메뉴 건너뛰기




Volumn 368, Issue 1632, 2013, Pages

Beyond the ENCODE project: Using genomics and epigenomics strategies to study enhancer evolution

Author keywords

Enhancer; Evolution; Genomics; Transcription

Indexed keywords

BIOCHEMISTRY; CHROMOSOME; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENOMICS; PROTEIN;

EID: 84887463729     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2013.0022     Document Type: Article
Times cited : (13)

References (62)
  • 1
    • 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
  • 2
    • 0042810698 scopus 로고    scopus 로고
    • A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly
    • (doi:10.1093/hmg/ddg180)
    • Lettice LA et al. 2003 A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet. 12, 1725-1735. (doi:10.1093/hmg/ ddg180)
    • (2003) Hum. Mol. Genet , vol.12 , pp. 1725-1735
    • Lettice, L.A.1
  • 3
    • 11144339384 scopus 로고    scopus 로고
    • Long-range control of gene expression: Emerging mechanisms and disruption in disease
    • (doi:10.1086/426833)
    • Kleinjan DA, van Heyningen V. 2005 Long-range control of gene expression: emerging mechanisms and disruption in disease. Am. J. Hum. Genet. 76, 8-32. (doi:10.1086/426833)
    • (2005) Am. J. Hum. Genet , vol.76 , pp. 8-32
    • Kleinjan, D.A.1    van Heyningen, V.2
  • 5
    • 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. 2011 A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279-283. (doi:10.1038/ nature09692)
    • (2011) Nature , vol.470 , pp. 279-283
    • Rada-Iglesias, A.1    Bajpai, R.2    Swigut, T.3    Brugmann, S.A.4    Flynn, R.A.5    Wysocka, J.6
  • 6
    • 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 , pp. 931-1021
    • Creyghton, M.P.1
  • 7
    • 58049191558 scopus 로고    scopus 로고
    • Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation
    • (doi:10.1016/j.stem.2008.11.011)
    • Cui K, Zang C, Roh T-Y, Schones DE, Childs RW, Peng W, Zhao K. 2009 Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 4, 80-93. (doi:10.1016/j.stem.2008.11.011)
    • (2009) Cell Stem Cell , vol.4 , pp. 80-93
    • Cui, K.1    Zang, C.2    Roh, T.-Y.3    Schones, D.E.4    Childs, R.W.5    Peng, W.6    Zhao, K.7
  • 8
    • 77949977555 scopus 로고    scopus 로고
    • Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages
    • (doi:10.1016/j.immuni.2010.02.008)
    • Ghisletti S et al. 2010 Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity 32, 317-328. (doi:10.1016/j.immuni.2010.02.008)
    • (2010) Immunity , vol.32 , pp. 317-328
    • Ghisletti, S.1
  • 9
    • 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
  • 10
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • (doi:10.1038/nature05874)
    • Birney E et al. 2007 Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816. (doi:10.1038/nature05874)
    • (2007) Nature , vol.447 , pp. 799-816
    • Birney, E.1
  • 11
    • 84860433173 scopus 로고    scopus 로고
    • Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function
    • (doi:10.1093/hmg/ dds034)
    • Sakabe NJ, Aneas I, Shen T, Shokri L, Park SY, Bulyk ML, Evans SM, Nobrega MA. 2012 Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. Hum. Mol. Genet. 21, 2194-2204. (doi:10.1093/hmg/ dds034)
    • (2012) Hum. Mol. Genet , vol.21 , pp. 2194-2204
    • Sakabe, N.J.1    Aneas, I.2    Shen, T.3    Shokri, L.4    Park, S.Y.5    Bulyk, M.L.6    Evans, S.M.7    Nobrega, M.A.8
  • 12
    • 53549125545 scopus 로고    scopus 로고
    • A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb
    • (doi:10.1101/gad.1693008)
    • Vokes SA, Ji H, Wong WH, McMahon AP. 2008 A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb. Genes Dev. 22, 2651-2663. (doi:10.1101/gad.1693008)
    • (2008) Genes Dev , vol.22 , pp. 2651-2663
    • Vokes, S.A.1    Ji, H.2    Wong, W.H.3    McMahon, A.P.4
  • 13
    • 33646510364 scopus 로고    scopus 로고
    • Genome-wide analysis of protein-DNA interactions
    • (doi:10.1146/annurev. genom.7.080505.115634)
    • Kim TH, Ren B. 2006 Genome-wide analysis of protein-DNA interactions. Annu. Rev. Genomics Hum. Genet. 7, 81-102. (doi:10.1146/annurev. genom.7.080505.115634)
    • (2006) Annu. Rev. Genomics Hum. Genet , vol.7 , pp. 81-102
    • Kim, T.H.1    Ren, B.2
  • 15
    • 40149098862 scopus 로고    scopus 로고
    • The evolution of combinatorial gene regulation in fungi
    • (doi:10.1371/journal.pbio.0060038)
    • Tuch BB, Galgoczy DJ, Hernday AD, Li H, Johnson AD. 2008 The evolution of combinatorial gene regulation in fungi. PLoS Biol. 6, e38. (doi:10.1371/journal.pbio.0060038)
    • (2008) PLoS Biol , vol.6
    • Tuch, B.B.1    Galgoczy, D.J.2    Hernday, A.D.3    Li, H.4    Johnson, A.D.5
  • 17
    • 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
  • 18
    • 77954100084 scopus 로고    scopus 로고
    • Transposable elements have rewired the core regulatory network of human embryonic stem cells
    • (doi:10.1038/ng.600)
    • Kunarso G, Chia NY, Jeyakani J, Hwang C, Lu X, Chan YS, Ng H-H, Bourque G. 2010 Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat. Genet. 42, 631-634. (doi:10.1038/ng.600)
    • (2010) Nat. Genet , vol.42 , pp. 631-634
    • Kunarso, G.1    Chia, N.Y.2    Jeyakani, J.3    Hwang, C.4    Lu, X.5    Chan, Y.S.6    Ng, H.-H.7    Bourque, G.8
  • 19
    • 33645381936 scopus 로고    scopus 로고
    • The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells
    • (doi:10.1038/ng1760)
    • Loh YH et al. 2006 The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat. Genet. 38, 431-440. (doi:10.1038/ng1760)
    • (2006) Nat. Genet , vol.38 , pp. 431-440
    • Loh, Y.H.1
  • 20
    • 42349088542 scopus 로고    scopus 로고
    • Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor
    • (doi:10.1371/journal.pone.0001061)
    • Conboy CM et al. 2007 Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor. PLoS ONE 2, e1061. (doi:10.1371/journal.pone.0001061)
    • (2007) PLoS ONE , vol.2
    • Conboy, C.M.1
  • 21
    • 77957220857 scopus 로고    scopus 로고
    • Comparative epigenomic analysis of murine and human adipogenesis
    • (doi:10.1016/j.cell.2010.09.006)
    • Mikkelsen TS, Xu Z, Zhang X, Wang L, Gimble JM, Lander ES, Rosen ED. 2010 Comparative epigenomic analysis of murine and human adipogenesis. Cell 143, 156-169. (doi:10.1016/j.cell.2010.09.006)
    • (2010) Cell , vol.143 , pp. 156-169
    • Mikkelsen, T.S.1    Xu, Z.2    Zhang, X.3    Wang, L.4    Gimble, J.M.5    Lander, E.S.6    Rosen, E.D.7
  • 22
    • 84863604466 scopus 로고    scopus 로고
    • Evolutionary conservation of histone modifications in mammals
    • (doi:10.1093/molbev/mss022)
    • Woo YH, Li WH. 2012 Evolutionary conservation of histone modifications in mammals. Mol. Biol. Evol. 29, 1757-1767. (doi:10.1093/molbev/mss022)
    • (2012) Mol. Biol. Evol , vol.29 , pp. 1757-1767
    • Woo, Y.H.1    Li, W.H.2
  • 23
    • 77950833803 scopus 로고    scopus 로고
    • Variation in transcription factor binding among humans
    • (doi:10.1126/science.1183621)
    • Kasowski M et al. 2010 Variation in transcription factor binding among humans. Science 328, 232-235. (doi:10.1126/science.1183621)
    • (2010) Science , vol.328 , pp. 232-235
    • Kasowski, M.1
  • 24
    • 77950854479 scopus 로고    scopus 로고
    • Heritable individual-specific and allele-specific chromatin signatures in humans
    • (doi:10.1126/science. 1184655)
    • McDaniell R et al. 2010 Heritable individual-specific and allele-specific chromatin signatures in humans. Science 328, 235-239. (doi:10.1126/science. 1184655)
    • (2010) Science , vol.328 , pp. 235-239
    • McDaniell, R.1
  • 25
    • 77951610155 scopus 로고    scopus 로고
    • Genetic analysis of variation in transcription factor binding in yeast
    • (doi:10.1038/nature08934)
    • Zheng W, Zhao H, Mancera E, Steinmetz LM, Snyder M. 2010 Genetic analysis of variation in transcription factor binding in yeast. Nature 464, 1187-1191. (doi:10.1038/nature08934)
    • (2010) Nature , vol.464 , pp. 1187-1191
    • Zheng, W.1    Zhao, H.2    Mancera, E.3    Steinmetz, L.M.4    Snyder, M.5
  • 26
    • 77950566643 scopus 로고    scopus 로고
    • Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species
    • (doi:10.1371/journal.pbio.1000343)
    • Bradley RK et al. 2010 Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol. 8, e1000343. (doi:10.1371/journal.pbio.1000343)
    • (2010) PLoS Biol , vol.8
    • Bradley, R.K.1
  • 27
    • 36448949026 scopus 로고    scopus 로고
    • Multivalent engagement of chromatin modifications by linked binding modules
    • (doi:10.1038/nrm2298)
    • Ruthenburg AJ, Li H, Patel DJ, Allis CD. 2007 Multivalent engagement of chromatin modifications by linked binding modules. Nat. Rev. Mol. Cell Biol. 8, 983-994. (doi:10.1038/nrm2298)
    • (2007) Nat. Rev. Mol. Cell Biol , vol.8 , pp. 983-994
    • Ruthenburg, A.J.1    Li, H.2    Patel, D.J.3    Allis, C.D.4
  • 28
    • 0035839136 scopus 로고    scopus 로고
    • Translating the histone code
    • (doi:10.1126/ science.1063127)
    • Jenuwein T, Allis CD. 2001 Translating the histone code. Science 293, 1074-1080. (doi:10.1126/ science.1063127)
    • (2001) Science , vol.293 , pp. 1074-1080
    • Jenuwein, T.1    Allis, C.D.2
  • 29
    • 79951784069 scopus 로고    scopus 로고
    • Genome-wide maps of transcription regulatory elements
    • (doi:10.1002/wsbm.70)
    • Sakabe NJ, Nobrega MA. 2010 Genome-wide maps of transcription regulatory elements. Wiley Interdiscip. Rev. Syst. Biol. Med. 2, 422-437. (doi:10.1002/wsbm.70)
    • (2010) Wiley Interdiscip. Rev. Syst. Biol. Med , vol.2 , pp. 422-437
    • Sakabe, N.J.1    Nobrega, M.A.2
  • 30
    • 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
  • 31
    • 84865121188 scopus 로고    scopus 로고
    • An encyclopedia of mouse DNA elements (mouse ENCODE)
    • (doi:10.1186/gb-2012-13-8-418)
    • Stamatoyannopoulos JA et al. 2007 An encyclopedia of mouse DNA elements (mouse ENCODE). Genome Biol. 13, 418. (doi:10.1186/gb-2012-13-8-418)
    • (2007) Genome Biol , vol.13 , pp. 418
    • Stamatoyannopoulos, J.A.1
  • 32
    • 78650331647 scopus 로고    scopus 로고
    • Identification of functional elements and regulatory circuits by Drosophila modENCODE
    • (doi:10.1126/science.1198374)
    • Roy S et al. 2010 Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330, 1787-1797. (doi:10.1126/science.1198374)
    • (2010) Science , vol.330 , pp. 1787-1797
    • Roy, S.1
  • 33
    • 78650410139 scopus 로고    scopus 로고
    • Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
    • (doi:10.1126/ science.1196914)
    • Gerstein MB et al. 2010 Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330, 1775-1787. (doi:10.1126/ science.1196914)
    • (2010) Science , vol.330 , pp. 1775-1787
    • Gerstein, M.B.1
  • 34
    • 84875275808 scopus 로고    scopus 로고
    • On the immortality of television sets: 'function' in the human genome according to the evolution-free gospel of ENCODE
    • (doi:10.1093/gbe/evt028)
    • Graur D, Zheng Y, Price N, Azevedo RB, Zufall RA, Elhaik E. 2013 On the immortality of television sets: 'function' in the human genome according to the evolution-free gospel of ENCODE. Genome Biol. Evol. 5, 578-590. (doi:10.1093/gbe/evt028)
    • (2013) Genome Biol. Evol , vol.5 , pp. 578-590
    • Graur, D.1    Zheng, Y.2    Price, N.3    Azevedo, R.B.4    Zufall, R.A.5    Elhaik, E.6
  • 35
    • 84875847924 scopus 로고    scopus 로고
    • Is junk DNA bunk? A critique of ENCODE
    • (doi:10.1073/pnas.1221376110)
    • Doolittle WF. 2013 Is junk DNA bunk? A critique of ENCODE. Proc. Natl Acad. Sci. USA 110, 5294-5300. (doi:10.1073/pnas.1221376110)
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 5294-5300
    • Doolittle, W.F.1
  • 36
    • 84868550433 scopus 로고    scopus 로고
    • The C-value paradox, junk DNA and ENCODE
    • (doi:10.1016/j. cub.2012.10.002)
    • Eddy SR. 2012 The C-value paradox, junk DNA and ENCODE. Curr Biol. 22, R898-R899. (doi:10.1016/j. cub.2012.10.002)
    • (2012) Curr Biol , vol.22
    • Eddy, S.R.1
  • 37
    • 84876031068 scopus 로고    scopus 로고
    • The ENCODE project: Missteps overshadowing a success
    • (doi:10.1016/j.cub.2013.03.023)
    • Eddy SR. 2013 The ENCODE project: missteps overshadowing a success. Curr. Biol. 23, R259-R261. (doi:10.1016/j.cub.2013.03.023)
    • (2013) Curr. Biol. , vol.23
    • Eddy, S.R.1
  • 38
    • 84872861423 scopus 로고    scopus 로고
    • Can ENCODE tell us how much junk DNA we carry in our genome
    • (doi:10.1016/j.bbrc.2012.12.074)
    • Niu DK, Jiang L. 2013 Can ENCODE tell us how much junk DNA we carry in our genome? Biochem. Biophys. Res. Commun. 430, 1340-1343. (doi:10.1016/j.bbrc.2012.12.074)
    • (2013) Biochem. Biophys. Res. Commun , vol.430 , pp. 1340-1343
    • Niu, D.K.1    Jiang, L.2
  • 39
    • 77957885770 scopus 로고    scopus 로고
    • Transcription factor binding variation in the evolution of gene regulation
    • (doi:10.1016/j.tig.2010. 08.005)
    • Dowell RD. 2010 Transcription factor binding variation in the evolution of gene regulation. Trends Genet. 26, 468-475. (doi:10.1016/j.tig.2010. 08.005)
    • (2010) Trends Genet , vol.26 , pp. 468-475
    • Dowell, R.D.1
  • 40
    • 33751381461 scopus 로고    scopus 로고
    • TimeTree: A public knowledge-base of divergence times among organisms
    • (doi:10.1093/bioinformatics/btl505)
    • Hedges SB, Dudley J, Kumar S. 2006 TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22, 2971-2972. (doi:10.1093/bioinformatics/btl505)
    • (2006) Bioinformatics , vol.22 , pp. 2971-2972
    • Hedges, S.B.1    Dudley, J.2    Kumar, S.3
  • 41
    • 79955471381 scopus 로고    scopus 로고
    • High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species
    • (doi:10.1038/ng.808)
    • He Q, Bardet AF, Patton B, Purvis J, Johnston J, Paulson A, Gogol M, Stark A, Zeitlinger J. 2011 High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat. Genet. 43, 414-420. (doi:10.1038/ng.808)
    • (2011) Nat. Genet , vol.43 , pp. 414-420
    • He, Q.1    Bardet, A.F.2    Patton, B.3    Purvis, J.4    Johnston, J.5    Paulson, A.6    Gogol, M.7    Stark, A.8    Zeitlinger, J.9
  • 42
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • (doi:10.1038/nature01644)
    • Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. 2003 Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241-254. (doi:10.1038/nature01644)
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 43
    • 73549108534 scopus 로고    scopus 로고
    • Switching the mechanism of mating type switching: A domesticated transposase supplants a domesticated homing endonuclease
    • (doi:10.1101/ gad.1886310)
    • Rusche LN, Rine J. 2010 Switching the mechanism of mating type switching: a domesticated transposase supplants a domesticated homing endonuclease. Genes Dev. 24, 10-14. (doi:10.1101/ gad.1886310)
    • (2010) Genes Dev , vol.24 , pp. 10-14
    • Rusche, L.N.1    Rine, J.2
  • 44
    • 25144525014 scopus 로고    scopus 로고
    • Core transcriptional regulatory circuitry in human embryonic stem cells
    • (doi:10.1016/j.cell.2005.08.020)
    • Boyer LA et al. 2005 Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947-956. (doi:10.1016/j.cell.2005.08.020)
    • (2005) Cell , vol.122 , pp. 947-956
    • Boyer, L.A.1
  • 45
    • 79958834622 scopus 로고    scopus 로고
    • Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes
    • (doi:10.1038/nsmb.2059)
    • Martin D et al. 2011 Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes. Nat. Struct. Mol. Biol. 18, 708-714. (doi:10.1038/nsmb.2059)
    • (2011) Nat. Struct. Mol. Biol , vol.18 , pp. 708-714
    • Martin, D.1
  • 46
    • 79955403252 scopus 로고    scopus 로고
    • Gene expression differences among primates are associated with changes in a histone epigenetic modification
    • (doi:10.1534/genetics.110.126177)
    • Cain CE, Blekhman R, Marioni JC, Gilad Y. 2011 Gene expression differences among primates are associated with changes in a histone epigenetic modification. Genetics 187, 1225-1234. (doi:10.1534/genetics.110.126177)
    • (2011) Genetics , vol.187 , pp. 1225-1234
    • Cain, C.E.1    Blekhman, R.2    Marioni, J.C.3    Gilad, Y.4
  • 47
    • 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
  • 48
    • 77958190479 scopus 로고    scopus 로고
    • Dramatic changes in transcription factor binding over evolutionary time
    • (doi:10.1186/gb- 2010-11-6-122)
    • Weirauch MT, Hughes TR. 2010 Dramatic changes in transcription factor binding over evolutionary time. Genome Biol. 11, 122. (doi:10.1186/gb- 2010-11-6-122)
    • (2010) Genome Biol , vol.11 , pp. 122
    • Weirauch, M.T.1    Hughes, T.R.2
  • 49
    • 77954960062 scopus 로고    scopus 로고
    • Phenotypic robustness conferred by apparently redundant transcriptional enhancers
    • (doi:10.1038/nature09158)
    • Frankel NS, Davis GK, Vargas D, Wang S, Payre FO, 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.S.1    Davis, G.K.2    Vargas, D.3    Wang, S.4    Payre, F.O.5    Stern, D.L.6
  • 50
    • 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
  • 51
    • 84871844925 scopus 로고    scopus 로고
    • DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila
    • 335, (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 , pp. 330-421
    • Fisher, W.W.1
  • 52
    • 40649126603 scopus 로고    scopus 로고
    • Transcription factor substitution during the evolution of fungal ribosome regulation
    • (doi:10. 1016/j.molcel.2008.02.006)
    • Hogues H, Lavoie H, Sellam A, Mangos M, Roemer T, Purisima E, Nantel A, Whiteway M. 2008 Transcription factor substitution during the evolution of fungal ribosome regulation. Mol. Cell 29, 552-562. (doi:10. 1016/j.molcel.2008.02.006)
    • (2008) Mol. Cell , vol.29 , pp. 552-562
    • Hogues, H.1    Lavoie, H.2    Sellam, A.3    Mangos, M.4    Roemer, T.5    Purisima, E.6    Nantel, A.7    Whiteway, M.8
  • 53
    • 33749173831 scopus 로고    scopus 로고
    • Evolution of alternative transcriptional circuits with identical logic
    • (doi:10.1038/ nature05099)
    • Tsong AE, Tuch BB, Li H, Johnson AD. 2006 Evolution of alternative transcriptional circuits with identical logic. Nature 443, 415-420. (doi:10.1038/ nature05099)
    • (2006) Nature , vol.443 , pp. 415-420
    • Tsong, A.E.1    Tuch, B.B.2    Li, H.3    Johnson, A.D.4
  • 54
    • 34250204870 scopus 로고    scopus 로고
    • Transcriptional rewiring of fungal galactose-metabolism circuitry
    • (doi:10.1016/j.cub.2007.05.017)
    • Martchenko M, Levitin A, Hogues H, Nantel A, Whiteway M. 2007 Transcriptional rewiring of fungal galactose-metabolism circuitry. Curr. Biol. 17, 1007-1013. (doi:10.1016/j.cub.2007.05.017)
    • (2007) Curr. Biol , vol.17 , pp. 1007-1013
    • Martchenko, M.1    Levitin, A.2    Hogues, H.3    Nantel, A.4    Whiteway, M.5
  • 55
    • 0034069495 scopus 로고    scopus 로고
    • Gene Ontology: Tool for the unification of biology. The Gene Ontology Consortium
    • (doi:10.1038/75556)
    • Ashburner M et al. 2000 Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29. (doi:10.1038/75556)
    • (2000) Nat. Genet , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 56
    • 33847242598 scopus 로고    scopus 로고
    • Foxp3 occupancy and regulation of key target genes during T-cell stimulation
    • (doi:10.1038/nature05478)
    • Marson A et al. 2007 Foxp3 occupancy and regulation of key target genes during T-cell stimulation. Nature 445, 931-935. (doi:10.1038/nature05478)
    • (2007) Nature , vol.445 , pp. 931-935
    • Marson, A.1
  • 57
    • 67650663220 scopus 로고    scopus 로고
    • Backup in gene regulatory networks explains differences between binding and knockout results
    • (doi:10.1038/msb.2009.33)
    • Gitter A, Siegfried Z, Klutstein M, Fornes O, Oliva B, Simon I, Bar-Joseph Z. 2009 Backup in gene regulatory networks explains differences between binding and knockout results. Mol. Syst. Biol. 5, 276. (doi:10.1038/msb.2009.33)
    • (2009) Mol. Syst. Biol , vol.5 , pp. 276
    • Gitter, A.1    Siegfried, Z.2    Klutstein, M.3    Fornes, O.4    Oliva, B.5    Simon, I.6    Bar-Joseph, Z.7
  • 58
    • 70449638281 scopus 로고    scopus 로고
    • Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis
    • (doi:10.1016/j.molcel.2009.11.002)
    • Yu M et al. 2009 Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Mol. Cell 36, 682-695. (doi:10.1016/j.molcel.2009.11.002)
    • (2009) Mol. Cell , vol.36 , pp. 682-695
    • Yu, M.1
  • 59
    • 65349162170 scopus 로고    scopus 로고
    • Conservation of core gene expression in vertebrate tissues
    • (doi:10.1186/jbiol130)
    • Chan ET et al. 2009 Conservation of core gene expression in vertebrate tissues. J. Biol. 8, 33. (doi:10.1186/jbiol130)
    • (2009) J. Biol , vol.8 , pp. 33
    • Chan, E.T.1
  • 60
    • 80054976678 scopus 로고    scopus 로고
    • The evolution of gene expression levels in mammalian organs
    • (doi:10.1038/nature10532)
    • Brawand D et al. 2011 The evolution of gene expression levels in mammalian organs. Nature 478, 343-348. (doi:10.1038/nature10532)
    • (2011) Nature , vol.478 , pp. 343-348
    • Brawand, D.1
  • 61
    • 84871410405 scopus 로고    scopus 로고
    • The evolutionary landscape of alternative splicing in vertebrate species
    • (doi:10.1126/ science.1230612)
    • Barbosa-Morais NL et al. 2012 The evolutionary landscape of alternative splicing in vertebrate species. Science 338, 1587-1593. (doi:10.1126/ science.1230612)
    • (2012) Science , vol.338 , pp. 1587-1593
    • Barbosa-Morais, N.L.1
  • 62
    • 75149143994 scopus 로고    scopus 로고
    • Conserved expression without conserved regulatory sequence: The more things change, the more they stay the same
    • (doi:10.1016/j.tig.2009.12.002)
    • Weirauch MT, Hughes TR. 2010 Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same. Trends Genet. 26, 66-74. (doi:10.1016/j.tig.2009.12.002)
    • (2010) Trends Genet , vol.26 , pp. 66-74
    • Weirauch, M.T.1    Hughes, T.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.