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Volumn 155, Issue 7, 2013, Pages 1521-1531

Rapid and pervasive changes in genome-wide enhancer usage during mammalian development

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BINDING SITE; BRAIN FUNCTION; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DEVELOPMENTAL STAGE; EMBRYO DEVELOPMENT; ENHANCER REGION; EPIGENETICS; FOREBRAIN; GENE EXPRESSION; GENETIC CONSERVATION; IN VIVO STUDY; MOUSE; NERVOUS SYSTEM DEVELOPMENT; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; TRANSGENIC MOUSE; ACETYLATION; ANIMAL; ANTIBODY SPECIFICITY; GENE EXPRESSION REGULATION; GENETIC ASSOCIATION; GENETIC EPIGENESIS; METABOLISM; MOLECULAR EVOLUTION;

EID: 84894598129     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2013.11.033     Document Type: Article
Times cited : (278)

References (81)
  • 2
    • 1242319291 scopus 로고    scopus 로고
    • Early expression of sodium channel transcripts and sodium current by cajal-retzius cells in the preplate of the embryonic mouse neocortex
    • M. Albrieux, J.-C. Platel, A. Dupuis, M. Villaz, and W.J. Moody Early expression of sodium channel transcripts and sodium current by cajal-retzius cells in the preplate of the embryonic mouse neocortex J. Neurosci. 24 2004 1719 1725
    • (2004) J. Neurosci. , vol.24 , pp. 1719-1725
    • Albrieux, M.1    Platel, J.-C.2    Dupuis, A.3    Villaz, M.4    Moody, W.J.5
  • 3
    • 0025224615 scopus 로고
    • Cellular migration patterns in the developing mouse cerebral cortex
    • C.P. Austin, and C.L. Cepko Cellular migration patterns in the developing mouse cerebral cortex Development 110 1990 713 732
    • (1990) Development , vol.110 , pp. 713-732
    • Austin, C.P.1    Cepko, C.L.2
  • 4
    • 82955247074 scopus 로고    scopus 로고
    • Sequentially acting Sox transcription factors in neural lineage development
    • M. Bergsland, D. Ramsköld, C. Zaouter, S. Klum, R. Sandberg, and J. Muhr Sequentially acting Sox transcription factors in neural lineage development Genes Dev. 25 2011 2453 2464
    • (2011) Genes Dev. , vol.25 , pp. 2453-2464
    • Bergsland, M.1    Ramsköld, D.2    Zaouter, C.3    Klum, S.4    Sandberg, R.5    Muhr, J.6
  • 5
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium
    • B.E. Bernstein, E. Birney, I. Dunham, E.D. Green, C. Gunter, M. Snyder ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome Nature 489 2012 57 74
    • (2012) Nature , vol.489 , pp. 57-74
    • Bernstein, B.E.1    Birney, E.2    Dunham, I.3    Green, E.D.4    Gunter, C.5    Snyder, M.6
  • 9
    • 0038485530 scopus 로고    scopus 로고
    • Heart development: Molecular insights into cardiac specification and early morphogenesis
    • T. Brand Heart development: molecular insights into cardiac specification and early morphogenesis Dev. Biol. 258 2003 1 19
    • (2003) Dev. Biol. , vol.258 , pp. 1-19
    • Brand, T.1
  • 10
    • 39749191367 scopus 로고    scopus 로고
    • The developmental genetics of congenital heart disease
    • B.G. Bruneau The developmental genetics of congenital heart disease Nature 451 2008 943 948
    • (2008) Nature , vol.451 , pp. 943-948
    • Bruneau, B.G.1
  • 11
    • 0034574349 scopus 로고    scopus 로고
    • Gene expression changes during murine postnatal brain development
    • RESEARCH0005
    • M. Clinton, J. Manson, D. McBride, and G. Miele Gene expression changes during murine postnatal brain development Genome Biol. 1 2000 RESEARCH0005
    • (2000) Genome Biol. , vol.1
    • Clinton, M.1    Manson, J.2    McBride, D.3    Miele, G.4
  • 12
    • 84861911346 scopus 로고    scopus 로고
    • Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb
    • J. Cotney, J. Leng, S. Oh, L.E. DeMare, S.K. Reilly, M.B. Gerstein, and J.P. Noonan Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb Genome Res. 22 2012 1069 1080
    • (2012) Genome Res. , vol.22 , pp. 1069-1080
    • Cotney, J.1    Leng, J.2    Oh, S.3    Demare, L.E.4    Reilly, S.K.5    Gerstein, M.B.6    Noonan, J.P.7
  • 14
    • 84859238629 scopus 로고    scopus 로고
    • Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: A multi-ethnic meta-analysis of 45,891 individuals
    • DIAGRAM+ Consortium MAGIC Consortium GLGC Investigators MuTHER Consortium DIAGRAM Consortium GIANT Consortium Global B Pgen Consortium Procardis Consortium MAGIC investigators GLGC Consortium
    • Z. Dastani, M.-F. Hivert, N. Timpson, J.R.B. Perry, X. Yuan, R.A. Scott, P. Henneman, I.M. Heid, J.R. Kizer, L.-P. Lyytikäinen DIAGRAM+ Consortium MAGIC Consortium GLGC Investigators MuTHER Consortium DIAGRAM Consortium GIANT Consortium Global B Pgen Consortium Procardis Consortium MAGIC investigators GLGC Consortium Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals PLoS Genet. 8 2012 e1002607
    • (2012) PLoS Genet. , vol.8 , pp. 1002607
    • Dastani, Z.1    Hivert, M.-F.2    Timpson, N.3    Perry, J.R.B.4    Yuan, X.5    Scott, R.A.6    Henneman, P.7    Heid, I.M.8    Kizer, J.R.9    Lyytikäinen, L.-P.10
  • 16
    • 78650141540 scopus 로고    scopus 로고
    • A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns
    • T. Domazet-Lošo, and D. Tautz A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns Nature 468 2010 815 818
    • (2010) Nature , vol.468 , pp. 815-818
    • Domazet-Lošo, T.1    Tautz, D.2
  • 17
    • 0028324080 scopus 로고
    • Insulin-like growth factor i stimulates myofibril development and decreases smooth muscle alpha-actin of adult cardiomyocytes
    • M.Y. Donath, J. Zapf, M. Eppenberger-Eberhardt, E.R. Froesch, and H.M. Eppenberger Insulin-like growth factor I stimulates myofibril development and decreases smooth muscle alpha-actin of adult cardiomyocytes Proc. Natl. Acad. Sci. USA 91 1994 1686 1690
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 1686-1690
    • Donath, M.Y.1    Zapf, J.2    Eppenberger-Eberhardt, M.3    Froesch, E.R.4    Eppenberger, H.M.5
  • 22
    • 0036301401 scopus 로고    scopus 로고
    • Patterning the vertebrate heart
    • R.P. Harvey Patterning the vertebrate heart Nat. Rev. Genet. 3 2002 544 556
    • (2002) Nat. Rev. Genet. , vol.3 , pp. 544-556
    • Harvey, R.P.1
  • 24
    • 77952567987 scopus 로고    scopus 로고
    • Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    • S. Heinz, C. Benner, N. Spann, E. Bertolino, Y.C. Lin, P. Laslo, J.X. Cheng, C. Murre, H. Singh, and C.K. Glass Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities Mol. Cell 38 2010 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    Laslo, P.6    Cheng, J.X.7    Murre, C.8    Singh, H.9    Glass, C.K.10
  • 29
    • 0034457922 scopus 로고    scopus 로고
    • A targeted partial invalidation of the insulin-like growth factor i receptor gene in mice causes a postnatal growth deficit
    • M. Holzenberger, P. Leneuve, G. Hamard, B. Ducos, L. Perin, M. Binoux, and Y. Le Bouc A targeted partial invalidation of the insulin-like growth factor I receptor gene in mice causes a postnatal growth deficit Endocrinology 141 2000 2557 2566
    • (2000) Endocrinology , vol.141 , pp. 2557-2566
    • Holzenberger, M.1    Leneuve, P.2    Hamard, G.3    Ducos, B.4    Perin, L.5    Binoux, M.6    Le Bouc, Y.7
  • 32
    • 84859462157 scopus 로고    scopus 로고
    • The genomic basis of adaptive evolution in threespine sticklebacks
    • Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team
    • F.C. Jones, M.G. Grabherr, Y.F. Chan, P. Russell, E. Mauceli, J. Johnson, R. Swofford, M. Pirun, M.C. Zody, S. White Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team The genomic basis of adaptive evolution in threespine sticklebacks Nature 484 2012 55 61
    • (2012) Nature , vol.484 , pp. 55-61
    • Jones, F.C.1    Grabherr, M.G.2    Chan, Y.F.3    Russell, P.4    Mauceli, E.5    Johnson, J.6    Swofford, R.7    Pirun, M.8    Zody, M.C.9    White, S.10
  • 35
    • 0016669094 scopus 로고
    • Evolution at two levels in humans and chimpanzees
    • M.C. King, and A.C. Wilson Evolution at two levels in humans and chimpanzees Science 188 1975 107 116
    • (1975) Science , vol.188 , pp. 107-116
    • King, M.C.1    Wilson, A.C.2
  • 39
    • 77956495708 scopus 로고    scopus 로고
    • Transcriptional enhancers in animal development and evolution
    • M. Levine Transcriptional enhancers in animal development and evolution Curr. Biol. 20 2010 R754 R763
    • (2010) Curr. Biol. , vol.20
    • Levine, M.1
  • 40
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 44
    • 33749361499 scopus 로고    scopus 로고
    • Gene regulatory networks in the evolution and development of the heart
    • E.N. Olson Gene regulatory networks in the evolution and development of the heart Science 313 2006 1922 1927
    • (2006) Science , vol.313 , pp. 1922-1927
    • Olson, E.N.1
  • 45
    • 0035261381 scopus 로고    scopus 로고
    • Genomic strategies to identify mammalian regulatory sequences
    • L.A. Pennacchio, and E.M. Rubin Genomic strategies to identify mammalian regulatory sequences Nat. Rev. Genet. 2 2001 100 109
    • (2001) Nat. Rev. Genet. , vol.2 , pp. 100-109
    • Pennacchio, L.A.1    Rubin, E.M.2
  • 52
    • 84861932338 scopus 로고    scopus 로고
    • Cis-regulatory control of corticospinal system development and evolution
    • S. Shim, K.Y. Kwan, M. Li, V. Lefebvre, and N. Sestan Cis-regulatory control of corticospinal system development and evolution Nature 486 2012 74 79
    • (2012) Nature , vol.486 , pp. 74-79
    • Shim, S.1    Kwan, K.Y.2    Li, M.3    Lefebvre, V.4    Sestan, N.5
  • 53
    • 76249102739 scopus 로고    scopus 로고
    • Organogenesis and development of the liver
    • K. Si-Tayeb, F.P. Lemaigre, and S.A. Duncan Organogenesis and development of the liver Dev. Cell 18 2010 175 189
    • (2010) Dev. Cell , vol.18 , pp. 175-189
    • Si-Tayeb, K.1    Lemaigre, F.P.2    Duncan, S.A.3
  • 54
    • 0031746740 scopus 로고    scopus 로고
    • Multiple coupling of human D5 dopamine receptors to guanine nucleotide binding proteins Gs and Gz
    • A. Sidhu, K. Kimura, M. Uh, B.H. White, and S. Patel Multiple coupling of human D5 dopamine receptors to guanine nucleotide binding proteins Gs and Gz J. Neurochem. 70 1998 2459 2467
    • (1998) J. Neurochem. , vol.70 , pp. 2459-2467
    • Sidhu, A.1    Kimura, K.2    Uh, M.3    White, B.H.4    Patel, S.5
  • 56
    • 0028909220 scopus 로고
    • Embryonic expression of the chicken Sox2, Sox3 and Sox11 genes suggests an interactive role in neuronal development
    • D. Uwanogho, M. Rex, E.J. Cartwright, G. Pearl, C. Healy, P.J. Scotting, and P.T. Sharpe Embryonic expression of the chicken Sox2, Sox3 and Sox11 genes suggests an interactive role in neuronal development Mech. Dev. 49 1995 23 36
    • (1995) Mech. Dev. , vol.49 , pp. 23-36
    • Uwanogho, D.1    Rex, M.2    Cartwright, E.J.3    Pearl, G.4    Healy, C.5    Scotting, P.J.6    Sharpe, P.T.7
  • 60
    • 84858779229 scopus 로고    scopus 로고
    • HaploReg: A resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants
    • L.D. Ward, and M. Kellis HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants Nucleic Acids Res. 40 Database issue 2012 D930 D934
    • (2012) Nucleic Acids Res. , vol.40 , Issue.DATABASE ISSUE
    • Ward, L.D.1    Kellis, M.2
  • 61
    • 0017699030 scopus 로고
    • Differential control of the synthesis of two hemoglobin beta chains in normal mice
    • J.B. Whitney 3rd Differential control of the synthesis of two hemoglobin beta chains in normal mice Cell 12 1977 863 871
    • (1977) Cell , vol.12 , pp. 863-871
    • Whitney III, J.B.1
  • 62
  • 64
    • 17844371936 scopus 로고    scopus 로고
    • Embryonic development of the liver
    • R. Zhao, and S.A. Duncan Embryonic development of the liver Hepatology 41 2005 956 967
    • (2005) Hepatology , vol.41 , pp. 956-967
    • Zhao, R.1    Duncan, S.A.2
  • 67
    • 84855901401 scopus 로고    scopus 로고
    • Harvard Stem Cell Institute Cambridge, MA
    • A.M. Zorn Liver Development 2008 Harvard Stem Cell Institute Cambridge, MA
    • (2008) Liver Development
    • Zorn, A.M.1
  • 68
    • 39049086371 scopus 로고    scopus 로고
    • Qualifying the relationship between sequence conservation and molecular function
    • G.M. Cooper, and C.D. Brown Qualifying the relationship between sequence conservation and molecular function Genome Res. 18 2008 201 205
    • (2008) Genome Res. , vol.18 , pp. 201-205
    • Cooper, G.M.1    Brown, C.D.2
  • 69
    • 22244452677 scopus 로고    scopus 로고
    • Distribution and intensity of constraint in mammalian genomic sequence
    • NISC Comparative Sequencing Program
    • G.M. Cooper, E.A. Stone, G. Asimenos, E.D. Green, S. Batzoglou, A. Sidow NISC Comparative Sequencing Program Distribution and intensity of constraint in mammalian genomic sequence Genome Res. 15 2005 901 913
    • (2005) Genome Res. , vol.15 , pp. 901-913
    • Cooper, G.M.1    Stone, E.A.2    Asimenos, G.3    Green, E.D.4    Batzoglou, S.5    Sidow, A.6
  • 70
    • 78651237647 scopus 로고    scopus 로고
    • Identifying a high fraction of the human genome to be under selective constraint using GERP++
    • E.V. Davydov, D.L. Goode, M. Sirota, G.M. Cooper, A. Sidow, and S. Batzoglou Identifying a high fraction of the human genome to be under selective constraint using GERP++ PLoS Comput. Biol. 6 2010 e1001025
    • (2010) PLoS Comput. Biol. , vol.6 , pp. 1001025
    • Davydov, E.V.1    Goode, D.L.2    Sirota, M.3    Cooper, G.M.4    Sidow, A.5    Batzoglou, S.6
  • 71
    • 80051992044 scopus 로고    scopus 로고
    • Using MACS to identify peaks from ChIP-Seq data
    • Unit2.14
    • J. Feng, T. Liu, and Y. Zhang Using MACS to identify peaks from ChIP-Seq data Curr Protoc Bioinformatics Chapter 2 2011 Unit2.14
    • (2011) Curr Protoc Bioinformatics , vol.2 CHAPTER
    • Feng, J.1    Liu, T.2    Zhang, Y.3
  • 72
    • 0032128201 scopus 로고    scopus 로고
    • Conspiracy of silence among repeated transgenes
    • S. Henikoff Conspiracy of silence among repeated transgenes Bioessays 20 1998 532 535
    • (1998) Bioessays , vol.20 , pp. 532-535
    • Henikoff, S.1
  • 73
    • 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 Nat. Immunol. 12 2011 918 922
    • (2011) Nat. Immunol. , vol.12 , pp. 918-922
    • Kidder, B.L.1    Hu, G.2    Zhao, K.3
  • 74
    • 0033796352 scopus 로고    scopus 로고
    • Variegation associated with lacZ in transgenic animals: A warning note
    • L. Montoliu, S. Chávez, and M. Vidal Variegation associated with lacZ in transgenic animals: a warning note Transgenic Res. 9 2000 237 239
    • (2000) Transgenic Res. , vol.9 , pp. 237-239
    • Montoliu, L.1    Chávez, S.2    Vidal, M.3
  • 77
    • 0036133289 scopus 로고    scopus 로고
    • Expression from a Dlx gene enhancer marks adult mouse cortical GABAergic neurons
    • T. Stühmer, L. Puelles, M. Ekker, and J.L.R. Rubenstein Expression from a Dlx gene enhancer marks adult mouse cortical GABAergic neurons Cereb. Cortex 12 2002 75 85
    • (2002) Cereb. Cortex , vol.12 , pp. 75-85
    • Stühmer, T.1    Puelles, L.2    Ekker, M.3    Rubenstein, J.L.R.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.