메뉴 건너뛰기




Volumn 368, Issue 1620, 2013, Pages

Effects of gene regulatory reprogramming on gene expression in human and mouse developing hearts

Author keywords

Cis regulatory evolution; Gene regulation; Lineage specific heart enhancers

Indexed keywords

CARDIOVASCULAR DISEASE; GENE EXPRESSION; GENOME; RODENT;

EID: 84891390867     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2012.0366     Document Type: Article
Times cited : (5)

References (35)
  • 1
    • 67249117049 scopus 로고    scopus 로고
    • Potential etiologic and functional implications of genomewide association loci for human diseases and traits
    • (doi:10. 1073/pnas.0903103106)
    • Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. 2009 Potential etiologic and functional implications of genomewide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA 106, 9362-9367.(doi:10. 1073/pnas.0903103106)
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 9362-9367
    • Hindorff, L.A.1    Sethupathy, P.2    Junkins, H.A.3    Ramos, E.M.4    Mehta, J.P.5    Collins, F.S.6    Manolio, T.A.7
  • 2
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • The ENCODE Project Consortium, (doi:10.1038/nature11247)
    • The ENCODE Project Consortium. 2012 An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74.(doi:10.1038/nature11247)
    • (2012) Nature , vol.489 , pp. 57-74
  • 3
    • 84866775366 scopus 로고    scopus 로고
    • Evidence of abundant purifying selection in humans for recently acquired regulatory functions
    • (doi:10.1126/science.1225057)
    • Ward LD, Kellis M. 2012 Evidence of abundant purifying selection in humans for recently acquired regulatory functions. Science 337, 1675-1678.(doi:10.1126/science.1225057)
    • (2012) Science , vol.337 , pp. 1675-1678
    • Ward, L.D.1    Kellis, M.2
  • 4
    • 38849149795 scopus 로고    scopus 로고
    • 2007 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
    • (doi:10. 1101/gr.6761107)
    • Miller W et al. 2007 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 17, 1797-1808.(doi:10. 1101/gr.6761107)
    • Genome Res , vol.17 , pp. 1797-1808
    • Miller, W.1
  • 5
    • 77953062527 scopus 로고    scopus 로고
    • Five vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
    • (doi:10. 1126/science.1186176)
    • Schmidt D et al. 2010 Five vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328, 1036-1040.(doi:10. 1126/science.1186176)
    • (2010) Science , vol.328 , pp. 1036-1040
    • Schmidt, D.1
  • 6
    • 33847057226 scopus 로고    scopus 로고
    • The evolutionary significance of cis-regulatory mutations
    • (doi:10.1038/nrg2063)
    • Wray GA. 2007 The evolutionary significance of cis-regulatory mutations. Nat. Rev. Gen. 8, 206-216.(doi:10.1038/nrg2063)
    • (2007) Nat. Rev. Gen. , vol.8 , pp. 206-216
    • Wray, G.A.1
  • 7
    • 34250358295 scopus 로고    scopus 로고
    • Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
    • (doi:10.1101/gr.5592107)
    • King DC, Taylor J, Zhang Y, Cheng Y, Martin J, ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis, Chiaromonte F, Miller W, Hardison RC. 2007 Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. Genome Res. 17, 775-786.(doi:10.1101/gr.5592107)
    • (2007) Genome Res , vol.17 , pp. 775-786
    • King, D.C.1    Taylor, J.2    Zhang, Y.3    Cheng, Y.4    Martin, J.5
  • 8
    • 0041903634 scopus 로고    scopus 로고
    • Identification of conserved regulatory elements by comparative genome analysis
    • (doi:10.1186/ 1475-4924-2-13)
    • Lenhard B, Sandelin A, Mendoza L, Engstrom P, Jareborg N, Wasserman WW. 2003 Identification of conserved regulatory elements by comparative genome analysis. J. Biol. 2, 13-23.(doi:10.1186/ 1475-4924-2-13)
    • (2003) J. Biol , vol.2 , pp. 13-23
    • Lenhard, B.1    Sandelin, A.2    Mendoza, L.3    Engstrom, P.4    Jareborg, N.5    Wasserman, W.W.6
  • 9
    • 0242418246 scopus 로고    scopus 로고
    • Phylogenetic shadowing of primate sequences to find functional regions of the human genome
    • (doi:10.1126/science. 1081331)
    • Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM. 2003 Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299, 1391-1394.(doi:10.1126/science. 1081331)
    • (2003) Science , vol.299 , pp. 1391-1394
    • Boffelli, D.1    McAuliffe, J.2    Ovcharenko, D.3    Lewis, K.D.4    Ovcharenko, I.5    Pachter, L.6    Rubin, E.M.7
  • 10
    • 33745409293 scopus 로고    scopus 로고
    • DNase-chip: A highresolution method to identify DNase I hypersensitive sites using tiled microarrays
    • (doi:10.1038/ nmeth888)
    • Crawford GE et al. 2006 DNase-chip: a highresolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat. Methods 3, 503-509.(doi:10.1038/ nmeth888)
    • (2006) Nat. Methods , vol.3 , pp. 503-509
    • Crawford, G.E.1
  • 11
    • 34250369627 scopus 로고    scopus 로고
    • FAIRE (formaldehyde-assisted isolation of regulatory elements) isolates active regulatory elements from human chromatin
    • (doi:10.1101/gr.5533506)
    • 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.(doi:10.1101/gr.5533506)
    • (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
  • 12
    • 0035312871 scopus 로고    scopus 로고
    • Transcription factors: Bound to activate or repress
    • (doi:10.1016/S0968-0004(01)01812-6)
    • Latchman DS. 2001 Transcription factors: bound to activate or repress. Trends Biochem. Sci. 26, 211-213.(doi:10.1016/S0968-0004(01)01812-6)
    • (2001) Trends Biochem. Sci , vol.26 , pp. 211-213
    • Latchman, D.S.1
  • 13
    • 0029825698 scopus 로고    scopus 로고
    • Interaction and functional collaboration of p300/CBP and bHLH proteins in muscle and B-cell differentiation
    • (doi:10. 1101/gad.10.19.2478)
    • Eckner R, Yao TP, Oldread E, Livingston DM. 1996 Interaction and functional collaboration of p300/CBP and bHLH proteins in muscle and B-cell differentiation. Genes Dev. 10, 2478-2490.(doi:10. 1101/gad.10.19.2478)
    • (1996) Genes Dev , vol.10 , pp. 2478-2490
    • Eckner, R.1    Yao, T.P.2    Oldread, E.3    Livingston, D.M.4
  • 14
    • 0031604766 scopus 로고    scopus 로고
    • Recruitment of CBP/p300 by the IFNβ enhanceosome is required for synergistic activation of transcription
    • (doi:10. 1016/S1097-2765(00)80028-3)
    • Merika M, Williams AJ, Chen G, Collins T, Thanos D. 1998 Recruitment of CBP/p300 by the IFNβ enhanceosome is required for synergistic activation of transcription. Mol. Cell 1, 277-287.(doi:10. 1016/S1097-2765(00)80028-3)
    • (1998) Mol. Cell , vol.1 , pp. 277-287
    • Merika, M.1    Williams, A.J.2    Chen, G.3    Collins, T.4    Thanos, D.5
  • 15
    • 34249026300 scopus 로고    scopus 로고
    • High-resolution profiling of histone methylations in the human genome
    • (doi:10.1016/j.cell. 2007.05.009)
    • Barski A, Cuddapah S, Cui K, Schones DE, Wang Z, Wei G, Chepelevi I, Zhao K. 2007 High-resolution profiling of histone methylations in the human genome. Cell 129, 823-837.(doi:10.1016/j.cell. 2007.05.009)
    • (2007) Cell , vol.129 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3    Schones, D.E.4    Wang, Z.5    Wei, G.6    Chepelevi, I.7    Zhao, K.8
  • 16
    • 33750352462 scopus 로고    scopus 로고
    • Transcriptional regulatory elements in the human genome
    • (doi:10.1146/ annurev.genom.7.080505.115623)
    • Maston G, Evans S, Green M. 2006 Transcriptional regulatory elements in the human genome. Annu. Rev. Genomics Hum. Genet. 7, 29-59.(doi:10.1146/ annurev.genom.7.080505.115623)
    • (2006) Annu. Rev. Genomics Hum. Genet , vol.7 , pp. 29-59
    • Maston, G.1    Evans, S.2    Green, M.3
  • 17
    • 33847334699 scopus 로고    scopus 로고
    • Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
    • (doi:10.1038/ng1966)
    • Heintzman ND et al. 2007 Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39, 311-318.(doi:10.1038/ng1966)
    • (2007) Nat. Genet , vol.39 , pp. 311-318
    • Heintzman, N.D.1
  • 18
    • 60149091656 scopus 로고    scopus 로고
    • ChIP-seq accurately predicts tissuespecific activity of enhancers
    • (doi:10.1038/nature07730)
    • Visel A et al. 2009 ChIP-seq accurately predicts tissuespecific activity of enhancers. Nature 457, 854-858.(doi:10.1038/nature07730)
    • (2009) Nature , vol.457 , pp. 854-858
    • Visel, A.1
  • 19
    • 77956641239 scopus 로고    scopus 로고
    • ChIP-seq identification of weakly conserved heart enhancers
    • (doi:10.1038/ng.650)
    • Blow MJ et al. 2010 ChIP-seq identification of weakly conserved heart enhancers. Nat. Genet. 42, 806-810.(doi:10.1038/ng.650)
    • (2010) Nat. Genet , vol.42 , pp. 806-810
    • Blow, M.J.1
  • 20
    • 84655164920 scopus 로고    scopus 로고
    • Large-scale discovery of enhancers from human heart tissue
    • (doi:10.1038/ng.1006)
    • May D et al. 2011 Large-scale discovery of enhancers from human heart tissue. Nat. Genet. 44, 89-93.(doi:10.1038/ng.1006)
    • (2011) Nat. Genet , vol.44 , pp. 89-93
    • May, D.1
  • 21
    • 67349122904 scopus 로고    scopus 로고
    • The development and structure of the ventricles in the human heart
    • (doi:10.1007/ s00246-009-9390-9)
    • Henderson DJ, Anderson RH. 2009 The development and structure of the ventricles in the human heart. Pediatr. Cardiol. 30, 588-596.(doi:10.1007/ s00246-009-9390-9)
    • (2009) Pediatr. Cardiol , vol.30 , pp. 588-596
    • Henderson, D.J.1    Anderson, R.H.2
  • 22
    • 33644874573 scopus 로고    scopus 로고
    • The UCSC Genome Browser Database: Update 2006
    • (doi:10.1093/nar/gkj144)
    • Hinrichs AS et al. 2006 The UCSC Genome Browser Database: Update 2006. Nucleic Acids Res. 34, D590-D598.(doi:10.1093/nar/gkj144)
    • (2006) Nucleic Acids Res , vol.34
    • Hinrichs, A.S.1
  • 23
    • 19944430797 scopus 로고    scopus 로고
    • Genomic maps and comparative analysis of histone modifications in human and mouse
    • (doi:10. 1016/j.cell.2005.01.001)
    • Bernstein BE et al. 2005 Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120, 169-181.(doi:10. 1016/j.cell.2005.01.001)
    • (2005) Cell , vol.120 , pp. 169-181
    • Bernstein, B.E.1
  • 24
    • 78650758676 scopus 로고    scopus 로고
    • Histone H3K27ac separates active from poised enhancers and predicts developmental state
    • (doi:10.1073/pnas.1016071107)
    • Creyghton MP et al. 2010 Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107, 21931-21936.(doi:10.1073/pnas.1016071107)
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 21931-21936
    • Creyghton, M.P.1
  • 25
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • (doi:10.1038/nature09906)
    • Ernst J et al. 2011 Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49.(doi:10.1038/nature09906)
    • (2011) Nature , vol.473 , pp. 43-49
    • Ernst, J.1
  • 26
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population-scale sequencing
    • (doi:10.1038/nature09534)
    • Altshuler DL et al. 2010 A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073.(doi:10.1038/nature09534)
    • (2010) Nature , vol.467 , pp. 1061-1073
    • Altshuler, D.L.1
  • 27
    • 78651289449 scopus 로고    scopus 로고
    • Ensembl 2011
    • (doi:10.1093/nar/gkq1064)
    • Flicek P et al. 2010 Ensembl 2011. Nucleic Acids Res. 39, D800-D806.(doi:10.1093/nar/gkq1064)
    • (2010) Nucleic Acids Res , vol.39
    • Flicek, P.1
  • 29
    • 71749120382 scopus 로고    scopus 로고
    • Finding distal regulatory elements in the human genome
    • (doi:10.1016/j.gde. 2009.09.006)
    • Heintzman ND, Ren B. 2009 Finding distal regulatory elements in the human genome. Curr. Opin. Genet. Dev. 19, 541-549.(doi:10.1016/j.gde. 2009.09.006)
    • (2009) Curr. Opin. Genet. Dev , vol.19 , pp. 541-549
    • Heintzman, N.D.1    Ren, B.2
  • 30
    • 77957946016 scopus 로고    scopus 로고
    • Genomics of longrange regulatory elements
    • (doi:10.1146/annurevgenom- 082509-141651)
    • Noonan JP, McCallion AS. 2010 Genomics of longrange regulatory elements. Annu. Rev. Genomics Hum. Genet. 11, 1-23.(doi:10.1146/annurevgenom- 082509-141651)
    • (2010) Annu. Rev. Genomics Hum. Genet , vol.11 , pp. 1-23
    • Noonan, J.P.1    McCallion, A.S.2
  • 31
    • 77957903560 scopus 로고    scopus 로고
    • The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation
    • (doi:10.1186/1471-2164-11-581)
    • Lin Z, Wu WS, Liang H, Woo Y, Li WH. 2010 The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation. BMC Genomics 11, 581-591.(doi:10.1186/1471-2164-11-581)
    • (2010) BMC Genomics , vol.11 , pp. 581-591
    • Lin, Z.1    Wu, W.S.2    Liang, H.3    Woo, Y.4    Li, W.H.5
  • 32
    • 0023272370 scopus 로고
    • Proximal and distal regulatory elements that influence in vivo expression of a cell cycledependent human H4 histone gene
    • (doi:10.1073/pnas. 84.12.3982)
    • Kroeger P, Stewart C, Schaap T, van Wjnen A, Hirshman J, Helms S, Stein G, Stein J. 1987 Proximal and distal regulatory elements that influence in vivo expression of a cell cycledependent human H4 histone gene. Proc. Natl Acad. Sci. USA 84, 3982-3986.(doi:10.1073/pnas. 84.12.3982)
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 3982-3986
    • Kroeger, P.1    Stewart, C.2    Schaap, T.3    van Wjnen, A.4    Hirshman, J.5    Helms, S.6    Stein, G.7    Stein, J.8
  • 33
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the encode pilot project
    • The ENCODE Project Consortium, (doi:10.1038/nature05874)
    • The ENCODE Project Consortium. 2007 Identification and analysis of functional elements in 1% of the human genome by the encode pilot project. Nature 447, 799-816.(doi:10.1038/nature05874)
    • (2007) Nature , vol.447 , pp. 799-816
  • 34
    • 3242878193 scopus 로고    scopus 로고
    • ECR Browser: A tool for visualizing and accessing data from comparisons of multiple vertebrate genomes
    • (doi:10.1093/nar/gkh355)
    • Ovcharenko I, Nobrega MA, Loots GG, Stubbs L. 2004 ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Res. 32, W280-W286.(doi:10.1093/nar/gkh355)
    • (2004) Nucleic Acids Res , vol.32
    • Ovcharenko, I.1    Nobrega, M.A.2    Loots, G.G.3    Stubbs, L.4
  • 35
    • 77956331627 scopus 로고    scopus 로고
    • Integrating common and rare genetic variation in diverse human populations
    • (doi:10.1038/ nature09298)
    • Altshuler DL et al. 2010 Integrating common and rare genetic variation in diverse human populations. Nature 467, 52-58.(doi:10.1038/ nature09298)
    • (2010) Nature , vol.467 , pp. 52-58
    • Altshuler, D.L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.