메뉴 건너뛰기




Volumn 32, Issue 5, 2016, Pages 269-283

Evolution of Epigenetic Regulation in Vertebrate Genomes

Author keywords

Epigenome evolution; Gene regulation; Vertebrate genomics

Indexed keywords

HISTONE; TRANSCRIPTION FACTOR;

EID: 84963731960     PISSN: 01689525     EISSN: 13624555     Source Type: Journal    
DOI: 10.1016/j.tig.2016.03.001     Document Type: Review
Times cited : (57)

References (105)
  • 1
    • 84891478098 scopus 로고    scopus 로고
    • Chromatin organization and global regulation of Hox gene clusters
    • Montavon T., Duboule D. Chromatin organization and global regulation of Hox gene clusters. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 2013, 368:20120367.
    • (2013) Philos. Trans. R. Soc. Lond. B: Biol. Sci. , vol.368 , pp. 20120367
    • Montavon, T.1    Duboule, D.2
  • 2
    • 80053555789 scopus 로고    scopus 로고
    • More than just a focus: the chromatin response to DNA damage and its role in genome integrity maintenance
    • Lukas J., et al. More than just a focus: the chromatin response to DNA damage and its role in genome integrity maintenance. Nat. Cell Biol. 2011, 13:1161-1169.
    • (2011) Nat. Cell Biol. , vol.13 , pp. 1161-1169
    • Lukas, J.1
  • 3
    • 79955482843 scopus 로고    scopus 로고
    • Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development
    • Okamoto I., et al. Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development. Nature 2011, 472:370-374.
    • (2011) Nature , vol.472 , pp. 370-374
    • Okamoto, I.1
  • 4
    • 66049083160 scopus 로고    scopus 로고
    • X inactivation and the complexities of silencing a sex chromosome
    • Chow J., Heard E. X inactivation and the complexities of silencing a sex chromosome. Curr. Opin. Cell Biol. 2009, 21:359-366.
    • (2009) Curr. Opin. Cell Biol. , vol.21 , pp. 359-366
    • Chow, J.1    Heard, E.2
  • 5
    • 84864867828 scopus 로고    scopus 로고
    • Establishment of epigenetic patterns in development
    • Leeb M., Wutz A. Establishment of epigenetic patterns in development. Chromosoma 2012, 121:251-262.
    • (2012) Chromosoma , vol.121 , pp. 251-262
    • Leeb, M.1    Wutz, A.2
  • 6
    • 0024870633 scopus 로고
    • The biological homology concept
    • Wagner G.P. The biological homology concept. Annu. Rev. Ecol. Syst. 1989, 20:51-69.
    • (1989) Annu. Rev. Ecol. Syst. , vol.20 , pp. 51-69
    • Wagner, G.P.1
  • 7
    • 78650410139 scopus 로고    scopus 로고
    • Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
    • Gerstein M.B., et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 2010, 330:1775-1787.
    • (2010) Science , vol.330 , pp. 1775-1787
    • Gerstein, M.B.1
  • 8
    • 78650331647 scopus 로고    scopus 로고
    • Identification of functional elements and regulatory circuits by Drosophila modENCODE
    • Consortium modENCODE., et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010, 330:1787-1797.
    • (2010) Science , vol.330 , pp. 1787-1797
    • Consortium, M.1
  • 9
    • 84923362619 scopus 로고    scopus 로고
    • Integrative analysis of 111 reference human epigenomes
    • Consortium R.E., et al. Integrative analysis of 111 reference human epigenomes. Nature 2015, 518:317-330.
    • (2015) Nature , vol.518 , pp. 317-330
    • Consortium, R.E.1
  • 10
    • 84865121188 scopus 로고    scopus 로고
    • An encyclopedia of mouse DNA elements (Mouse ENCODE)
    • Mouse ENCODE Consortium, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012, 13:418.
    • (2012) Genome Biol. , vol.13 , pp. 418
  • 11
    • 0014421064 scopus 로고
    • Evolutionary rate at the molecular level
    • Kimura M. Evolutionary rate at the molecular level. Nature 1968, 217:624-626.
    • (1968) Nature , vol.217 , pp. 624-626
    • Kimura, M.1
  • 12
    • 33751316959 scopus 로고    scopus 로고
    • In vivo enhancer analysis of human conserved non-coding sequences
    • Pennacchio L.A., et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 2006, 444:499-502.
    • (2006) Nature , vol.444 , pp. 499-502
    • Pennacchio, L.A.1
  • 13
    • 84866150923 scopus 로고    scopus 로고
    • Human developmental enhancers conserved between deuterostomes and protostomes
    • Clarke S.L., et al. Human developmental enhancers conserved between deuterostomes and protostomes. PLoS Genet. 2012, 8:e1002852.
    • (2012) PLoS Genet. , vol.8
    • Clarke, S.L.1
  • 14
    • 34250365369 scopus 로고    scopus 로고
    • Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    • Margulies E.H., et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007, 17:760-774.
    • (2007) Genome Res. , vol.17 , pp. 760-774
    • Margulies, E.H.1
  • 15
    • 39049086371 scopus 로고    scopus 로고
    • Qualifying the relationship between sequence conservation and molecular function
    • Cooper G.M., Brown C.D. Qualifying the relationship between sequence conservation and molecular function. Genome Res. 2008, 18:201-205.
    • (2008) Genome Res. , vol.18 , pp. 201-205
    • Cooper, G.M.1    Brown, C.D.2
  • 16
    • 0016669094 scopus 로고
    • Evolution at two levels in humans and chimpanzees
    • King M.C., Wilson A.C. Evolution at two levels in humans and chimpanzees. Science 1975, 188:107-116.
    • (1975) Science , vol.188 , pp. 107-116
    • King, M.C.1    Wilson, A.C.2
  • 17
    • 33847057226 scopus 로고    scopus 로고
    • The evolutionary significance of cis-regulatory mutations
    • Wray G.A. The evolutionary significance of cis-regulatory mutations. Nat. Rev. Genet. 2007, 8:206-216.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 206-216
    • Wray, G.A.1
  • 18
    • 77953271655 scopus 로고    scopus 로고
    • Comparative assessment of methods for aligning multiple genome sequences
    • Chen X., Tompa M. Comparative assessment of methods for aligning multiple genome sequences. Nat. Biotechnol. 2010, 28:567-572.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 567-572
    • Chen, X.1    Tompa, M.2
  • 19
    • 0014690698 scopus 로고
    • Gene regulation for higher cells: a theory
    • Britten R.J., Davidson E.H. Gene regulation for higher cells: a theory. Science 1969, 165:349-357.
    • (1969) Science , vol.165 , pp. 349-357
    • Britten, R.J.1    Davidson, E.H.2
  • 21
    • 77954100084 scopus 로고    scopus 로고
    • Transposable elements have rewired the core regulatory network of human embryonic stem cells
    • Kunarso G., et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat. Genet. 2010, 42:631-634.
    • (2010) Nat. Genet. , vol.42 , pp. 631-634
    • Kunarso, G.1
  • 22
    • 77956641239 scopus 로고    scopus 로고
    • ChIP-Seq identification of weakly conserved heart enhancers
    • Blow M.J., et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat. Genet. 2010, 42:806-810.
    • (2010) Nat. Genet. , vol.42 , pp. 806-810
    • Blow, M.J.1
  • 23
    • 84929320904 scopus 로고    scopus 로고
    • Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility
    • Dogan N., et al. Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. Epigenetics Chromatin 2015, 8:16.
    • (2015) Epigenetics Chromatin , vol.8 , pp. 16
    • Dogan, N.1
  • 24
    • 0028143457 scopus 로고
    • Comparative analysis of Igf-2/H19 imprinted domain: identification of a highly conserved intergenic DNase I hypersensitive region
    • Koide T., et al. Comparative analysis of Igf-2/H19 imprinted domain: identification of a highly conserved intergenic DNase I hypersensitive region. Genomics 1994, 24:1-8.
    • (1994) Genomics , vol.24 , pp. 1-8
    • Koide, T.1
  • 25
    • 0031593199 scopus 로고    scopus 로고
    • Locus control regions of mammalian β-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights
    • Hardison R., et al. Locus control regions of mammalian β-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights. Gene 1997, 205:73-94.
    • (1997) Gene , vol.205 , pp. 73-94
    • Hardison, R.1
  • 26
    • 0344011426 scopus 로고    scopus 로고
    • Differential transcription factor occupancy but evolutionarily conserved chromatin features at the human and mouse M-CSF (CSF-1) receptor loci
    • Follows G.A., et al. Differential transcription factor occupancy but evolutionarily conserved chromatin features at the human and mouse M-CSF (CSF-1) receptor loci. Nucleic Acids Res. 2003, 31:5805-5816.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5805-5816
    • Follows, G.A.1
  • 27
    • 33751234242 scopus 로고    scopus 로고
    • The human and mouse H19 imprinting control regions harbor an evolutionarily conserved silencer element that functions on transgenes in Drosophila
    • Arney K.L., et al. The human and mouse H19 imprinting control regions harbor an evolutionarily conserved silencer element that functions on transgenes in Drosophila. Dev. Genes Evol. 2006, 216:811-819.
    • (2006) Dev. Genes Evol. , vol.216 , pp. 811-819
    • Arney, K.L.1
  • 28
    • 48249141249 scopus 로고    scopus 로고
    • Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians
    • Smits G., et al. Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians. Nat. Genet. 2008, 40:971-976.
    • (2008) Nat. Genet. , vol.40 , pp. 971-976
    • Smits, G.1
  • 29
    • 0033634728 scopus 로고    scopus 로고
    • M6P/IGF2R imprinting evolution in mammals
    • Killian J.K., et al. M6P/IGF2R imprinting evolution in mammals. Mol. Cell 2000, 5:707-716.
    • (2000) Mol. Cell , vol.5 , pp. 707-716
    • Killian, J.K.1
  • 30
    • 84926098534 scopus 로고    scopus 로고
    • Sequence-level mechanisms of human epigenome evolution
    • Prendergast J.G.D., et al. Sequence-level mechanisms of human epigenome evolution. Genome Biol. Evol. 2014, 6:1758-1771.
    • (2014) Genome Biol. Evol. , vol.6 , pp. 1758-1771
    • Prendergast, J.G.D.1
  • 31
    • 84884678913 scopus 로고    scopus 로고
    • Dynamics of DNA methylation in recent human and great ape evolution
    • Hernando-Herraez I., et al. Dynamics of DNA methylation in recent human and great ape evolution. PLoS Genet. 2013, 9:e1003763-e1003812.
    • (2013) PLoS Genet. , vol.9 , pp. e1003763-e1003812
    • Hernando-Herraez, I.1
  • 32
    • 84949024094 scopus 로고    scopus 로고
    • The interplay between DNA methylation and sequence divergence in recent human evolution
    • Hernando-Herraez I., et al. The interplay between DNA methylation and sequence divergence in recent human evolution. Nucleic Acids Res. 2015, 43:8204-8214.
    • (2015) Nucleic Acids Res. , vol.43 , pp. 8204-8214
    • Hernando-Herraez, I.1
  • 33
    • 84924561748 scopus 로고    scopus 로고
    • Evolutionary changes in promoter and enhancer activity during human corticogenesis
    • Reilly S.K., et al. Evolutionary changes in promoter and enhancer activity during human corticogenesis. Science 2015, 347:1155-1159.
    • (2015) Science , vol.347 , pp. 1155-1159
    • Reilly, S.K.1
  • 34
    • 84861977900 scopus 로고    scopus 로고
    • Comparative epigenomic annotation of regulatory DNA
    • Xiao S., et al. Comparative epigenomic annotation of regulatory DNA. Cell 2012, 149:1381-1392.
    • (2012) Cell , vol.149 , pp. 1381-1392
    • Xiao, S.1
  • 35
    • 33745772571 scopus 로고    scopus 로고
    • New methods for detecting lineage-specific selection
    • Springer Berlin Heidelberg
    • Siepel A., et al. New methods for detecting lineage-specific selection. Research in Computational Molecular Biology 2006, Vol. 3909:190-205. Springer Berlin Heidelberg.
    • (2006) Research in Computational Molecular Biology , vol.3909 , pp. 190-205
    • Siepel, A.1
  • 36
    • 84879911829 scopus 로고    scopus 로고
    • The evolution of lineage-specific regulatory activities in the human embryonic limb
    • Cotney J., et al. The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell 2013, 154:185-196.
    • (2013) Cell , vol.154 , pp. 185-196
    • Cotney, J.1
  • 37
    • 0026001046 scopus 로고
    • CpG islands: features and distribution in the genomes of vertebrates
    • Aïssani B., Bernardi G. CpG islands: features and distribution in the genomes of vertebrates. Gene 1991, 106:173-183.
    • (1991) Gene , vol.106 , pp. 173-183
    • Aïssani, B.1    Bernardi, G.2
  • 38
    • 84879049092 scopus 로고    scopus 로고
    • Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates
    • Long H.K., et al. Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. Elife 2013, 2:e00348.
    • (2013) Elife , vol.2
    • Long, H.K.1
  • 39
    • 0021924990 scopus 로고
    • Effect of regional DNA methylation on gene expression
    • Keshet I., et al. Effect of regional DNA methylation on gene expression. Proc. Natl. Acad. Sci. U.S.A. 1985, 82:2560-2564.
    • (1985) Proc. Natl. Acad. Sci. U.S.A. , vol.82 , pp. 2560-2564
    • Keshet, I.1
  • 40
    • 0023057868 scopus 로고
    • In vitro methylation inhibits the promotor activity of a cloned intracisternal A-particle LTR
    • Feenastr A., et al. In vitro methylation inhibits the promotor activity of a cloned intracisternal A-particle LTR. Nucleic Acids Res. 1986, 14:4343-4352.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 4343-4352
    • Feenastr, A.1
  • 41
    • 38949212693 scopus 로고    scopus 로고
    • A novel CpG island set identifies tissue-specific methylation at developmental gene loci
    • Illingworth R., et al. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 2008, 6:e22.
    • (2008) PLoS Biol. , vol.6 , pp. e22
    • Illingworth, R.1
  • 42
    • 79952265169 scopus 로고    scopus 로고
    • A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues
    • Pai A.A., et al. A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PLoS Genet. 2011, 7:e1001316.
    • (2011) PLoS Genet. , vol.7
    • Pai, A.A.1
  • 43
    • 0036144048 scopus 로고    scopus 로고
    • DNA methylation patterns and epigenetic memory
    • Bird A. DNA methylation patterns and epigenetic memory. Genes Dev. 2002, 16:6-21.
    • (2002) Genes Dev. , vol.16 , pp. 6-21
    • Bird, A.1
  • 44
    • 84923345958 scopus 로고    scopus 로고
    • Intermediate DNA methylation is a conserved signature of genome regulation
    • Elliott G., et al. Intermediate DNA methylation is a conserved signature of genome regulation. Nat. Commun. 2015, 6:6363.
    • (2015) Nat. Commun. , vol.6 , pp. 6363
    • Elliott, G.1
  • 45
    • 43749098985 scopus 로고    scopus 로고
    • DNA methylation landscapes: provocative insights from epigenomics
    • Suzuki M.M., Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet. 2008, 9:465-476.
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 465-476
    • Suzuki, M.M.1    Bird, A.2
  • 46
    • 80054994283 scopus 로고    scopus 로고
    • Identification of genetic elements that autonomously determine DNA methylation states
    • Lienert F., et al. Identification of genetic elements that autonomously determine DNA methylation states. Nat. Genet. 2011, 43:1091-1097.
    • (2011) Nat. Genet. , vol.43 , pp. 1091-1097
    • Lienert, F.1
  • 47
    • 84899093961 scopus 로고    scopus 로고
    • DNA methylation and evolution of duplicate genes
    • Keller T.E., Yi S.V. DNA methylation and evolution of duplicate genes. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:5932-5937.
    • (2014) Proc. Natl. Acad. Sci. U.S.A. , vol.111 , pp. 5932-5937
    • Keller, T.E.1    Yi, S.V.2
  • 48
    • 0027960055 scopus 로고
    • Sp1 sites in the mouse Aprt gene promoter are required to prevent methylation of the CpG island
    • Macleod D., et al. Sp1 sites in the mouse Aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev. 1994, 8:2282-2292.
    • (1994) Genes Dev. , vol.8 , pp. 2282-2292
    • Macleod, D.1
  • 49
    • 84892690160 scopus 로고    scopus 로고
    • Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions
    • Feldmann A., et al. Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions. PLoS Genet. 2013, 9:e1003994.
    • (2013) PLoS Genet. , vol.9
    • Feldmann, A.1
  • 50
    • 84922621952 scopus 로고    scopus 로고
    • Function and information content of DNA methylation
    • Schübeler D. Function and information content of DNA methylation. Nature 2015, 517:321-326.
    • (2015) Nature , vol.517 , pp. 321-326
    • Schübeler, D.1
  • 51
    • 84922295278 scopus 로고    scopus 로고
    • Enhancer evolution across 20 mammalian species
    • Villar D., et al. Enhancer evolution across 20 mammalian species. Cell 2015, 160:554-566.
    • (2015) Cell , vol.160 , pp. 554-566
    • Villar, D.1
  • 52
    • 77952734605 scopus 로고    scopus 로고
    • Conservation and divergence of methylation patterning in plants and animals
    • Feng S., et al. Conservation and divergence of methylation patterning in plants and animals. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:8689-8694.
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 8689-8694
    • Feng, S.1
  • 53
    • 77952355762 scopus 로고    scopus 로고
    • Genome-wide evolutionary analysis of eukaryotic DNA methylation
    • Zemach A., et al. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 2010, 328:916-919.
    • (2010) Science , vol.328 , pp. 916-919
    • Zemach, A.1
  • 54
    • 69949132191 scopus 로고    scopus 로고
    • Chromatin organization marks exon-intron structure
    • Schwartz S., et al. Chromatin organization marks exon-intron structure. Nat. Struct. Mol. Biol. 2009, 16:990-995.
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 990-995
    • Schwartz, S.1
  • 55
    • 84859033105 scopus 로고    scopus 로고
    • DNA methylation rebalances gene dosage after mammalian gene duplications
    • Chang A.Y-F., Liao B-Y. DNA methylation rebalances gene dosage after mammalian gene duplications. Mol. Biol. Evol. 2012, 29:133-144.
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 133-144
    • Chang, A.Y.-F.1    Liao, B.-Y.2
  • 56
    • 84866081028 scopus 로고    scopus 로고
    • Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution
    • Zeng J., et al. Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution. Am. J. Hum. Genet. 2012, 91:455-465.
    • (2012) Am. J. Hum. Genet. , vol.91 , pp. 455-465
    • Zeng, J.1
  • 57
    • 84940752163 scopus 로고    scopus 로고
    • Early developmental and evolutionary origins of gene body DNA methylation patterns in mammalian placentas
    • Schroeder D.I., et al. Early developmental and evolutionary origins of gene body DNA methylation patterns in mammalian placentas. PLoS Genet. 2015, 11:e1005442.
    • (2015) PLoS Genet. , vol.11
    • Schroeder, D.I.1
  • 58
    • 61349098460 scopus 로고    scopus 로고
    • Differential chromatin marking of introns and expressed exons by H3K36me3
    • Kolasinska-Zwierz P., et al. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat. Genet. 2009, 41:376-381.
    • (2009) Nat. Genet. , vol.41 , pp. 376-381
    • Kolasinska-Zwierz, P.1
  • 59
    • 77149175671 scopus 로고    scopus 로고
    • Regulation of alternative splicing by histone modifications
    • Luco R.F., et al. Regulation of alternative splicing by histone modifications. Science 2010, 327:996-1000.
    • (2010) Science , vol.327 , pp. 996-1000
    • Luco, R.F.1
  • 60
    • 84956647649 scopus 로고    scopus 로고
    • Regulation of mismatch repair by histone code and posttranslational modifications in eukaryotic cells
    • Li F., et al. Regulation of mismatch repair by histone code and posttranslational modifications in eukaryotic cells. DNA Repair 2016, 38:68-74.
    • (2016) DNA Repair , vol.38 , pp. 68-74
    • Li, F.1
  • 61
    • 84938830634 scopus 로고    scopus 로고
    • Chromatin signature identifies monoallelic gene expression across mammalian cell types
    • Nag A., et al. Chromatin signature identifies monoallelic gene expression across mammalian cell types. G3 2015, 5:1713-1720.
    • (2015) G3 , vol.5 , pp. 1713-1720
    • Nag, A.1
  • 62
    • 65549104157 scopus 로고    scopus 로고
    • Histone modifications at human enhancers reflect global cell-type-specific gene expression
    • Heintzman N.D., et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 2009, 459:108-112.
    • (2009) Nature , vol.459 , pp. 108-112
    • Heintzman, N.D.1
  • 63
    • 84890397089 scopus 로고    scopus 로고
    • Predicting enhancer transcription and activity from chromatin modifications
    • Zhu Y., et al. Predicting enhancer transcription and activity from chromatin modifications. Nucleic Acids Res. 2013, 41:10032-10043.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 10032-10043
    • Zhu, Y.1
  • 64
    • 84355163093 scopus 로고    scopus 로고
    • DNA-binding factors shape the mouse methylome at distal regulatory regions
    • Stadler M.B., et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 2011, 480:490-495.
    • (2011) Nature , vol.480 , pp. 490-495
    • Stadler, M.B.1
  • 66
    • 84872020892 scopus 로고    scopus 로고
    • Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state
    • Wilczynski B., et al. Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state. PLoS Comput. Biol. 2012, 8:e1002798.
    • (2012) PLoS Comput. Biol. , vol.8
    • Wilczynski, B.1
  • 67
    • 84891390867 scopus 로고    scopus 로고
    • Effects of gene regulatory reprogramming on gene expression in human and mouse developing hearts
    • Hsu C-H., Ovcharenko I. Effects of gene regulatory reprogramming on gene expression in human and mouse developing hearts. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 2013, 368:20120366.
    • (2013) Philos. Trans. R. Soc. Lond. B: Biol. Sci. , vol.368 , pp. 20120366
    • Hsu, C.-H.1    Ovcharenko, I.2
  • 68
    • 77957220857 scopus 로고    scopus 로고
    • Comparative epigenomic analysis of murine and human adipogenesis
    • Mikkelsen T.S., et al. Comparative epigenomic analysis of murine and human adipogenesis. Cell 2010, 143:156-169.
    • (2010) Cell , vol.143 , pp. 156-169
    • Mikkelsen, T.S.1
  • 69
    • 84948457844 scopus 로고    scopus 로고
    • Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest
    • Prescott S.L., et al. Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. Cell 2015, 163:68-83.
    • (2015) Cell , vol.163 , pp. 68-83
    • Prescott, S.L.1
  • 70
    • 84904250693 scopus 로고    scopus 로고
    • Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period
    • Tena J.J., et al. Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period. Genome Res. 2014, 24:1075-1085.
    • (2014) Genome Res. , vol.24 , pp. 1075-1085
    • Tena, J.J.1
  • 71
    • 84868484735 scopus 로고    scopus 로고
    • Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest
    • Rada-Iglesias A., et al. Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest. Cell Stem Cell 2012, 11:633-648.
    • (2012) Cell Stem Cell , vol.11 , pp. 633-648
    • Rada-Iglesias, A.1
  • 72
    • 84925680345 scopus 로고    scopus 로고
    • Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework
    • Yokoyama K.D., et al. Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework. PLoS Comput. Biol. 2014, 10:e1003771.
    • (2014) PLoS Comput. Biol. , vol.10
    • Yokoyama, K.D.1
  • 73
    • 84881141882 scopus 로고    scopus 로고
    • Cooperativity and rapid evolution of cobound transcription factors in closely related mammals
    • Stefflova K., et al. Cooperativity and rapid evolution of cobound transcription factors in closely related mammals. Cell 2013, 154:530-540.
    • (2013) Cell , vol.154 , pp. 530-540
    • Stefflova, K.1
  • 74
    • 0028853170 scopus 로고
    • NF-E2 and GATA binding motifs are required for the formation of DNase I hypersensitive site 4 of the human beta-globin locus control region
    • Stamatoyannopoulos J.A., et al. NF-E2 and GATA binding motifs are required for the formation of DNase I hypersensitive site 4 of the human beta-globin locus control region. EMBO J. 1995, 14:106-116.
    • (1995) EMBO J. , vol.14 , pp. 106-116
    • Stamatoyannopoulos, J.A.1
  • 75
    • 84911494217 scopus 로고    scopus 로고
    • Principles of regulatory information conservation between mouse and human
    • Cheng Y., et al. Principles of regulatory information conservation between mouse and human. Nature 2014, 515:371-375.
    • (2014) Nature , vol.515 , pp. 371-375
    • Cheng, Y.1
  • 76
    • 84911936991 scopus 로고    scopus 로고
    • Widespread contribution of transposable elements to the innovation of gene regulatory networks
    • Sundaram V., et al. Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res. 2014, 24:1963-1976.
    • (2014) Genome Res. , vol.24 , pp. 1963-1976
    • Sundaram, V.1
  • 77
    • 34249818182 scopus 로고    scopus 로고
    • Tissue-specific transcriptional regulation has diverged significantly between human and mouse
    • Odom D.T., et al. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat. Genet. 2007, 39:730-732.
    • (2007) Nat. Genet. , vol.39 , pp. 730-732
    • Odom, D.T.1
  • 78
    • 77953062527 scopus 로고    scopus 로고
    • Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
    • Schmidt D., et al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 2010, 328:1036-1040.
    • (2010) Science , vol.328 , pp. 1036-1040
    • Schmidt, D.1
  • 79
    • 84864073098 scopus 로고    scopus 로고
    • Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection
    • Shibata Y., et al. Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLoS Genet. 2012, 8:e1002789.
    • (2012) PLoS Genet. , vol.8
    • Shibata, Y.1
  • 80
    • 84911462077 scopus 로고    scopus 로고
    • A comparative encyclopedia of DNA elements in the mouse genome
    • Yue F., et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature 2014, 515:355-364.
    • (2014) Nature , vol.515 , pp. 355-364
    • Yue, F.1
  • 81
    • 19944430797 scopus 로고    scopus 로고
    • Genomic maps and comparative analysis of histone modifications in human and mouse
    • Bernstein B.E., et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 2005, 120:169-181.
    • (2005) Cell , vol.120 , pp. 169-181
    • Bernstein, B.E.1
  • 82
    • 84928236059 scopus 로고    scopus 로고
    • Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates
    • Chalopin D., et al. Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biol. Evol. 2015, 7:567-580.
    • (2015) Genome Biol. Evol. , vol.7 , pp. 567-580
    • Chalopin, D.1
  • 83
    • 33646928347 scopus 로고    scopus 로고
    • A distal enhancer and an ultraconserved exon are derived from a novel retroposon
    • Bejerano G., et al. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 2006, 441:87-90.
    • (2006) Nature , vol.441 , pp. 87-90
    • Bejerano, G.1
  • 84
    • 84877749322 scopus 로고    scopus 로고
    • Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong?
    • de Souza F.S.J., et al. Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong?. Mol. Biol. Evol. 2013, 30:1239-1251.
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 1239-1251
    • de Souza, F.S.J.1
  • 85
    • 42349096534 scopus 로고    scopus 로고
    • Transposable elements and the evolution of regulatory networks
    • Feschotte C. Transposable elements and the evolution of regulatory networks. Nat. Rev. Genet. 2008, 9:397-405.
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 397-405
    • Feschotte, C.1
  • 86
    • 0035986888 scopus 로고    scopus 로고
    • Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover
    • Dermitzakis E.T., Clark A.G. Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover. Mol. Biol. Evol. 2002, 19:1114-1121.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1114-1121
    • Dermitzakis, E.T.1    Clark, A.G.2
  • 87
    • 33744824906 scopus 로고    scopus 로고
    • Evolutionary turnover of mammalian transcription start sites
    • Frith M.C. Evolutionary turnover of mammalian transcription start sites. Genome Res. 2006, 16:713-722.
    • (2006) Genome Res. , vol.16 , pp. 713-722
    • Frith, M.C.1
  • 88
    • 84911470871 scopus 로고    scopus 로고
    • Conservation of trans-acting circuitry during mammalian regulatory evolution
    • Stergachis A.B., et al. Conservation of trans-acting circuitry during mammalian regulatory evolution. Nature 2014, 515:365-370.
    • (2014) Nature , vol.515 , pp. 365-370
    • Stergachis, A.B.1
  • 89
    • 0028104109 scopus 로고
    • Spl elements protect a CpG island from de novo methylation
    • Brandeis M., et al. Spl elements protect a CpG island from de novo methylation. Nature 1994, 371:435-438.
    • (1994) Nature , vol.371 , pp. 435-438
    • Brandeis, M.1
  • 90
    • 59149084538 scopus 로고    scopus 로고
    • The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
    • Irizarry R.A., et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet. 2009, 41:178-186.
    • (2009) Nat. Genet. , vol.41 , pp. 178-186
    • Irizarry, R.A.1
  • 91
    • 76549135113 scopus 로고    scopus 로고
    • Colloquium paper: stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease
    • Feinberg A.P., Irizarry R.A. Colloquium paper: stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:1757-1764.
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 1757-1764
    • Feinberg, A.P.1    Irizarry, R.A.2
  • 92
    • 84855278198 scopus 로고    scopus 로고
    • Combinatorial binding in human and mouse embryonic stem cells identifies conserved enhancers active in early embryonic development
    • Göke J., et al. Combinatorial binding in human and mouse embryonic stem cells identifies conserved enhancers active in early embryonic development. PLoS Comput. Biol. 2011, 7:e1002304.
    • (2011) PLoS Comput. Biol. , vol.7
    • Göke, J.1
  • 93
    • 51149203927 scopus 로고
    • Canalization of development and the inheritance of acquired characters
    • Waddington C.H. Canalization of development and the inheritance of acquired characters. Nature 1942, 150:563-565.
    • (1942) Nature , vol.150 , pp. 563-565
    • Waddington, C.H.1
  • 94
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.S.1
  • 95
    • 84882766972 scopus 로고    scopus 로고
    • Developmental fate and cellular maturity encoded in human regulatory DNA landscapes
    • Stergachis A.B., et al. Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell 2013, 154:888-903.
    • (2013) Cell , vol.154 , pp. 888-903
    • Stergachis, A.B.1
  • 96
    • 0026546877 scopus 로고
    • A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands
    • Frommer M., et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. U.S.A. 1992, 89:1827-1831.
    • (1992) Proc. Natl. Acad. Sci. U.S.A. , vol.89 , pp. 1827-1831
    • Frommer, M.1
  • 97
    • 27144500218 scopus 로고    scopus 로고
    • Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis
    • Meissner A., et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005, 33:5868-5877.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 5868-5877
    • Meissner, A.1
  • 98
    • 77954504873 scopus 로고    scopus 로고
    • Conserved role of intragenic DNA methylation in regulating alternative promoters
    • Maunakea A.K., et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 2010, 466:253-257.
    • (2010) Nature , vol.466 , pp. 253-257
    • Maunakea, A.K.1
  • 99
    • 84863256915 scopus 로고    scopus 로고
    • Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA
    • Blackledge N.P., et al. Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA. Nucleic Acids Res. 2012, 40:e32.
    • (2012) Nucleic Acids Res. , vol.40 , pp. e32
    • Blackledge, N.P.1
  • 100
    • 34249026300 scopus 로고    scopus 로고
    • High-resolution profiling of histone methylations in the human genome
    • Barski A., 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
  • 101
    • 84865755978 scopus 로고    scopus 로고
    • The accessible chromatin landscape of the human genome
    • Thurman R.E., et al. The accessible chromatin landscape of the human genome. Nature 2012, 489:75-82.
    • (2012) Nature , vol.489 , pp. 75-82
    • Thurman, R.E.1
  • 102
    • 0036645169 scopus 로고    scopus 로고
    • Transcription factor complex formation and chromatin fine structure alterations at the murine c-Fms (CSF-1 receptor) locus during maturation of myeloid precursor cells
    • Tagoh H., et al. Transcription factor complex formation and chromatin fine structure alterations at the murine c-Fms (CSF-1 receptor) locus during maturation of myeloid precursor cells. Genes Dev. 2002, 16:1721-1737.
    • (2002) Genes Dev. , vol.16 , pp. 1721-1737
    • Tagoh, H.1
  • 103
    • 1642512344 scopus 로고    scopus 로고
    • Evolution of eyes and photoreceptor cell types
    • Arendt D. Evolution of eyes and photoreceptor cell types. Int. J. Dev. Biol. 2003, 47:563-571.
    • (2003) Int. J. Dev. Biol. , vol.47 , pp. 563-571
    • Arendt, D.1
  • 104
    • 34249034031 scopus 로고    scopus 로고
    • The developmental genetics of homology
    • Wagner G.P. The developmental genetics of homology. Nat. Rev. Genet. 2007, 8:473-479.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 473-479
    • Wagner, G.P.1
  • 105
    • 84876940752 scopus 로고    scopus 로고
    • Divergence of mammalian higher order chromatin structure is associated with developmental loci
    • Chambers E.V., et al. Divergence of mammalian higher order chromatin structure is associated with developmental loci. PLoS Comput. Biol. 2013, 9:e1003017.
    • (2013) PLoS Comput. Biol. , vol.9
    • Chambers, E.V.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.