메뉴 건너뛰기




Volumn 368, Issue 1632, 2013, Pages

Deep conservation of cis-regulatory elements in metazoans

Author keywords

Cis regulatory element; Development; Evolution; Gene regulatory networks

Indexed keywords

COMMON ANCESTRY; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENOME; METAZOAN; MORPHOLOGY; PROTEIN;

EID: 84887450841     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2013.0020     Document Type: Article
Times cited : (26)

References (123)
  • 1
    • 84873729683 scopus 로고    scopus 로고
    • FGF signaling induces mesoderm in the hemichordate Saccoglossus kowalevskii
    • (doi:10.1242/dev.083790)
    • Green SA, Norris RP, Terasaki M, Lowe CJ. 2013 FGF signaling induces mesoderm in the hemichordate Saccoglossus kowalevskii. Development 140, 1024-1033. (doi:10.1242/dev.083790)
    • (2013) Development , vol.140 , pp. 1024-1033
    • Green, S.A.1    Norris, R.P.2    Terasaki, M.3    Lowe, C.J.4
  • 2
    • 84872017259 scopus 로고    scopus 로고
    • A framework for the establishment of a cnidarian gene regulatory network for 'Endomesoderm' specification: The inputs of B-Catenin/TCF signaling
    • doi:10.1371/journal.pgen.1003164)
    • Röttinger E, Dahlin P, Martindale MQ. 2012 A framework for the establishment of a cnidarian gene regulatory network for 'Endomesoderm' specification: the inputs of B-Catenin/TCF signaling. PLoS Genet. 8, e1003164. (doi:10.1371/journal. pgen.1003164)
    • (2012) PLoS Genet , vol.8
    • Röttinger, E.1    Dahlin, P.2    Martindale, M.Q.3
  • 3
    • 68349090353 scopus 로고    scopus 로고
    • A developmental perspective: Changes in the position of the blastopore during bilaterian evolution
    • doi:10.1016/j.devcel.2009.07.024)
    • Martindale MQ, Hejnol A. 2009 A developmental perspective: changes in the position of the blastopore during bilaterian evolution. Dev. Cell 17, 162-174. (doi:10.1016/j.devcel.2009.07.024)
    • (2009) Dev. Cell , vol.17 , pp. 162-174
    • Martindale, M.Q.1    Hejnol, A.2
  • 5
    • 33748589190 scopus 로고    scopus 로고
    • Dorsoventral patterning in hemichordates: Insights into early chordate evolution
    • doi:10.1371/journal.pbio.0040291)
    • Lowe CJ et al. 2006 Dorsoventral patterning in hemichordates: insights into early chordate evolution. PLoS Biol. 4, e291. (doi:10.1371/journal. pbio.0040291)
    • (2006) PLoS Biol , vol.4
    • Lowe, C.J.1
  • 6
    • 0038826956 scopus 로고    scopus 로고
    • Anteroposterior patterning in hemichordates and the origins of the chordate nervous system
    • doi:10.1016/S0092-8674(03)00469-0)
    • Lowe CJ, Wu M, Salic A, Evans L, Lander E, Stange- Thomann N, Gruber CE, Gerhart J, Kirschner M. 2003 Anteroposterior patterning in hemichordates and the origins of the chordate nervous system. Cell 113, 853-865. (doi:10.1016/S0092-8674(03)00469-0)
    • (2003) Cell , vol.113 , pp. 853-865
    • Lowe, C.J.1    Wu, M.2    Salic, A.3    Evans, L.4    Lander, E.5    Stange- Thomann, N.6    Gruber, C.E.7    Gerhart, J.8    Kirschner, M.9
  • 8
    • 79951769532 scopus 로고    scopus 로고
    • Noggin and noggin-like genes control dorsoventral axis regeneration in planarians
    • doi:10.1016/j.cub.2011.01.016)
    • Molina MD, Neto A, Maeso I, Gomez-Skarmeta JL, Salo E, Cebria F. 2011 Noggin and noggin-like genes control dorsoventral axis regeneration in planarians. Curr. Biol. 21, 300-305. (doi:10.1016/j.cub.2011. 01.016)
    • (2011) Curr. Biol , vol.21 , pp. 300-305
    • Molina, M.D.1    Neto, A.2    Maeso, I.3    Gomez-Skarmeta, J.L.4    Salo, E.5    Cebria, F.6
  • 9
    • 79951771552 scopus 로고    scopus 로고
    • A Bmp/Admp regulatory circuit controls maintenance and regeneration of dorsal-ventral polarity in planarians
    • doi:10.1016/j.cub.2011.01.017)
    • Gavinõ MA, Reddien PW. 2011 A Bmp/Admp regulatory circuit controls maintenance and regeneration of dorsal-ventral polarity in planarians. Curr. Biol. 21, 294-299. (doi:10.1016/j.cub.2011. 01.017)
    • (2011) Curr. Biol , vol.21 , pp. 294-299
    • Gavinõ, M.A.1    Reddien, P.W.2
  • 10
    • 70349658094 scopus 로고    scopus 로고
    • Eye evolution: Common use and independent recruitment of genetic components
    • doi:10.1098/rstb.2009.0079
    • Vopalensky P, Kozmik Z. 2009 Eye evolution: common use and independent recruitment of genetic components. Phil. Trans. R. Soc. B 364, 2819-2832. (doi:10.1098/rstb.2009.0079)
    • (2009) Phil. Trans. R. Soc. B , vol.364 , pp. 2819-2832
    • Vopalensky, P.1    Kozmik, Z.2
  • 11
    • 34250900443 scopus 로고    scopus 로고
    • Conserved sensory-neurosecretory cell types in annelid and fish forebrain: Insights into hypothalamus evolution
    • doi:10.1016/j.cell.2007.04.041)
    • Tessmar-Raible K, Raible F, Christodoulou F, Guy K, Rembold M, Hausen H, Arendt D. 2007 Conserved sensory-neurosecretory cell types in annelid and fish forebrain: insights into hypothalamus evolution. Cell 129, 1389-1400. (doi:10.1016/j.cell.2007.04.041)
    • (2007) Cell , vol.129 , pp. 1389-1400
    • Tessmar-Raible, K.1    Raible, F.2    Christodoulou, F.3    Guy, K.4    Rembold, M.5    Hausen, H.6    Arendt, D.7
  • 12
    • 33749402982 scopus 로고    scopus 로고
    • The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: Evidence from the starlet sea anemone, Nematostella vectensis
    • doi:10.1186/gb-2006-7-7-r64
    • Ryan J, Burton P, Mazza M, Kwong G, Mullikin J, Finnerty J. 2006 The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: evidence from the starlet sea anemone, Nematostella vectensis. Genome Biol. 7, R64. (doi:10.1186/gb-2006-7-7-r64)
    • (2006) Genome Biol , vol.7
    • Ryan, J.1    Burton, P.2    Mazza, M.3    Kwong, G.4    Mullikin, J.5    Finnerty, J.6
  • 13
    • 19944432478 scopus 로고    scopus 로고
    • Unexpected complexity of the Wnt gene family in a sea anemone
    • doi:10.1038/nature03158)
    • Kusserow A et al. 2005 Unexpected complexity of the Wnt gene family in a sea anemone. Nature 433, 156-160. (doi:10.1038/nature03158)
    • (2005) Nature , vol.433 , pp. 156-160
    • Kusserow, A.1
  • 14
    • 34447300950 scopus 로고    scopus 로고
    • Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization
    • doi:10.1126/science.1139158
    • Putnam NH et al. 2007 Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317, 86-94. (doi:10. 1126/science.1139158)
    • (2007) Science , vol.317 , pp. 86-94
    • Putnam, N.H.1
  • 15
    • 84872893458 scopus 로고    scopus 로고
    • Insights into bilaterian evolution from three spiralian genomes
    • doi:10.1038/nature11696
    • Simakov O et al. 2013 Insights into bilaterian evolution from three spiralian genomes. Nature 493, 526-531. (doi:10.1038/nature11696)
    • (2013) Nature , vol.493 , pp. 526-531
    • Simakov, O.1
  • 17
    • 79952681078 scopus 로고    scopus 로고
    • Evolution of gene regulatory networks controlling body plan development
    • doi:10.1016/j.cell.2011.02.017)
    • Peter IS, Davidson EH. 2011 Evolution of gene regulatory networks controlling body plan development. Cell 144, 970-985. (doi:10.1016/j. cell.2011.02.017)
    • (2011) Cell , vol.144 , pp. 970-985
    • Peter, I.S.1    Davidson, E.H.2
  • 18
    • 33749325080 scopus 로고    scopus 로고
    • Genomic evolution of Hox gene clusters
    • doi:10.1126/science.1132040)
    • Lemons D, McGinnis W. 2006 Genomic evolution of Hox gene clusters. Science 313, 1918-1922. (doi:10.1126/science.1132040)
    • (2006) Science , vol.313 , pp. 1918-1922
    • Lemons, D.1    McGinnis, W.2
  • 19
    • 84866315760 scopus 로고    scopus 로고
    • Development of the larval anterior neurogenic domains of Terebratalia transversa (Brachiopoda) provides insights into the diversification of larval apical organs and the spiralian nervous system
    • (doi:10.1186/2041-9139-3-3)
    • Santagata S, Resh C, Hejnol A, Martindale M, Passamaneck Y. 2012 Development of the larval anterior neurogenic domains of Terebratalia transversa (Brachiopoda) provides insights into the diversification of larval apical organs and the spiralian nervous system. EvoDevo 3, 3. (doi:10. 1186/2041-9139-3-3)
    • (2012) EvoDevo , vol.3 , pp. 3
    • Santagata, S.1    Resh, C.2    Hejnol, A.3    Martindale, M.4    Passamaneck, Y.5
  • 20
    • 79955092263 scopus 로고    scopus 로고
    • Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer
    • doi:10.1186/2041-9139-1-7)
    • Irimia M, Pineiro C, Maeso I, Gomez-Skarmeta J, Casares F, Garcia-Fernandez J. 2010 Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer. EvoDevo 1, 7. (doi:10.1186/2041-9139-1-7)
    • (2010) EvoDevo , vol.1 , pp. 7
    • Irimia, M.1    Pineiro, C.2    Maeso, I.3    Gomez-Skarmeta, J.4    Casares, F.5    Garcia-Fernandez, J.6
  • 21
    • 84858187883 scopus 로고    scopus 로고
    • Ancient deuterostome origins of vertebrate brain signalling centres
    • doi:10.1038/nature10838)
    • Pani AM, Mullarkey EE, Aronowicz J, Assimacopoulos S, Grove EA, Lowe CJ. 2012 Ancient deuterostome origins of vertebrate brain signalling centres. Nature 483, 289-294. (doi:10.1038/nature10838)
    • (2012) Nature , vol.483 , pp. 289-294
    • Pani, A.M.1    Mullarkey, E.E.2    Aronowicz, J.3    Assimacopoulos, S.4    Grove, E.A.5    Lowe, C.J.6
  • 22
    • 84869763293 scopus 로고    scopus 로고
    • Concept of neural genoarchitecture and its genomic fundament
    • doi:10.3389/fnana.2012.00047)
    • Puelles L, Ferran JL. 2012 Concept of neural genoarchitecture and its genomic fundament. Front. Neuroanat. 6, 47. (doi:10.3389/fnana.2012.00047)
    • (2012) Front. Neuroanat , vol.6 , pp. 47
    • Puelles, L.1    Ferran, J.L.2
  • 23
    • 34247098755 scopus 로고    scopus 로고
    • Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in bilateria
    • doi:10.1016/j.cell.2007.02.040)
    • Denes AS, Jekely G, Steinmetz PR, Raible F, Snyman H, Prud'homme B, Ferrier DE, Balavoine G, Arendt D. 2007 Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in bilateria. Cell 129, 277-288. (doi:10. 1016/j.cell.2007.02.040)
    • (2007) Cell , vol.129 , pp. 277-288
    • Denes, A.S.1    Jekely, G.2    Steinmetz, P.R.3    Raible, F.4    Snyman, H.5    Prud'homme, B.6    Ferrier, D.E.7    Balavoine, G.8    Arendt, D.9
  • 24
    • 70349336077 scopus 로고    scopus 로고
    • Conserved noncoding elements and the evolution of animal body plans
    • doi:10.1002/bies.200900014)
    • Vavouri T, Lehner B. 2009 Conserved noncoding elements and the evolution of animal body plans. Bioessays 31, 727-735. (doi:10.1002/bies. 200900014)
    • (2009) Bioessays , vol.31 , pp. 727-735
    • Vavouri, T.1    Lehner, B.2
  • 25
    • 33751316959 scopus 로고    scopus 로고
    • In vivo enhancer analysis of human conserved non-coding sequences
    • doi:10.1038/nature05295)
    • Pennacchio LA et al. 2006 In vivo enhancer analysis of human conserved non-coding sequences. Nature 444, 499-502. (doi:10.1038/nature05295)
    • (2006) Nature , vol.444 , pp. 499-502
    • Pennacchio, L.A.1
  • 26
    • 20044366725 scopus 로고    scopus 로고
    • Highly conserved non-coding sequences are associated with vertebrate development
    • doi:10.1371/journal.pbio.0030007)
    • Woolfe A et al. 2005 Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3, e7. (doi:10.1371/journal. pbio.0030007)
    • (2005) PLoS Biol , vol.3
    • Woolfe, A.1
  • 27
    • 79952163548 scopus 로고    scopus 로고
    • Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes
    • (doi:10.1093/molbev/msq304)
    • Lee AP, Kerk SY, Tan YY, Brenner S, Venkatesh B. 2011 Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes. Mol. Biol. Evol. 28, 1205-1215. (doi:10. 1093/molbev/msq304)
    • (2011) Mol. Biol. Evol , vol.28 , pp. 1205-1215
    • Lee, A.P.1    Kerk, S.Y.2    Tan, Y.Y.3    Brenner, S.4    Venkatesh, B.5
  • 28
    • 74249085481 scopus 로고    scopus 로고
    • Early evolution of conserved regulatory sequences associated with development in vertebrates
    • (doi:10.1371/journal.pgen.1000762)
    • McEwen GK, Goode DK, Parker HJ, Woolfe A, Callaway H, Elgar G. 2009 Early evolution of conserved regulatory sequences associated with development in vertebrates. PLoS Genet. 5, e1000762. (doi:10.1371/journal.pgen.1000762)
    • (2009) PLoS Genet , vol.5
    • McEwen, G.K.1    Goode, D.K.2    Parker, H.J.3    Woolfe, A.4    Callaway, H.5    Elgar, G.6
  • 29
    • 84876044425 scopus 로고    scopus 로고
    • Highly conserved elements discovered in vertebrates are present in nonsyntenic loci of tunicates, act as enhancers and can be transcribed during development
    • doi:10.1093/nar/gkt030)
    • Sanges R et al. 2013 Highly conserved elements discovered in vertebrates are present in nonsyntenic loci of tunicates, act as enhancers and can be transcribed during development. Nucleic Acids Res. 41, 3600-3618. (doi:10.1093/nar/gkt030)
    • (2013) Nucleic Acids Res , vol.41 , pp. 3600-3618
    • Sanges, R.1
  • 30
    • 84866150923 scopus 로고    scopus 로고
    • Human developmental enhancers conserved between deuterostomes and protostomes
    • (doi:10.1371/journal.pgen.1002852)
    • Clarke SL, VanderMeer JE, Wenger AM, Schaar BT, Ahituv N, Bejerano G. 2012 Human developmental enhancers conserved between deuterostomes and protostomes. PLoS Genet. 8, e1002852. (doi:10. 1371/journal.pgen.1002852)
    • (2012) PLoS Genet , vol.8
    • Clarke, S.L.1    Vandermeer, J.E.2    Wenger, A.M.3    Schaar, B.T.4    Ahituv, N.5    Bejerano, G.6
  • 31
    • 70350741353 scopus 로고    scopus 로고
    • Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
    • (doi:10.1101/gr.093237.109)
    • Hufton AL, Mathia S, Braun H, Georgi U, Lehrach H, Vingron M, Poustka AJ, Panopoulou G. 2009 Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. Genome Res. 19, 2036-2051. (doi:10. 1101/gr.093237.109)
    • (2009) Genome Res , vol.19 , pp. 2036-2051
    • Hufton, A.L.1    Mathia, S.2    Braun, H.3    Georgi, U.4    Lehrach, H.5    Vingron, M.6    Poustka, A.J.7    Panopoulou, G.8
  • 32
    • 45749086679 scopus 로고    scopus 로고
    • The amphioxus genome and the evolution of the chordate karyotype
    • doi:10.1038/nature06967)
    • Putnam NH et al. 2008 The amphioxus genome and the evolution of the chordate karyotype. Nature 453, 1064-1071. (doi:10.1038/nature06967)
    • (2008) Nature , vol.453 , pp. 1064-1071
    • Putnam, N.H.1
  • 33
    • 46449117597 scopus 로고    scopus 로고
    • The amphioxus genome illuminates vertebrate origins and cephalochordate biology
    • doi:10.1101/gr.073676.107)
    • Holland LZ et al. 2008 The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res. 18, 1100-1111. (doi:10. 1101/gr.073676.107)
    • (2008) Genome Res , vol.18 , pp. 1100-1111
    • Holland, L.Z.1
  • 34
    • 38849112675 scopus 로고    scopus 로고
    • Genomic regulatory blocks underlie extensive microsynteny conservation in insects
    • (doi:10.1101/gr.6669607)
    • Engstrom PG, Ho Sui SJ, Drivenes O, Becker TS, Lenhard B. 2007 Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res. 17, 1898-1908. (doi:10.1101/gr. 6669607)
    • (2007) Genome Res , vol.17 , pp. 1898-1908
    • Engstrom, P.G.1    Ho Sui, S.J.2    Drivenes, O.3    Becker, T.S.4    Lenhard, B.5
  • 35
    • 34447500684 scopus 로고    scopus 로고
    • Parallel evolution of conserved noncoding elements that target a common set of developmental regulatory genes from worms to humans
    • (doi:10.1186/gb-2007-8-2-r15)
    • Vavouri T, Walter K, Gilks WR, Lehner B, Elgar G. 2007 Parallel evolution of conserved noncoding elements that target a common set of developmental regulatory genes from worms to humans. Genome Biol. 8, R15. (doi:10.1186/gb- 2007-8-2-r15)
    • (2007) Genome Biol , vol.8
    • Vavouri, T.1    Walter, K.2    Gilks, W.R.3    Lehner, B.4    Elgar, G.5
  • 36
    • 80052152362 scopus 로고    scopus 로고
    • Transphyletic conservation of developmental regulatory state in animal evolution
    • (doi:10.1073/pnas.1109037108)
    • Royo JL et al. 2011 Transphyletic conservation of developmental regulatory state in animal evolution. Proc. Natl Acad. Sci. USA 108, 14 186-14 191. (doi:10.1073/pnas.1109037108)
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , Issue.14 , pp. 186-191
    • Royo, J.L.1
  • 39
    • 22144473057 scopus 로고    scopus 로고
    • Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
    • doi:10.1186/1471-2164-5-99)
    • Sandelin A, Bailey P, Bruce S, Engstrom PG, Klos JM, Wasserman WW, Ericson J, Lenhard B. 2004 Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 5, 99. (doi:10.1186/1471-2164-5-99)
    • (2004) BMC Genomics , vol.5 , pp. 99
    • Sandelin, A.1    Bailey, P.2    Bruce, S.3    Engstrom, P.G.4    Klos, J.M.5    Wasserman, W.W.6    Ericson, J.7    Lenhard, B.8
  • 40
    • 80052781416 scopus 로고    scopus 로고
    • Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved noncoding regions
    • doi:10.1371/journal.pone.0024824)
    • Royo JL, Hidalgo C, Roncero Y, Seda MA, Akalin A, Lenhard B, Casares F, Gomez-Skarmeta JL. 2011 Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved noncoding regions. PLoS ONE 6, e24824. (doi:10.1371/ journal.pone.0024824)
    • (2011) PLoS ONE , vol.6
    • Royo, J.L.1    Hidalgo, C.2    Roncero, Y.3    Seda, M.A.4    Akalin, A.5    Lenhard, B.6    Casares, F.7    Gomez-Skarmeta, J.L.8
  • 41
    • 0034756824 scopus 로고    scopus 로고
    • Comparative genomics of the SOX9 region in human and Fugu rubripes: Conservation of short regulatory sequence elements within large intergenic regions
    • doi:10.1006/geno.2001.6648)
    • Bagheri-Fam S, Ferraz C, Demaille J, Scherer G, Pfeifer D. 2001 Comparative genomics of the SOX9 region in human and Fugu rubripes: conservation of short regulatory sequence elements within large intergenic regions. Genomics 78, 73-82. (doi:10. 1006/geno.2001.6648)
    • (2001) Genomics , vol.78 , pp. 73-82
    • Bagheri-Fam, S.1    Ferraz, C.2    Demaille, J.3    Scherer, G.4    Pfeifer, D.5
  • 44
    • 0037397910 scopus 로고    scopus 로고
    • Regulatory roles of conserved intergenic domains in vertebrate Dlx bigene clusters
    • doi:10.1101/gr.716103)
    • Ghanem N, Jarinova O, Amores A, Long Q, Hatch G, Park BK, Rubenstein JL, Ekker M. 2003 Regulatory roles of conserved intergenic domains in vertebrate Dlx bigene clusters. Genome Res. 13, 533-543. (doi:10.1101/gr.716103)
    • (2003) Genome Res , vol.13 , pp. 533-543
    • Ghanem, N.1    Jarinova, O.2    Amores, A.3    Long, Q.4    Hatch, G.5    Park, B.K.6    Rubenstein, J.L.7    Ekker, M.8
  • 45
    • 0033972132 scopus 로고    scopus 로고
    • Analysis of vertebrate SCL loci identifies conserved enhancers
    • doi:10.1038/72635)
    • Gottgens B et al. 2000 Analysis of vertebrate SCL loci identifies conserved enhancers. Nat. Biotechnol. 18, 181-186. (doi:10.1038/72635)
    • (2000) Nat. Biotechnol , vol.18 , pp. 181-186
    • Gottgens, B.1
  • 46
    • 0142084743 scopus 로고    scopus 로고
    • Scanning human gene deserts for long-range enhancers
    • doi:10.1126/science.1088328)
    • Nobrega MA, Ovcharenko I, Afzal V, Rubin EM. 2003 Scanning human gene deserts for long-range enhancers. Science 302, 413. (doi:10.1126/science. 1088328)
    • (2003) Science , vol.302 , pp. 413
    • Nobrega, M.A.1    Ovcharenko, I.2    Afzal, V.3    Rubin, E.M.4
  • 47
    • 0038613098 scopus 로고    scopus 로고
    • A global control region defines a chromosomal regulatory landscape containing the HoxD cluster
    • doi:10.1016/S0092-8674(03)00310-6)
    • Spitz F, Gonzalez F, Duboule D. 2003 A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113, 405-417. (doi:10.1016/S0092-8674(03)00310-6)
    • (2003) Cell , vol.113 , pp. 405-417
    • Spitz, F.1    Gonzalez, F.2    Duboule, D.3
  • 48
    • 38649123306 scopus 로고    scopus 로고
    • Ultraconservation identifies a small subset of extremely constrained developmental enhancers
    • doi:10.1038/ng.2007.55)
    • Visel A et al. 2008 Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat. Genet. 40, 158-160. (doi:10.1038/ng.2007.55)
    • (2008) Nat. Genet , vol.40 , pp. 158-160
    • Visel, A.1
  • 49
    • 84871117732 scopus 로고    scopus 로고
    • Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression
    • doi:10.1186/1471-2164-13-713)
    • Ariza-Cosano A, Visel A, Pennacchio LA, Fraser HB, Gomez-Skarmeta JL, Irimia M, Bessa J. 2012 Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression. BMC Genomics 13, 713. (doi:10.1186/1471-2164-13-713)
    • (2012) BMC Genomics , vol.13 , pp. 713
    • Ariza-Cosano, A.1    Visel, A.2    Pennacchio, L.A.3    Fraser, H.B.4    Gomez-Skarmeta, J.L.5    Irimia, M.6    Bessa, J.7
  • 50
    • 75649100190 scopus 로고    scopus 로고
    • Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish
    • doi:10.1007/s00438-009-0503-1)
    • Navratilova P, Fredman D, Lenhard B, Becker TS. 2010 Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish. Mol. Genet. Genomics 283, 171-184. (doi:10.1007/ s00438-009-0503-1)
    • (2010) Mol. Genet. Genomics , vol.283 , pp. 171-184
    • Navratilova, P.1    Fredman, D.2    Lenhard, B.3    Becker, T.S.4
  • 51
    • 60549097668 scopus 로고    scopus 로고
    • Systematic human/ zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes
    • doi:10.1016/j.ydbio.2008.10.044)
    • Navratilova P, Fredman D, Hawkins TA, Turner K, Lenhard B, Becker TS. 2009 Systematic human/ zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Dev. Biol. 327, 526-540. (doi:10.1016/j.ydbio.2008.10.044)
    • (2009) Dev. Biol , vol.327 , pp. 526-540
    • Navratilova, P.1    Fredman, D.2    Hawkins, T.A.3    Turner, K.4    Lenhard, B.5    Becker, T.S.6
  • 52
    • 70449529760 scopus 로고    scopus 로고
    • Cisregulation and chromosomal rearrangement of the fgf8 locus after the teleost/tetrapod split
    • doi:10.1016/j.ydbio.2009.09.029)
    • Komisarczuk AZ, Kawakami K, Becker TS. 2009 Cisregulation and chromosomal rearrangement of the fgf8 locus after the teleost/tetrapod split. Dev. Biol. 336, 301-312. (doi:10.1016/j.ydbio.2009.09.029)
    • (2009) Dev. Biol , vol.336 , pp. 301-312
    • Komisarczuk, A.Z.1    Kawakami, K.2    Becker, T.S.3
  • 53
    • 77957225928 scopus 로고    scopus 로고
    • The importance of being cis: Evolution of orthologous fish and mammalian enhancer activity
    • doi:10.1093/molbev/msq128)
    • Ritter DI, Li Q, Kostka D, Pollard KS, Guo S, Chuang JH. 2010 The importance of being cis: evolution of orthologous fish and mammalian enhancer activity. Mol. Biol. Evol. 27, 2322-2332. (doi:10.1093/ molbev/msq128)
    • (2010) Mol. Biol. Evol , vol.27 , pp. 2322-2332
    • Ritter, D.I.1    Li, Q.2    Kostka, D.3    Pollard, K.S.4    Guo, S.5    Chuang, J.H.6
  • 54
    • 22344454794 scopus 로고    scopus 로고
    • Ultraconserved elements in insect genomes: A highly conserved intronic sequence implicated in the control of homothorax mRNA splicing
    • doi:10.1101/gr.3545105)
    • Glazov EA, Pheasant M, McGraw EA, Bejerano G, Mattick JS. 2005 Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Res. 15, 800-808. (doi:10.1101/gr.3545105)
    • (2005) Genome Res , vol.15 , pp. 800-808
    • Glazov, E.A.1    Pheasant, M.2    McGraw, E.A.3    Bejerano, G.4    Mattick, J.S.5
  • 55
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • doi:10.1101/gr.3715005)
    • Siepel A et al. 2005 Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050. (doi:10. 1101/gr.3715005)
    • (2005) Genome Res , vol.15 , pp. 1034-1050
    • Siepel, A.1
  • 56
    • 84875065227 scopus 로고    scopus 로고
    • Characterization of genomic regulatory domains conserved across the genus Drosophila
    • doi:10.1093/gbe/evs089)
    • Sahagun V, Ranz JM. 2012 Characterization of genomic regulatory domains conserved across the genus Drosophila. Genome Biol. Evol. 4, 1054-1060. (doi:10.1093/gbe/evs089)
    • (2012) Genome Biol. Evol , vol.4 , pp. 1054-1060
    • Sahagun, V.1    Ranz, J.M.2
  • 57
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • doi:10.1038/nature01262)
    • Waterston RH et al. 2002 Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562. (doi:10.1038/nature01262)
    • (2002) Nature , vol.420 , pp. 520-562
    • Waterston, R.H.1
  • 58
    • 0038354776 scopus 로고    scopus 로고
    • Insights from human/mouse genome comparisons
    • doi:10.1007/s00335-002-4001-1)
    • Pennacchio LA. 2003 Insights from human/mouse genome comparisons. Mamm. Genome 14, 429-436. (doi:10.1007/s00335-002-4001-1)
    • (2003) Mamm. Genome , vol.14 , pp. 429-436
    • Pennacchio, L.A.1
  • 59
    • 34247342594 scopus 로고    scopus 로고
    • Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) Genome
    • doi:10.1371/journal.pbio.0050101)
    • Venkatesh B et al. 2007 Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) Genome. PLoS Biol. 5, e101. (doi:10.1371/journal.pbio.0050101)
    • (2007) PLoS Biol , vol.5
    • Venkatesh, B.1
  • 60
    • 80054916668 scopus 로고    scopus 로고
    • Evolutionary crossroads in developmental biology: Amphioxus
    • doi:10.1242/dev.066720)
    • Bertrand S, Escriva H. 2011 Evolutionary crossroads in developmental biology: amphioxus. Development 138, 4819-4830. (doi:10.1242/dev.066720)
    • (2011) Development , vol.138 , pp. 4819-4830
    • Bertrand, S.1    Escriva, H.2
  • 61
    • 67651223442 scopus 로고    scopus 로고
    • From the American to the European amphioxus: Towards experimental evo-devo at the origin of chordates
    • (doi:10.1387/ijdb.072436jg)
    • Garcia-Fernandez J et al. 2009 From the American to the European amphioxus: towards experimental evo-devo at the origin of chordates. Int. J. Dev. Biol. 53, 1359-1366. (doi:10.1387/ijdb.072436jg)
    • (2009) Int. J. Dev. Biol , vol.53 , pp. 1359-1366
    • Garcia-Fernandez, J.1
  • 62
    • 3042740671 scopus 로고    scopus 로고
    • Comparative genomics at the vertebrate extremes
    • doi:10.1038/nrg1350)
    • Boffelli D, Nobrega MA, Rubin EM. 2004 Comparative genomics at the vertebrate extremes. Nat. Rev. Genet. 5, 456-465. (doi:10.1038/ nrg1350)
    • (2004) Nat. Rev. Genet , vol.5 , pp. 456-465
    • Boffelli, D.1    Nobrega, M.A.2    Rubin, E.M.3
  • 64
    • 48749122180 scopus 로고    scopus 로고
    • Identification of DPPA4 and other genes as putative Sox2:Oct-3/4 target genes using a combination of in silico analysis and transcription-based assays
    • doi:10.1002/jcp.21440)
    • Chakravarthy H, Boer B, Desler M, Mallanna SK, McKeithan TW, Rizzino A. 2008 Identification of DPPA4 and other genes as putative Sox2:Oct-3/4 target genes using a combination of in silico analysis and transcription-based assays. J. Cell. Physiol. 216, 651-662. (doi:10.1002/jcp.21440)
    • (2008) J. Cell. Physiol , vol.216 , pp. 651-662
    • Chakravarthy, H.1    Boer, B.2    Desler, M.3    Mallanna, S.K.4    McKeithan, T.W.5    Rizzino, A.6
  • 65
    • 33747743032 scopus 로고    scopus 로고
    • Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage
    • doi:10.1186/gb-2006-7-7-r56)
    • Sanges R, Kalmar E, Claudiani P, D'Amato M, Muller F, Stupka E. 2006 Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage. Genome Biol. 7, R56. (doi:10.1186/gb- 2006-7-7-r56)
    • (2006) Genome Biol , vol.7
    • Sanges, R.1    Kalmar, E.2    Claudiani, P.3    D'Amato, M.4    Muller, F.5    Stupka, E.6
  • 66
    • 47649129807 scopus 로고    scopus 로고
    • Convergent evolution of clustering of Iroquois homeobox genes across metazoans
    • doi:10.1093/molbev/msn109)
    • Irimia M, Maeso I, Garcia-Fernandez J. 2008 Convergent evolution of clustering of Iroquois homeobox genes across metazoans. Mol. Biol. Evol. 25, 1521-1525. (doi:10.1093/molbev/msn109)
    • (2008) Mol. Biol. Evol , vol.25 , pp. 1521-1525
    • Irimia, M.1    Maeso, I.2    Garcia-Fernandez, J.3
  • 67
    • 0035986888 scopus 로고    scopus 로고
    • Evolution of transcription factor binding sites in mammalian gene regulatory regions: Conservation and turnover
    • (doi:10.1093/oxfordjournals.molbev.a004169)
    • Dermitzakis ET, Clark AG. 2002 Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover. Mol. Biol. Evol. 19, 1114-1121. (doi:10.1093/ oxfordjournals.molbev.a004169)
    • (2002) Mol. Biol. Evol , vol.19 , pp. 1114-1121
    • Dermitzakis, E.T.1    Clark, A.G.2
  • 68
    • 0037498017 scopus 로고    scopus 로고
    • Turnover of binding sites for transcription factors involved in early Drosophila development
    • doi:10.1016/S0378-1119(03)00556-0)
    • Costas J, Casares F, Vieira J. 2003 Turnover of binding sites for transcription factors involved in early Drosophila development. Gene 310, 215-220. (doi:10.1016/S0378-1119(03)00556-0)
    • (2003) Gene , vol.310 , pp. 215-220
    • Costas, J.1    Casares, F.2    Vieira, J.3
  • 69
    • 34249818182 scopus 로고    scopus 로고
    • Tissue-specific transcriptional regulation has diverged significantly between human and mouse
    • doi:10.1038/ng2047)
    • Odom DT et al. 2007 Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat. Genet. 39, 730-732. (doi:10.1038/ng2047)
    • (2007) Nat. Genet , vol.39 , pp. 730-732
    • Odom, D.T.1
  • 70
    • 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
  • 71
    • 51149097760 scopus 로고    scopus 로고
    • Shadow enhancers as a source of evolutionary novelty
    • doi:10.1126/science.1160631)
    • Hong JW, Hendrix DA, Levine MS. 2008 Shadow enhancers as a source of evolutionary novelty. Science 321, 1314. (doi:10.1126/science.1160631)
    • (2008) Science , vol.321 , pp. 1314
    • Hong, J.W.1    Hendrix, D.A.2    Levine, M.S.3
  • 72
    • 77954960062 scopus 로고    scopus 로고
    • Phenotypic robustness conferred by apparently redundant transcriptional enhancers
    • doi:10.1038/nature09158)
    • Frankel N, Davis GK, Vargas D, Wang S, Payre F, Stern DL. 2010 Phenotypic robustness conferred by apparently redundant transcriptional enhancers. Nature 466, 490-493. (doi:10.1038/nature09158)
    • (2010) Nature , vol.466 , pp. 490-493
    • Frankel, N.1    Davis, G.K.2    Vargas, D.3    Wang, S.4    Payre, F.5    Stern, D.L.6
  • 73
    • 33846490910 scopus 로고    scopus 로고
    • Patterning the zebrafish diencephalon by the conserved zinc-finger protein Fezl
    • doi:10.1242/dev.02705)
    • Jeong JY, Einhorn Z, Mathur P, Chen L, Lee S, Kawakami K, Guo S. 2007 Patterning the zebrafish diencephalon by the conserved zinc-finger protein Fezl. Development 134, 127-136. (doi:10.1242/dev. 02705)
    • (2007) Development , vol.134 , pp. 127-136
    • Jeong, J.Y.1    Einhorn, Z.2    Mathur, P.3    Chen, L.4    Lee, S.5    Kawakami, K.6    Guo, S.7
  • 74
    • 84879911829 scopus 로고    scopus 로고
    • The evolution of lineage-specific regulatory activities in the human embryonic limb
    • doi:10.1016/j.cell.2013.05.056)
    • Cotney J, Leng J, Yin J, Reilly SK, DeMare LE, Emera D, Ayoub AE, Rakic P, Noonan JP. 2013 The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell 154, 185-196. (doi:10.1016/j.cell.2013.05.056)
    • (2013) Cell , vol.154 , pp. 185-196
    • Cotney, J.1    Leng, J.2    Yin, J.3    Reilly, S.K.4    Demare, L.E.5    Emera, D.6    Ayoub, A.E.7    Rakic, P.8    Noonan, J.P.9
  • 75
    • 0032498230 scopus 로고    scopus 로고
    • The enhanceosome and transcriptional synergy
    • doi:10.1016/S0092-8674(00)80893-4)
    • Carey M. 1998 The enhanceosome and transcriptional synergy. Cell 92, 5-8. (doi:10.1016/ S0092-8674(00)80893-4)
    • (1998) Cell , vol.92 , pp. 5-8
    • Carey, M.1
  • 76
    • 77951874066 scopus 로고    scopus 로고
    • Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
    • doi:10.1101/gr.104471.109)
    • Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, Ovcharenko I. 2010 Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res. 20, 565-577. (doi:10.1101/gr.104471. 109)
    • (2010) Genome Res , vol.20 , pp. 565-577
    • Gotea, V.1    Visel, A.2    Westlund, J.M.3    Nobrega, M.A.4    Pennacchio, L.A.5    Ovcharenko, I.6
  • 77
    • 84887463729 scopus 로고    scopus 로고
    • Beyond the ENCODE project: Using genomics and epigenomics strategies to study enhancer evolution
    • doi:10.1098/rstb.2013.0022)
    • Sakabe NJ, Nobrega MA. 2013 Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution. Phil. Trans. R. Soc. B 368, 20130022. (doi:10.1098/rstb.2013.0022)
    • (2013) Phil. Trans. R. Soc. B , vol.368 , pp. 20130022
    • Sakabe, N.J.1    Nobrega, M.A.2
  • 78
    • 84871844925 scopus 로고    scopus 로고
    • DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila
    • doi:10.1073/pnas.1209589110)
    • Fisher WW et al. 2012 DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proc. Natl Acad. Sci. USA 109, 21 330-21 335. (doi:10.1073/pnas.1209589110)
    • (2012) Proc. Natl Acad. Sci. USA 109 , vol.21 , Issue.335 , pp. 330-421
    • Fisher, W.W.1
  • 79
    • 84867444899 scopus 로고    scopus 로고
    • ENCODE: The human encyclopaedia
    • doi:10.1038/489046a)
    • Maher B. 2012 ENCODE: the human encyclopaedia. Nature 489, 46-48. (doi:10.1038/489046a)
    • (2012) Nature , vol.489 , pp. 46-48
    • Maher, B.1
  • 80
    • 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
  • 81
    • 65549104157 scopus 로고    scopus 로고
    • Histone modifications at human enhancers reflect global cell-type-specific gene expression
    • doi:10.1038/nature07829)
    • Heintzman ND et al. 2009 Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108-112. (doi:10. 1038/nature07829)
    • (2009) Nature , vol.459 , pp. 108-112
    • Heintzman, N.D.1
  • 82
    • 70249088327 scopus 로고    scopus 로고
    • Genomic views of distant-acting enhancers
    • (doi:10.1038/nature08451)
    • Visel A, Rubin EM, Pennacchio LA. 2009 Genomic views of distant-acting enhancers. Nature 461, 199-205. (doi:10.1038/nature08451)
    • (2009) Nature , vol.461 , pp. 199-205
    • Visel, A.1    Rubin, E.M.2    Pennacchio, L.A.3
  • 84
    • 84864462544 scopus 로고    scopus 로고
    • A map of the cis-regulatory sequences in the mouse genome
    • (doi:10.1038/nature11243)
    • Shen Y et al. 2012 A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116-120. (doi:10.1038/nature11243)
    • (2012) Nature , vol.488 , pp. 116-120
    • Shen, Y.1
  • 85
    • 77952367798 scopus 로고    scopus 로고
    • Widespread transcription at neuronal activity-regulated enhancers
    • doi:10.1038/nature09033)
    • Kim TK et al. 2010 Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182-187. (doi:10.1038/nature09033)
    • (2010) Nature , vol.465 , pp. 182-187
    • Kim, T.K.1
  • 86
    • 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, 21 931-21 936. (doi:10.1073/pnas.1016071107)
    • (2010) Proc. Natl Acad. Sci. USA 107 , vol.21 , Issue.936 , pp. 931-1021
    • Creyghton, M.P.1
  • 87
    • 80053622239 scopus 로고    scopus 로고
    • Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency
    • doi:10.1038/cr.2011.146)
    • Hawkins RD et al. 2011 Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Cell Res. 21, 1393-1409. (doi:10.1038/cr.2011.146)
    • (2011) Cell Res , vol.21 , pp. 1393-1409
    • Hawkins, R.D.1
  • 88
    • 79951516056 scopus 로고    scopus 로고
    • A unique chromatin signature uncovers early developmental enhancers in humans
    • doi:10.1038/nature09692)
    • Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. 2010 A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 278-283. (doi:10.1038/ nature09692)
    • (2010) Nature , vol.470 , pp. 278-283
    • Rada-Iglesias, A.1    Bajpai, R.2    Swigut, T.3    Brugmann, S.A.4    Flynn, R.A.5    Wysocka, J.6
  • 89
    • 84856239091 scopus 로고    scopus 로고
    • Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
    • doi:10.1038/ng.1064)
    • Bonn S et al. 2012 Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat. Genet. 44, 148-156. (doi:10.1038/ ng.1064)
    • (2012) Nat. Genet , vol.44 , pp. 148-156
    • Bonn, S.1
  • 90
    • 84865755978 scopus 로고    scopus 로고
    • The accessible chromatin landscape of the human genome
    • doi:10.1038/nature11232)
    • Thurman RE et al. 2012 The accessible chromatin landscape of the human genome. Nature 489, 75-82. (doi:10.1038/nature11232)
    • (2012) Nature , vol.489 , pp. 75-82
    • Thurman, R.E.1
  • 91
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • doi:10.1038/nature11247)
    • Dunham I et al. 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
    • Dunham, I.1
  • 92
    • 84865739425 scopus 로고    scopus 로고
    • Architecture of the human regulatory network derived from ENCODE data
    • doi:10.1038/nature11245)
    • Gerstein MB et al. 2012 Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91-100. (doi:10.1038/nature11245)
    • (2012) Nature , vol.489 , pp. 91-100
    • Gerstein, M.B.1
  • 93
    • 84865708757 scopus 로고    scopus 로고
    • An expansive human regulatory lexicon encoded in transcription factor footprints
    • doi:10.1038/nature11212)
    • Neph S et al. 2012 An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489, 83-90. (doi:10.1038/ nature11212)
    • (2012) Nature , vol.489 , pp. 83-90
    • Neph, S.1
  • 94
    • 84865754452 scopus 로고    scopus 로고
    • Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
    • doi:10.1186/gb-2012-13-9-r48)
    • Yip KY et al. 2012 Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol. 13, R48. (doi:10.1186/gb- 2012-13-9-r48)
    • (2012) Genome Biol , vol.13
    • Yip, K.Y.1
  • 95
    • 84867095528 scopus 로고    scopus 로고
    • A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development
    • doi:10.1016/j.cell.2012.08.027)
    • Paige SL et al. 2012 A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development. Cell 151, 221-232. (doi:10.1016/j.cell.2012.08.027)
    • (2012) Cell , vol.151 , pp. 221-232
    • Paige, S.L.1
  • 96
    • 84867073340 scopus 로고    scopus 로고
    • Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage
    • doi:10.1016/j.cell.2012.07.035)
    • Wamstad JA et al. 2012 Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell 151, 206-220. (doi:10. 1016/j.cell.2012.07.035)
    • (2012) Cell , vol.151 , pp. 206-220
    • Wamstad, J.A.1
  • 97
    • 84868484735 scopus 로고    scopus 로고
    • Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest
    • doi:10.1016/j.stem.2012.07.006)
    • Rada-Iglesias A, Bajpai R, Prescott S, Brugmann SA, Swigut T, Wysocka J. 2012 Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest. Cell Stem Cell 11, 633-648. (doi:10.1016/j.stem.2012.07.006)
    • (2012) Cell Stem Cell , vol.11 , pp. 633-648
    • Rada-Iglesias, A.1    Bajpai, R.2    Prescott, S.3    Brugmann, S.A.4    Swigut, T.5    Wysocka, J.6
  • 98
    • 84878292277 scopus 로고    scopus 로고
    • Transcriptional and epigenetic dynamics during specification of human embryonic stem cells
    • doi:10.1016/j.cell.2013.04.037)
    • Gifford CA et al. 2013 Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell 153, 1149-1163. (doi:10.1016/j. cell.2013.04.037)
    • (2013) Cell , vol.153 , pp. 1149-1163
    • Gifford, C.A.1
  • 99
    • 84878282421 scopus 로고    scopus 로고
    • Epigenomic analysis of multilineage differentiation of human embryonic stem cells
    • (doi:10.1016/j.cell.2013.04.022)
    • Xie W et al. 2013 Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134-1148. (doi:10.1016/j. cell.2013.04.022)
    • (2013) Cell , vol.153 , pp. 1134-1148
    • Xie, W.1
  • 100
    • 78650141540 scopus 로고    scopus 로고
    • A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns
    • (doi:10.1038/nature09632)
    • Domazet-Loso T, Tautz D. 2010 A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature 468, 815-818. (doi:10. 1038/nature09632)
    • (2010) Nature , vol.468 , pp. 815-818
    • Domazet-Loso, T.1    Tautz, D.2
  • 101
    • 79953113902 scopus 로고    scopus 로고
    • Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis
    • (doi:10.1038/ncomms1248)
    • Irie N, Kuratani S. 2011 Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis. Nat. Commun. 2, 248. (doi:10.1038/ ncomms1248)
    • (2011) Nat. Commun , vol.2 , pp. 248
    • Irie, N.1    Kuratani, S.2
  • 102
    • 84860903672 scopus 로고    scopus 로고
    • Developmental milestones punctuate gene expression in the Caenorhabditis embryo
    • doi:10.1016/j.devcel.2012.04.004)
    • Levin M, Hashimshony T, Wagner F, Yanai I. 2012 Developmental milestones punctuate gene expression in the Caenorhabditis embryo. Dev. Cell 22, 1101-1108. (doi:10.1016/j.devcel.2012.04.004)
    • (2012) Dev. Cell , vol.22 , pp. 1101-1108
    • Levin, M.1    Hashimshony, T.2    Wagner, F.3    Yanai, I.4
  • 104
    • 0018199224 scopus 로고
    • DNAse footprinting: A simple method for the detection of protein-DNA binding specificity
    • doi:10.1093/nar/5.9.3157)
    • Galas DJ, Schmitz A. 1978 DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res. 5, 3157-3170. (doi:10.1093/nar/5.9.3157)
    • (1978) Nucleic Acids Res , vol.5 , pp. 3157-3170
    • Galas, D.J.1    Schmitz, A.2
  • 105
    • 63849308888 scopus 로고    scopus 로고
    • Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
    • doi:10.1038/nmeth.1313)
    • Hesselberth JR et al. 2009 Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat. Methods 6, 283-289. (doi:10. 1038/nmeth.1313)
    • (2009) Nat. Methods , vol.6 , pp. 283-289
    • Hesselberth, J.R.1
  • 106
    • 84866361701 scopus 로고    scopus 로고
    • Circuitry and dynamics of human transcription factor regulatory networks
    • doi:10.1016/j.cell.2012.04.040)
    • Neph S, Stergachis AB, Reynolds A, Sandstrom R, Borenstein E, Stamatoyannopoulos JA. 2012 Circuitry and dynamics of human transcription factor regulatory networks. Cell 150, 1274-1286. (doi:10. 1016/j.cell.2012.04.040)
    • (2012) Cell , vol.150 , pp. 1274-1286
    • Neph, S.1    Stergachis, A.B.2    Reynolds, A.3    Sandstrom, R.4    Borenstein, E.5    Stamatoyannopoulos, J.A.6
  • 107
    • 39049130281 scopus 로고    scopus 로고
    • Global control regions and regulatory landscapes in vertebrate development and evolution
    • doi:10.S0065-2660(07)00006-5)
    • Spitz F, Duboule D. 2008 Global control regions and regulatory landscapes in vertebrate development and evolution. Adv. Genet. 61, 175-205. (doi:10. S0065-2660(07)00006-5)
    • (2008) Adv. Genet , vol.61 , pp. 175-205
    • Spitz, F.1    Duboule, D.2
  • 108
    • 84862755561 scopus 로고    scopus 로고
    • Landscapes and archipelagos: Spatial organization of gene regulation in vertebrates
    • doi:10.1016/j.tcb.2012.04.003)
    • Montavon T, Duboule D. 2012 Landscapes and archipelagos: spatial organization of gene regulation in vertebrates. Trends Cell Biol. 22, 347-354. (doi:10.1016/j.tcb.2012.04.003)
    • (2012) Trends Cell Biol , vol.22 , pp. 347-354
    • Montavon, T.1    Duboule, D.2
  • 109
    • 10144238527 scopus 로고    scopus 로고
    • Identification of a hot spot for microdeletions in patients with X-linked deafness type 3 (DFN3)900 kb proximal to the DFN3 gene POU3F4
    • doi:10.1093/hmg/5.9.1229)
    • de Kok YJ et al. 1996 Identification of a hot spot for microdeletions in patients with X-linked deafness type 3 (DFN3)900 kb proximal to the DFN3 gene POU3F4. Hum. Mol. Genet. 5, 1229-1235. (doi:10. 1093/hmg/5.9.1229)
    • (1996) Hum. Mol. Genet , vol.5 , pp. 1229-1235
    • de Kok, Y.J.1
  • 110
    • 23044477774 scopus 로고    scopus 로고
    • Inversion-induced disruption of the Hoxd cluster leads to the partition of regulatory landscapes
    • doi:10.1038/ng1597)
    • Spitz F, Herkenne C, Morris MA, Duboule D. 2005 Inversion-induced disruption of the Hoxd cluster leads to the partition of regulatory landscapes. Nat. Genet. 37, 889-893. (doi:10.1038/ng1597)
    • (2005) Nat. Genet , vol.37 , pp. 889-893
    • Spitz, F.1    Herkenne, C.2    Morris, M.A.3    Duboule, D.4
  • 111
    • 33645073400 scopus 로고    scopus 로고
    • A functional screen for sonic hedgehog regulatory elements across a 1 Mb interval identifies long-range ventral forebrain enhancers
    • doi:10.1242/dev.02239)
    • Jeong Y, El-Jaick K, Roessler E, Muenke M, Epstein DJ. 2006 A functional screen for sonic hedgehog regulatory elements across a 1 Mb interval identifies long-range ventral forebrain enhancers. Development 133, 761-772. (doi:10.1242/dev. 02239)
    • (2006) Development , vol.133 , pp. 761-772
    • Jeong, Y.1    El-Jaick, K.2    Roessler, E.3    Muenke, M.4    Epstein, D.J.5
  • 116
    • 70149102036 scopus 로고    scopus 로고
    • Conservation of enhancer location in divergent insects
    • (doi:10.1073/pnas.0905754106)
    • Cande J, Goltsev Y, Levine MS. 2009 Conservation of enhancer location in divergent insects. Proc. Natl Acad. Sci. USA 106, 14 414-14 419. (doi:10.1073/ pnas.0905754106)
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , Issue.14 , pp. 414-419
    • Cande, J.1    Goltsev, Y.2    Levine, M.S.3
  • 117
    • 34248153777 scopus 로고    scopus 로고
    • Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
    • (doi:10.1101/gr.6086307)
    • Kikuta H et al. 2007 Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res. 17, 545-555. (doi:10.1101/gr.6086307)
    • (2007) Genome Res , vol.17 , pp. 545-555
    • Kikuta, H.1
  • 118
    • 84859541999 scopus 로고    scopus 로고
    • An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
    • (doi:10.1101/gr.132233.111)
    • Maeso I et al. 2012 An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement. Genome Res. 22, 642-655. (doi:10.1101/gr.132233. 111)
    • (2012) Genome Res , vol.22 , pp. 642-655
    • Maeso, I.1
  • 119
    • 84870512646 scopus 로고    scopus 로고
    • Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints
    • doi:10.1101/gr.139725.112)
    • Irimia M et al. 2012 Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints. Genome Res. 22, 2356-2367. (doi:10.1101/gr.139725.112)
    • (2012) Genome Res , vol.22 , pp. 2356-2367
    • Irimia, M.1
  • 120
    • 84882611819 scopus 로고    scopus 로고
    • Ancient cis-regulatory constraints and the evolution of genome architecture
    • doi:10.1016/j.tig.2013.05.008)
    • Irimia M, Maeso I, Roy SW, Fraser HB. 2013 Ancient cis-regulatory constraints and the evolution of genome architecture. Trends Genet. 29, 521-528. (doi:10.1016/j.tig.2013.05.008)
    • (2013) Trends Genet , vol.29 , pp. 521-528
    • Irimia, M.1    Maeso, I.2    Roy, S.W.3    Fraser, H.B.4
  • 121
    • 57849155689 scopus 로고    scopus 로고
    • Evolution of Otx paralogue usages in early patterning of the vertebrate head
    • doi:10.1016/j.ydbio.2008.09.018)
    • Suda Y, Kurokawa D, Takeuchi M, Kajikawa E, Kuratani S, Amemiya C, Aizawa S. 2009 Evolution of Otx paralogue usages in early patterning of the vertebrate head. Dev. Biol. 325, 282-295. (doi:10. 1016/j.ydbio.2008.09.018)
    • (2009) Dev. Biol , vol.325 , pp. 282-295
    • Suda, Y.1    Kurokawa, D.2    Takeuchi, M.3    Kajikawa, E.4    Kuratani, S.5    Amemiya, C.6    Aizawa, S.7
  • 122
    • 0031919446 scopus 로고    scopus 로고
    • Tripartite organization of the ancestral chordate brain and the antiquity of placodes: Insights from ascidian Pax-2/5/8, Hox and Otx genes
    • Wada H, Saiga H, Satoh N, Holland PW. 1998 Tripartite organization of the ancestral chordate brain and the antiquity of placodes: insights from ascidian Pax-2/5/8, Hox and Otx genes. Development 125, 1113-1122.
    • (1998) Development , vol.125 , pp. 1113-1122
    • Wada, H.1    Saiga, H.2    Satoh, N.3    Holland, P.W.4
  • 123
    • 84872020892 scopus 로고    scopus 로고
    • Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state
    • doi:10.1371/journal. pcbi.1002798)
    • Wilczynski B, Liu YH, Yeo ZX, Furlong EE. 2012 Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state. PLoS Comput. Biol. 8, e1002798. (doi:10.1371/journal. pcbi.1002798)
    • (2012) PLoS Comput. Biol , vol.8
    • Wilczynski, B.1    Liu, Y.H.2    Yeo, Z.X.3    Furlong, E.E.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.