol.42 , pp. 826-836
    • Zhou, X.1    O'Shea, E.K.2
  • 2
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: representation and discovery
    • Stormo G.D. DNA binding sites: representation and discovery. Bioinformatics 2000, 16:16-23.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 3
    • 0030986188 scopus 로고    scopus 로고
    • The hardwiring of development: organization and function of genomic regulatory systems
    • Arnone M.I., Davidson E.H. The hardwiring of development: organization and function of genomic regulatory systems. Development 1997, 124:1851-1864.
    • (1997) Development , vol.124 , pp. 1851-1864
    • Arnone, M.I.1    Davidson, E.H.2
  • 4
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • Johnson D.S., Mortazavi A., Myers R.M., et al. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007, 316:1497-1502.
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3
  • 5
    • 34547633677 scopus 로고    scopus 로고
    • Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
    • Robertson G., Hirst M., Bainbridge M., et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 2007, 4:651-657.
    • (2007) Nat. Methods , vol.4 , pp. 651-657
    • Robertson, G.1    Hirst, M.2    Bainbridge, M.3
  • 6
    • 75949114262 scopus 로고    scopus 로고
    • W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data
    • Jin V.X., Apostolos J., Nagisetty N.S., et al. W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data. Bioinformatics 2009, 25:3191-3193.
    • (2009) Bioinformatics , vol.25 , pp. 3191-3193
    • Jin, V.X.1    Apostolos, J.2    Nagisetty, N.S.3
  • 7
    • 79958090979 scopus 로고    scopus 로고
    • DREME: motif discovery in transcription factor ChIP-seq data
    • Bailey T.L. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 2011, 27:1653-1659.
    • (2011) Bioinformatics , vol.27 , pp. 1653-1659
    • Bailey, T.L.1
  • 8
    • 77949916244 scopus 로고    scopus 로고
    • On the detection and refinement of transcription factor binding sites using ChIP-Seq data
    • Hu M., Yu J., Taylor J.M., et al. On the detection and refinement of transcription factor binding sites using ChIP-Seq data. Nucleic Acids Res. 2009, 38:2154-2167.
    • (2009) Nucleic Acids Res. , vol.38 , pp. 2154-2167
    • Hu, M.1    Yu, J.2    Taylor, J.M.3
  • 9
    • 77957802676 scopus 로고    scopus 로고
    • Systematic identification of conserved motif modules in the human genome
    • Cai X., Hou L., Su N., et al. Systematic identification of conserved motif modules in the human genome. BMC Genomics 2010, 11:567.
    • (2010) BMC Genomics , vol.11 , pp. 567
    • Cai, X.1    Hou, L.2    Su, N.3
  • 10
    • 84891390878 scopus 로고    scopus 로고
    • Chipmodule: systematic discovery of transcription factors and their cofactors from chip-seq data
    • Ding J., Cai X., Wang Y., et al. Chipmodule: systematic discovery of transcription factors and their cofactors from chip-seq data. Pac. Symp. Biocomput. 2013, 320-331.
    • (2013) Pac. Symp. Biocomput. , pp. 320-331
    • Ding, J.1    Cai, X.2    Wang, Y.3
  • 11
    • 77957818564 scopus 로고    scopus 로고
    • Deep and wide digging for binding motifs in ChIP-Seq data
    • Kulakovskiy I.V., Boeva V.A., Favorov A.V., et al. Deep and wide digging for binding motifs in ChIP-Seq data. Bioinformatics 2010, 26:2622-2623.
    • (2010) Bioinformatics , vol.26 , pp. 2622-2623
    • Kulakovskiy, I.V.1    Boeva, V.A.2    Favorov, A.V.3
  • 12
  • 13
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Dunham I., Kundaje A., Aldred S.F., et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.
    • (2012) Nature , vol.489 , pp. 57-74
    • Dunham, I.1    Kundaje, A.2    Aldred, S.F.3
  • 14
    • 84865859048 scopus 로고    scopus 로고
    • What does our genome encode?
    • Stamatoyannopoulos J.A. What does our genome encode?. Genome Res. 2012, 22:1602-1611.
    • (2012) Genome Res. , vol.22 , pp. 1602-1611
    • Stamatoyannopoulos, J.A.1
  • 15
    • 33847334699 scopus 로고    scopus 로고
    • Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
    • Heintzman N.D., Stuart R.K., Hon G., et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 2007, 39:311-318.
    • (2007) Nat. Genet. , vol.39 , pp. 311-318
    • Heintzman, N.D.1    Stuart, R.K.2    Hon, G.3
  • 16
    • 84857781464 scopus 로고    scopus 로고
    • Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization
    • Chepelev I., Wei G., Wangsa D., et al. Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization. Cell Res. 2012, 22:490-503.
    • (2012) Cell Res. , vol.22 , pp. 490-503
    • Chepelev, I.1    Wei, G.2    Wangsa, D.3
  • 17
    • 34249026300 scopus 로고    scopus 로고
    • High-resolution profiling of histone methylations in the human genome
    • Barski A., Cuddapah S., Cui K., et al. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129:823-837.
    • (2007) Cell , vol.129 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3
  • 18
    • 78650758676 scopus 로고    scopus 로고
    • Histone H3K27ac separates active from poised enhancers and predicts developmental state
    • Creyghton M.P., Cheng A.W., Welstead G.G., et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl. Acad. Sci. 2010, 107:21931-21936.
    • (2010) Proc. Natl. Acad. Sci. , vol.107 , pp. 21931-21936
    • Creyghton, M.P.1    Cheng, A.W.2    Welstead, G.G.3
  • 19
    • 79951516056 scopus 로고    scopus 로고
    • A unique chromatin signature uncovers early developmental enhancers in humans
    • Rada-Iglesias A., Bajpai R., Swigut T., et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 2010, 470:279-283.
    • (2010) Nature , vol.470 , pp. 279-283
    • Rada-Iglesias, A.1    Bajpai, R.2    Swigut, T.3
  • 21
    • 84865856641 scopus 로고    scopus 로고
    • Sequence and chromatin determinants of cell-type-specific transcription factor binding
    • Arvey A., Agius P., Noble W.S., et al. Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Res. 2012, 22:1723-1734.
    • (2012) Genome Res. , vol.22 , pp. 1723-1734
    • Arvey, A.1    Agius, P.2    Noble, W.S.3
  • 22
    • 84865777820 scopus 로고    scopus 로고
    • Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
    • Kundaje A., Kyriazopoulou-Panagiotopoulou S., Libbrecht M., et al. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res. 2012, 22:1735-1747.
    • (2012) Genome Res. , vol.22 , pp. 1735-1747
    • Kundaje, A.1    Kyriazopoulou-Panagiotopoulou, S.2    Libbrecht, M.3
  • 23
    • 84865852567 scopus 로고    scopus 로고
    • Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
    • Wang J., Zhuang J., Iyer S., et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012, 22:1798-1812.
    • (2012) Genome Res. , vol.22 , pp. 1798-1812
    • Wang, J.1    Zhuang, J.2    Iyer, S.3
  • 24
    • 84865739425 scopus 로고    scopus 로고
    • Architecture of the human regulatory network derived from ENCODE data
    • Gerstein M.B., Kundaje A., Hariharan M., et al. Architecture of the human regulatory network derived from ENCODE data. Nature 2012, 489:91-100.
    • (2012) Nature , vol.489 , pp. 91-100
    • Gerstein, M.B.1    Kundaje, A.2    Hariharan, M.3
  • 25
    • 55749094855 scopus 로고    scopus 로고
    • An integrated software system for analyzing ChIP-chip and ChIP-seq data
    • Ji H., Jiang H., Ma W., et al. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol. 2008, 26:1293-1300.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1293-1300
    • Ji, H.1    Jiang, H.2    Ma, W.3
  • 26
    • 53849146020 scopus 로고    scopus 로고
    • Model-based analysis of ChIP-Seq (MACS)
    • Zhang Y., Liu T., Meyer C.A., et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008, 9:R137.
    • (2008) Genome Biol. , vol.9
    • Zhang, Y.1    Liu, T.2    Meyer, C.A.3
  • 27
    • 0029960055 scopus 로고    scopus 로고
    • TRANSFAC: a database on transcription factors and their DNA binding sites
    • Wingender E., Dietze P., Karas H., et al. TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res. 1996, 24:238-241.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 238-241
    • Wingender, E.1    Dietze, P.2    Karas, H.3
  • 28
    • 79952598545 scopus 로고    scopus 로고
    • Identifying dispersed epigenomic domains from ChIP-Seq data
    • Song Q., Smith A.D. Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics 2011, 27:870-871.
    • (2011) Bioinformatics , vol.27 , pp. 870-871
    • Song, Q.1    Smith, A.D.2
  • 29
    • 67650711619 scopus 로고    scopus 로고
    • A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
    • Zang C., Schones D.E., Zeng C., et al. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 2009, 25:1952-1958.
    • (2009) Bioinformatics , vol.25 , pp. 1952-1958
    • Zang, C.1    Schones, D.E.2    Zeng, C.3
  • 30
    • 34250369627 scopus 로고    scopus 로고
    • FAIRE (formaldehyde-assisted isolation of regulatory elements) isolates active regulatory elements from human chromatin
    • Giresi P.G., Kim J., McDaniell R.M., et al. FAIRE (formaldehyde-assisted isolation of regulatory elements) isolates active regulatory elements from human chromatin. Genome Res. 2007, 17:877-885.
    • (2007) Genome Res. , vol.17 , pp. 877-885
    • Giresi, P.G.1    Kim, J.2    McDaniell, R.M.3
  • 31
    • 84865822182 scopus 로고    scopus 로고
    • Systematic localization of common disease-associated variation in regulatory DNA
    • Maurano M.T., Humbert R., Rynes E., et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 2012, 337:1190-1195.
    • (2012) Science , vol.337 , pp. 1190-1195
    • Maurano, M.T.1    Humbert, R.2    Rynes, E.3
  • 32
    • 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 L.L., et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 2011, 21:1757-1767.
    • (2011) Genome Res. , vol.21 , pp. 1757-1767
    • Song, L.1    Zhang, Z.2    Grasfeder, L.L.3
  • 33
    • 33745152719 scopus 로고    scopus 로고
    • Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression
    • Blanchette M., Bataille A.R., Chen X., et al. Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res. 2006, 16:656-668.
    • (2006) Genome Res. , vol.16 , pp. 656-668
    • Blanchette, M.1    Bataille, A.R.2    Chen, X.3
  • 34
    • 0001884644 scopus 로고
    • Individual comparisons by ranking methods
    • Wilcoxon F. Individual comparisons by ranking methods. Biom. Bull. 1945, 1:80-83.
    • (1945) Biom. Bull. , vol.1 , pp. 80-83
    • Wilcoxon, F.1
  • 35
    • 47049092561 scopus 로고    scopus 로고
    • Selective binding of sterol regulatory element-binding protein isoforms and co-regulatory proteins to promoters for lipid metabolic genes in liver
    • Bennett M.K., Seo Y.-K., Datta S., et al. Selective binding of sterol regulatory element-binding protein isoforms and co-regulatory proteins to promoters for lipid metabolic genes in liver. J. Biol. Chem. 2008, 283:15628-15637.
    • (2008) J. Biol. Chem. , vol.283 , pp. 15628-15637
    • Bennett, M.K.1    Seo, Y.-K.2    Datta, S.3
  • 36
    • 84856471735 scopus 로고    scopus 로고
    • SREBPs: metabolic integrators in physiology and metabolism
    • Jeon T.-I., Osborne T.F. SREBPs: metabolic integrators in physiology and metabolism. Trends Endocrinol. Metab. 2012, 23:65-72.
    • (2012) Trends Endocrinol. Metab. , vol.23 , pp. 65-72
    • Jeon, T.-I.1    Osborne, T.F.2
  • 37
    • 79960642153 scopus 로고    scopus 로고
    • Integrated expression profiling and genome-wide analysis of ChREBP targets reveals the dual role for ChREBP in glucose-regulated gene expression
    • Jeong Y.-S., Kim D., Lee Y.S., et al. Integrated expression profiling and genome-wide analysis of ChREBP targets reveals the dual role for ChREBP in glucose-regulated gene expression. PLoS One 2011, 6:e22544.
    • (2011) PLoS One , vol.6
    • Jeong, Y.-S.1    Kim, D.2    Lee, Y.S.3
  • 38
    • 84857707318 scopus 로고    scopus 로고
    • ChromHMM: automating chromatin-state discovery and characterization
    • Ernst J., Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods 2012, 9:215-216.
    • (2012) Nat. Methods , vol.9 , pp. 215-216
    • Ernst, J.1    Kellis, M.2
  • 39
    • 84862785201 scopus 로고    scopus 로고
    • Unsupervised pattern discovery in human chromatin structure through genomic segmentation
    • Hoffman M.M., Buske O.J., Wang J., et al. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat. Methods 2012, 9:473-476.
    • (2012) Nat. Methods , vol.9 , pp. 473-476
    • Hoffman, M.M.1    Buske, O.J.2    Wang, J.3
  • 40
    • 84864462544 scopus 로고    scopus 로고
    • A map of the cis-regulatory sequences in the mouse genome
    • Shen Y., Yue F., McCleary D.F., et al. A map of the cis-regulatory sequences in the mouse genome. Nature 2012, 488:116-120.
    • (2012) Nature , vol.488 , pp. 116-120
    • Shen, Y.1    Yue, F.2    McCleary, D.F.3
  • 41
    • 0036079158 scopus 로고    scopus 로고
    • The human genome browser at UCSC
    • Kent W.J., Sugnet C.W., Furey T.S., et al. The human genome browser at UCSC. Genome Res. 2002, 12:996-1006.
    • (2002) Genome Res. , vol.12 , pp. 996-1006
    • Kent, W.J.1    Sugnet, C.W.2    Furey, T.S.3
  • 42
    • 76249083492 scopus 로고    scopus 로고
    • Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq
    • Motallebipour M., Ameur A., Reddy Bysani M.S., et al. Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq. Genome Biol. 2009, 10:R129.
    • (2009) Genome Biol. , vol.10
    • Motallebipour, M.1    Ameur, A.2    Reddy Bysani, M.S.3
  • 43
    • 48249123867 scopus 로고    scopus 로고
    • Genome-wide occupancy of SREBF1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes
    • Reed B.D., Charos A.E., Szekely A.M., et al. Genome-wide occupancy of SREBF1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PLoS Genet. 2008, 4:e1000133.
    • (2008) PLoS Genet. , vol.4
    • Reed, B.D.1    Charos, A.E.2    Szekely, A.M.3
  • 45
    • 79952266465 scopus 로고    scopus 로고
    • Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    • Pique-Regi R.P., Degner J.F., Pai A.A., Gaffney D.G., Gilad Y., Pritchard J.K. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Research. 2011 Mar, 21(3):447-55.
    • (2011) Genome Research. , vol.21 , Issue.3 , pp. 447-455
    • Pique-Regi, R.P.1    Degner, J.F.2    Pai, A.A.3    Gaffney, D.G.4    Gilad, Y.5    Pritchard, J.K.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.