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Volumn 111, Issue 17, 2014, Pages 6131-6138

Defining functional DNA elements in the human genome

(30)  Kellis, Manolis a,b   Wold, Barbara c   Snyder, Michael P d   Bernstein, Bradley E b,e,f   Kundaje, Anshul a,b   Marinov, Georgi K c   Ward, Lucas D a,b   Birney, Ewan g   Crawford, Gregory E h   Dekker, Job i   Dunham, Ian g   Elnitski, Laura L j   Farnham, Peggy J k   Feingold, Elise A j   Gerstein, Mark l   Giddings, Morgan C m   Gilbert, David M n   Gingeras, Thomas R o   Green, Eric D j   Guigo, Roderic p   more..


Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; DNA; MICRORNA; PIWI INTERACTING RNA; REPETITIVE DNA; RNA POLYMERASE; SPACER DNA; TRANSCRIPTION FACTOR GATA 1; UNTRANSLATED RNA;

EID: 84899633396     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1318948111     Document Type: Review
Times cited : (528)

References (116)
  • 1
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International Human Genome Sequencing Consortium
    • Lander ES, et al.; International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409(6822):860-921.
    • (2001) Nature , vol.409 , Issue.6822 , pp. 860-921
    • Lander, E.S.1
  • 2
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Mouse Genome Sequencing Consortium
    • Waterston RH, et al.; Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420(6915):520-562.
    • (2002) Nature , vol.420 , Issue.6915 , pp. 520-562
    • Waterston, R.H.1
  • 3
    • 80054973803 scopus 로고    scopus 로고
    • A high-resolution map of human evolutionary constraint using 29 mammals
    • Lindblad-Toh K, et al. (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478(7370):476-482.
    • (2011) Nature , vol.478 , Issue.7370 , pp. 476-482
    • Lindblad-Toh, K.1
  • 4
    • 80555142991 scopus 로고    scopus 로고
    • What fraction of the human genome is functional?
    • Ponting CP, Hardison RC (2011) What fraction of the human genome is functional? Genome Res 21(11):1769-1776.
    • (2011) Genome Res , vol.21 , Issue.11 , pp. 1769-1776
    • Ponting, C.P.1    Hardison, R.C.2
  • 5
    • 84859462157 scopus 로고    scopus 로고
    • The genomic basis of adaptive evolution in threespine sticklebacks
    • Jones FC, et al. (2012) The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484(7392):55-61.
    • (2012) Nature , vol.484 , Issue.7392 , pp. 55-61
    • Jones, F.C.1
  • 6
    • 84874069538 scopus 로고    scopus 로고
    • Identifying recent adaptations in large-scale genomic data
    • 1000 Genomes Project
    • Grossman SR, et al.; 1000 Genomes Project (2013) Identifying recent adaptations in large-scale genomic data. Cell 152(4):703-713.
    • (2013) Cell , vol.152 , Issue.4 , pp. 703-713
    • Grossman, S.R.1
  • 7
    • 84880076219 scopus 로고    scopus 로고
    • Gene expression drives local adaptation in humans
    • Fraser HB (2013) Gene expression drives local adaptation in humans. Genome Res 23(7):1089-1096.
    • (2013) Genome Res , vol.23 , Issue.7 , pp. 1089-1096
    • Fraser, H.B.1
  • 8
    • 39749184167 scopus 로고    scopus 로고
    • The evolution of gene regulation underlies a morphological difference between two Drosophila sister species
    • Jeong S, et al. (2008) The evolution of gene regulation underlies a morphological difference between two Drosophila sister species. Cell 132(5):783-793.
    • (2008) Cell , vol.132 , Issue.5 , pp. 783-793
    • Jeong, S.1
  • 9
    • 46149104377 scopus 로고    scopus 로고
    • Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution
    • Carroll SB (2008) Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution. Cell 134(1):25-36.
    • (2008) Cell , vol.134 , Issue.1 , pp. 25-36
    • Carroll, S.B.1
  • 10
    • 74549118236 scopus 로고    scopus 로고
    • Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer
    • Chan YF, et al. (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science 327(5963):302-305.
    • (2010) Science , vol.327 , Issue.5963 , pp. 302-305
    • Chan, Y.F.1
  • 11
    • 11144339384 scopus 로고    scopus 로고
    • Long-range control of gene expression: Emerging mechanisms and disruption in disease
    • Kleinjan DA, van Heyningen V (2005) Long-range control of gene expression: Emerging mechanisms and disruption in disease. Am J Hum Genet 76(1):8-32.
    • (2005) Am J Hum Genet , vol.76 , Issue.1 , pp. 8-32
    • Kleinjan, D.A.1    Van Heyningen, V.2
  • 12
    • 39049171403 scopus 로고    scopus 로고
    • Long-range gene control and genetic disease
    • Kleinjan DA, Lettice LA (2008) Long-range gene control and genetic disease. Adv Genet 61:339-388.
    • (2008) Adv Genet , vol.61 , pp. 339-388
    • Kleinjan, D.A.1    Lettice, L.A.2
  • 13
    • 67249117049 scopus 로고    scopus 로고
    • Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
    • Hindorff LA, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106(23):9362-9367.
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.23 , pp. 9362-9367
    • Hindorff, L.A.1
  • 14
    • 84865822182 scopus 로고    scopus 로고
    • Systematic localization of common disease-associated variation in regulatory DNA
    • Maurano MT, et al. (2012) Systematic localization of common disease-associated variation in regulatory DNA. Science 337(6099): 1190-1195.
    • (2012) Science , vol.337 , Issue.6099 , pp. 1190-1195
    • Maurano, M.T.1
  • 15
    • 84865777825 scopus 로고    scopus 로고
    • Linking disease associations with regulatory information in the human genome
    • Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M (2012) Linking disease associations with regulatory information in the human genome. Genome Res 22(9):1748-1759.
    • (2012) Genome Res , vol.22 , Issue.9 , pp. 1748-1759
    • Schaub, M.A.1    Boyle, A.P.2    Kundaje, A.3    Batzoglou, S.4    Snyder, M.5
  • 16
    • 84858779229 scopus 로고    scopus 로고
    • HaploReg: A resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants
    • Ward LD, Kellis M (2012) HaploReg: A resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res 40(Database issue):D930-D934.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE
    • Ward, L.D.1    Kellis, M.2
  • 17
    • 0035986888 scopus 로고    scopus 로고
    • Evolution of transcription factor binding sites in Mammalian gene regulatory regions: Conservation and turnover
    • Dermitzakis ET, Clark AG (2002) Evolution of transcription factor binding sites in Mammalian gene regulatory regions: Conservation and turnover. Mol Biol Evol 19(7):1114-1121.
    • (2002) Mol Biol Evol , vol.19 , Issue.7 , pp. 1114-1121
    • Dermitzakis, E.T.1    Clark, A.G.2
  • 18
    • 0037498017 scopus 로고    scopus 로고
    • Turnover of binding sites for transcription factors involved in early Drosophila development
    • Costas J, Casares F, Vieira J (2003) Turnover of binding sites for transcription factors involved in early Drosophila development. Gene 310:215-220.
    • (2003) Gene , vol.310 , pp. 215-220
    • Costas, J.1    Casares, F.2    Vieira, J.3
  • 19
    • 33750442876 scopus 로고    scopus 로고
    • Large-scale turnover of functional transcription factor binding sites in Drosophila
    • Moses AM, et al. (2006) Large-scale turnover of functional transcription factor binding sites in Drosophila. PLOS Comput Biol 2(10):e130.
    • (2006) PLOS Comput Biol , vol.2 , Issue.10
    • Moses, A.M.1
  • 20
    • 0031889035 scopus 로고    scopus 로고
    • Functional analysis of eve stripe 2 enhancer evolution in Drosophila: Rules governing conservation and change
    • Ludwig MZ, Patel NH, Kreitman M (1998) Functional analysis of eve stripe 2 enhancer evolution in Drosophila: Rules governing conservation and change. Development 125(5):949-958.
    • (1998) Development , vol.125 , Issue.5 , pp. 949-958
    • Ludwig, M.Z.1    Patel, N.H.2    Kreitman, M.3
  • 21
    • 0142084743 scopus 로고    scopus 로고
    • Scanning human gene deserts for long-range enhancers
    • Nobrega MA, Ovcharenko I, Afzal V, Rubin EM (2003) Scanning human gene deserts for long-range enhancers. Science 302(5644): 413.
    • (2003) Science , vol.302 , Issue.5644 , pp. 413
    • Nobrega, M.A.1    Ovcharenko, I.2    Afzal, V.3    Rubin, E.M.4
  • 22
    • 34548697503 scopus 로고    scopus 로고
    • Deletion of ultraconserved elements yields viable mice
    • Ahituv N, et al. (2007) Deletion of ultraconserved elements yields viable mice. PLoS Biol 5(9):e234.
    • (2007) PLoS Biol , vol.5 , Issue.9
    • Ahituv, N.1
  • 23
    • 39049147650 scopus 로고    scopus 로고
    • Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b
    • McGaughey DM, et al. (2008) Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. Genome Res 18(2):252-260.
    • (2008) Genome Res , vol.18 , Issue.2 , pp. 252-260
    • McGaughey, D.M.1
  • 24
    • 84876569397 scopus 로고    scopus 로고
    • Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation
    • Vakhrusheva OA, Bazykin GA, Kondrashov AS (2013) Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation. Genome Biol Evol 5(3):532-541.
    • (2013) Genome Biol Evol , vol.5 , Issue.3 , pp. 532-541
    • Vakhrusheva, O.A.1    Bazykin, G.A.2    Kondrashov, A.S.3
  • 25
    • 84875847924 scopus 로고    scopus 로고
    • Is junk DNA bunk? A critique of ENCODE
    • Doolittle WF (2013) Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci USA 110(14):5294-5300.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.14 , pp. 5294-5300
    • Doolittle, W.F.1
  • 26
    • 84875275808 scopus 로고    scopus 로고
    • On the immortality of television sets: "Function" in the human genome according to the evolution-free gospel of ENCODE
    • Graur D, et al. (2013) On the immortality of television sets: "Function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 5(3):578-590.
    • (2013) Genome Biol Evol , vol.5 , Issue.3 , pp. 578-590
    • Graur, D.1
  • 27
    • 84868550433 scopus 로고    scopus 로고
    • The C-value paradox, junk DNA and ENCODE
    • Eddy SR (2012) The C-value paradox, junk DNA and ENCODE. Curr Biol 22(21):R898-R899.
    • (2012) Curr Biol , vol.22 , Issue.21
    • Eddy, S.R.1
  • 28
    • 84876031068 scopus 로고    scopus 로고
    • The ENCODE project: Missteps overshadowing a success
    • Eddy SR (2013) The ENCODE project: Missteps overshadowing a success. Curr Biol 23(7):R259-R261.
    • (2013) Curr Biol , vol.23 , Issue.7
    • Eddy, S.R.1
  • 29
    • 84899637780 scopus 로고    scopus 로고
    • The extent of functionality in the human genome
    • Mattick JS, et al. (2013) The extent of functionality in the human genome. HUGO J 7(1):2.
    • (2013) HUGO J , vol.7 , Issue.1 , pp. 2
    • Mattick, J.S.1
  • 30
    • 84872861423 scopus 로고    scopus 로고
    • Can ENCODE tell us how much junk DNA we carry in our genome?
    • Niu DK, Jiang L (2012) Can ENCODE tell us how much junk DNA we carry in our genome? Biochem Biophys Res Commun 430(4): 1340-1343.
    • (2012) Biochem Biophys Res Commun , vol.430 , Issue.4 , pp. 1340-1343
    • Niu, D.K.1    Jiang, L.2
  • 31
    • 84911006514 scopus 로고    scopus 로고
    • Junk or functional DNA?: ENCODE and the function controversy
    • 10.1007/s10539-014-9441-3
    • Germain PL, Ratti E, Boem F (2014) Junk or functional DNA?: ENCODE and the function controversy. Biology & Philosophy, 10.1007/s10539-014-9441-3.
    • (2014) Biology & Philosophy
    • Germain, P.L.1    Ratti, E.2    Boem, F.3
  • 32
    • 13444266370 scopus 로고    scopus 로고
    • Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
    • Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33(Database issue):D514-D517.
    • (2005) Nucleic Acids Res , vol.33 , Issue.DATABASE ISSUE
    • Hamosh, A.1    Scott, A.F.2    Amberger, J.S.3    Bocchini, C.A.4    McKusick, V.A.5
  • 33
    • 0033569405 scopus 로고    scopus 로고
    • A large-scale insertional mutagenesis screen in zebrafish
    • Amsterdam A, et al. (1999) A large-scale insertional mutagenesis screen in zebrafish. Genes Dev 13(20):2713-2724.
    • (1999) Genes Dev , vol.13 , Issue.20 , pp. 2713-2724
    • Amsterdam, A.1
  • 34
    • 12144289681 scopus 로고    scopus 로고
    • A large-scale RNAi screen in human cells identifies new components of the p53 pathway
    • Berns K, et al. (2004) A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428(6981): 431-437.
    • (2004) Nature , vol.428 , Issue.6981 , pp. 431-437
    • Berns, K.1
  • 35
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • Ernst J, et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473(7345):43-49.
    • (2011) Nature , vol.473 , Issue.7345 , pp. 43-49
    • Ernst, J.1
  • 36
    • 84877147962 scopus 로고    scopus 로고
    • Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
    • Kheradpour P, et al. (2013) Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res 23(5):800-811.
    • (2013) Genome Res , vol.23 , Issue.5 , pp. 800-811
    • Kheradpour, P.1
  • 37
    • 60149091656 scopus 로고    scopus 로고
    • ChIP-seq accurately predicts tissue-specific activity of enhancers
    • Visel A, et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457(7231):854-858.
    • (2009) Nature , vol.457 , Issue.7231 , pp. 854-858
    • Visel, A.1
  • 38
    • 84863230316 scopus 로고    scopus 로고
    • Massively parallel functional dissection of mammalian enhancers in vivo
    • Patwardhan RP, et al. (2012) Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol 30(3): 265-270.
    • (2012) Nat Biotechnol , vol.30 , Issue.3 , pp. 265-270
    • Patwardhan, R.P.1
  • 39
    • 84863229330 scopus 로고    scopus 로고
    • Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
    • Melnikov A, et al. (2012) Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat Biotechnol 30(3):271-277.
    • (2012) Nat Biotechnol , vol.30 , Issue.3 , pp. 271-277
    • Melnikov, A.1
  • 40
    • 47749087494 scopus 로고    scopus 로고
    • Tools for neuroanatomy and neurogenetics in Drosophila
    • Pfeiffer BD, et al. (2008) Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci USA 105(28): 9715-9720.
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.28 , pp. 9715-9720
    • Pfeiffer, B.D.1
  • 41
    • 84863116742 scopus 로고    scopus 로고
    • A systematic survey of loss-of-function variants in human proteincoding genes
    • 1000 Genomes Project Consortium
    • MacArthur DG, et al.; 1000 Genomes Project Consortium (2012) A systematic survey of loss-of-function variants in human proteincoding genes. Science 335(6070):823-828.
    • (2012) Science , vol.335 , Issue.6070 , pp. 823-828
    • Macarthur, D.G.1
  • 42
    • 36049018312 scopus 로고    scopus 로고
    • Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
    • Harvard FlyBase curators; Berkeley Drosophila Genome Project
    • Stark A, et al.; Harvard FlyBase curators; Berkeley Drosophila Genome Project (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450(7167):219-232.
    • (2007) Nature , vol.450 , Issue.7167 , pp. 219-232
    • Stark, A.1
  • 43
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • 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(6937):241-254.
    • (2003) Nature , vol.423 , Issue.6937 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 44
    • 15244358503 scopus 로고    scopus 로고
    • Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
    • Xie X, et al. (2005) Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 434(7031):338-345.
    • (2005) Nature , vol.434 , Issue.7031 , pp. 338-345
    • Xie, X.1
  • 45
    • 0041465867 scopus 로고    scopus 로고
    • Comparative analyses of multi-species sequences from targeted genomic regions
    • Thomas JW, et al. (2003) Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424(6950): 788-793.
    • (2003) Nature , vol.424 , Issue.6950 , pp. 788-793
    • Thomas, J.W.1
  • 46
    • 0038724989 scopus 로고    scopus 로고
    • Finding functional features in Saccharomyces genomes by phylogenetic footprinting
    • Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-76.
    • (2003) Science , vol.301 , Issue.5629 , pp. 71-76
    • Cliften, P.1
  • 47
    • 0242418246 scopus 로고    scopus 로고
    • Phylogenetic shadowing of primate sequences to find functional regions of the human genome
    • Boffelli D, et al. (2003) Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299(5611):1391-1394.
    • (2003) Science , vol.299 , Issue.5611 , pp. 1391-1394
    • Boffelli, D.1
  • 48
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Siepel A, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15(8): 1034-1050.
    • (2005) Genome Res , vol.15 , Issue.8 , pp. 1034-1050
    • Siepel, A.1
  • 49
    • 18344415808 scopus 로고    scopus 로고
    • Distinguishing regulatory DNA from neutral sites
    • Elnitski L, et al. (2003) Distinguishing regulatory DNA from neutral sites. Genome Res 13(1):64-72.
    • (2003) Genome Res , vol.13 , Issue.1 , pp. 64-72
    • Elnitski, L.1
  • 50
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • Bartel DP (2009) MicroRNAs: Target recognition and regulatory functions. Cell 136(2):215-233.
    • (2009) Cell , vol.136 , Issue.2 , pp. 215-233
    • Bartel, D.P.1
  • 51
    • 84861904178 scopus 로고    scopus 로고
    • Genome regulation by long noncoding RNAs
    • Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81:145-166.
    • (2012) Annu Rev Biochem , vol.81 , pp. 145-166
    • Rinn, J.L.1    Chang, H.Y.2
  • 52
    • 36749037521 scopus 로고    scopus 로고
    • The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race
    • Aravin AA, Hannon GJ, Brennecke J (2007) The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318(5851):761-764.
    • (2007) Science , vol.318 , Issue.5851 , pp. 761-764
    • Aravin, A.A.1    Hannon, G.J.2    Brennecke, J.3
  • 53
    • 84860369511 scopus 로고    scopus 로고
    • Small RNA in the nucleus: The RNA-chromatin ping-pong
    • Olovnikov I, Aravin AA, Fejes Toth K (2012) Small RNA in the nucleus: The RNA-chromatin ping-pong. Curr Opin Genet Dev 22(2): 164-171.
    • (2012) Curr Opin Genet Dev , vol.22 , Issue.2 , pp. 164-171
    • Olovnikov, I.1    Aravin, A.A.2    Fejes Toth, K.3
  • 54
    • 0023663887 scopus 로고
    • Position-independent, high-level expression of the human betaglobin gene in transgenic mice
    • Grosveld F, van Assendelft GB, Greaves DR, Kollias G (1987) Position-independent, high-level expression of the human betaglobin gene in transgenic mice. Cell 51(6):975-985.
    • (1987) Cell , vol.51 , Issue.6 , pp. 975-985
    • Grosveld, F.1    Van Assendelft, G.B.2    Greaves, D.R.3    Kollias, G.4
  • 55
    • 0345019804 scopus 로고    scopus 로고
    • Long-range transcriptional regulation of cytokine gene expression
    • Agarwal S, Rao A (1998) Long-range transcriptional regulation of cytokine gene expression. Curr Opin Immunol 10(3):345-352.
    • (1998) Curr Opin Immunol , vol.10 , Issue.3 , pp. 345-352
    • Agarwal, S.1    Rao, A.2
  • 56
    • 0032534894 scopus 로고    scopus 로고
    • Partial rescue of GATA-3 by yeast artificial chromosome transgenes
    • Lakshmanan G, Lieuw KH, Grosveld F, Engel JD (1998) Partial rescue of GATA-3 by yeast artificial chromosome transgenes. Dev Biol 204(2):451-463.
    • (1998) Dev Biol , vol.204 , Issue.2 , pp. 451-463
    • Lakshmanan, G.1    Lieuw, K.H.2    Grosveld, F.3    Engel, J.D.4
  • 58
    • 4444364399 scopus 로고    scopus 로고
    • Bioinformatics for the 'bench biologist': How to find regulatory regions in genomic DNA
    • Nardone J, Lee DU, Ansel KM, Rao A (2004) Bioinformatics for the 'bench biologist': How to find regulatory regions in genomic DNA. Nat Immunol 5(8):768-774.
    • (2004) Nat Immunol , vol.5 , Issue.8 , pp. 768-774
    • Nardone, J.1    Lee, D.U.2    Ansel, K.M.3    Rao, A.4
  • 59
    • 0023899769 scopus 로고
    • Nuclease hypersensitive sites in chromatin
    • Gross DS, Garrard WT (1988) Nuclease hypersensitive sites in chromatin. Annu Rev Biochem 57:159-197.
    • (1988) Annu Rev Biochem , vol.57 , pp. 159-197
    • Gross, D.S.1    Garrard, W.T.2
  • 60
    • 33745209016 scopus 로고    scopus 로고
    • Pursuing gene regulation 'logic' via RNA interference and chromatin immunoprecipitation
    • Li CC, Ramirez-Carrozzi VR, Smale ST (2006) Pursuing gene regulation 'logic' via RNA interference and chromatin immunoprecipitation. Nat Immunol 7(7):692-697.
    • (2006) Nat Immunol , vol.7 , Issue.7 , pp. 692-697
    • Li, C.C.1    Ramirez-Carrozzi, V.R.2    Smale, S.T.3
  • 61
    • 0036024955 scopus 로고    scopus 로고
    • Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation
    • Weinmann AS, Farnham PJ (2002) Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods 26(1):37-47.
    • (2002) Methods , vol.26 , Issue.1 , pp. 37-47
    • Weinmann, A.S.1    Farnham, P.J.2
  • 62
    • 0036024954 scopus 로고    scopus 로고
    • Dissecting long-range transcriptional mechanisms by chromatin immunoprecipitation
    • Johnson KD, Bresnick EH (2002) Dissecting long-range transcriptional mechanisms by chromatin immunoprecipitation. Methods 26(1):27-36.
    • (2002) Methods , vol.26 , Issue.1 , pp. 27-36
    • Johnson, K.D.1    Bresnick, E.H.2
  • 63
    • 79951516056 scopus 로고    scopus 로고
    • A unique chromatin signature uncovers early developmental enhancers in humans
    • Rada-Iglesias A, et al. (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470(7333):279-283.
    • (2011) Nature , vol.470 , Issue.7333 , pp. 279-283
    • Rada-Iglesias, A.1
  • 64
    • 78650758676 scopus 로고    scopus 로고
    • Histone H3K27ac separates active from poised enhancers and predicts developmental state
    • Creyghton MP, et al. (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA 107(50):21931-21936.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.50 , pp. 21931-21936
    • Creyghton, M.P.1
  • 65
    • 56549129538 scopus 로고    scopus 로고
    • Chromatin structure analyses identify miRNA promoters
    • Ozsolak F, et al. (2008) Chromatin structure analyses identify miRNA promoters. Genes Dev 22(22):3172-3183.
    • (2008) Genes Dev , vol.22 , Issue.22 , pp. 3172-3183
    • Ozsolak, F.1
  • 66
    • 0036726369 scopus 로고    scopus 로고
    • Global analysis of gene expression in yeast
    • Horak CE, Snyder M (2002) Global analysis of gene expression in yeast. Funct Integr Genomics 2(4-5):171-180.
    • (2002) Funct Integr Genomics , vol.2 , Issue.4-5 , pp. 171-180
    • Horak, C.E.1    Snyder, M.2
  • 67
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCyclopedia of DNA Elements) Project
    • ENCODE Project Consortium
    • ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306(5696):636-640.
    • (2004) Science , vol.306 , Issue.5696 , pp. 636-640
  • 68
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • ENCODE Project Consortium
    • Birney E, et al.; ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146):799-816.
    • (2007) Nature , vol.447 , Issue.7146 , pp. 799-816
    • Birney, E.1
  • 69
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium
    • ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57-74.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 57-74
  • 70
    • 70449696134 scopus 로고    scopus 로고
    • Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
    • Cheng Y, et al. (2009) Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res 19(12): 2172-2184.
    • (2009) Genome Res , vol.19 , Issue.12 , pp. 2172-2184
    • Cheng, Y.1
  • 71
    • 80052805267 scopus 로고    scopus 로고
    • Histone modification: Cause or cog?
    • Henikoff S, Shilatifard A (2011) Histone modification: Cause or cog? Trends Genet 27(10):389-396.
    • (2011) Trends Genet , vol.27 , Issue.10 , pp. 389-396
    • Henikoff, S.1    Shilatifard, A.2
  • 72
    • 84864452351 scopus 로고    scopus 로고
    • Systematic dissection of roles for chromatin regulators in a yeast stress response
    • Weiner A, et al. (2012) Systematic dissection of roles for chromatin regulators in a yeast stress response. PLoS Biol 10(7):e1001369.
    • (2012) PLoS Biol , vol.10 , Issue.7
    • Weiner, A.1
  • 73
    • 0000822856 scopus 로고
    • The genetic organization of chromosomes
    • Thomas CA, Jr. (1971) The genetic organization of chromosomes. Annu Rev Genet 5:237-256.
    • (1971) Annu Rev Genet , vol.5 , pp. 237-256
    • Thomas Jr., C.A.1
  • 74
    • 0035090476 scopus 로고    scopus 로고
    • Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma
    • Gregory TR (2001) Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol Rev Camb Philos Soc 76(1):65-101.
    • (2001) Biol Rev Camb Philos Soc , vol.76 , Issue.1 , pp. 65-101
    • Gregory, T.R.1
  • 75
    • 84855455959 scopus 로고    scopus 로고
    • Rates and fitness consequences of new mutations in humans
    • Keightley PD (2012) Rates and fitness consequences of new mutations in humans. Genetics 190(2):295-304.
    • (2012) Genetics , vol.190 , Issue.2 , pp. 295-304
    • Keightley, P.D.1
  • 76
    • 0346875454 scopus 로고
    • Origin, development and maturation of organelles and organelle systems of the cell surface in Paramecium
    • Ehret CF, De Haller G (1963) Origin, development and maturation of organelles and organelle systems of the cell surface in Paramecium. J Ultrastruct Res 23(Suppl 6):1-42.
    • (1963) J Ultrastruct Res , vol.23 , Issue.SUPPL. 6 , pp. 1-42
    • Ehret, C.F.1    De Haller, G.2
  • 77
    • 0015271630 scopus 로고
    • So much "junk" DNA in our genome
    • Ohno S (1972) So much "junk" DNA in our genome. Brookhaven Symp Biol 23:366-370.
    • (1972) Brookhaven Symp Biol , vol.23 , pp. 366-370
    • Ohno, S.1
  • 79
    • 33644503176 scopus 로고    scopus 로고
    • A large family of ancient repeat elements in the human genome is under strong selection
    • Kamal M, Xie X, Lander ES (2006) A large family of ancient repeat elements in the human genome is under strong selection. Proc Natl Acad Sci USA 103(8):2740-2745.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.8 , pp. 2740-2745
    • Kamal, M.1    Xie, X.2    Lander, E.S.3
  • 80
    • 34249937354 scopus 로고    scopus 로고
    • Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
    • Lowe CB, Bejerano G, Haussler D (2007) Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci USA 104(19):8005-8010.
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.19 , pp. 8005-8010
    • Lowe, C.B.1    Bejerano, G.2    Haussler, D.3
  • 81
    • 80051914599 scopus 로고    scopus 로고
    • Three periods of regulatory innovation during vertebrate evolution
    • Lowe CB, et al. (2011) Three periods of regulatory innovation during vertebrate evolution. Science 333(6045):1019-1024.
    • (2011) Science , vol.333 , Issue.6045 , pp. 1019-1024
    • Lowe, C.B.1
  • 83
    • 84877749322 scopus 로고    scopus 로고
    • Exaptation of transposable elements into novel cis-regulatory elements: Is the evidence always strong?
    • de Souza FS, Franchini LF, Rubinstein M (2013) Exaptation of transposable elements into novel cis-regulatory elements: Is the evidence always strong? Mol Biol Evol 30(6):1239-1251.
    • (2013) Mol Biol Evol , vol.30 , Issue.6 , pp. 1239-1251
    • De Souza, F.S.1    Franchini, L.F.2    Rubinstein, M.3
  • 84
    • 33745620751 scopus 로고    scopus 로고
    • Functional noncoding sequences derived from SINEs in the mammalian genome
    • Nishihara H, Smit AF, Okada N (2006) Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res 16(7):864-874.
    • (2006) Genome Res , vol.16 , Issue.7 , pp. 864-874
    • Nishihara, H.1    Smit, A.F.2    Okada, N.3
  • 85
    • 79960911703 scopus 로고    scopus 로고
    • The reality of pervasive transcription
    • discussion e1001102
    • Clark MB, et al. (2011) The reality of pervasive transcription. PLoS Biol, 9(7):e1000625, discussion e1001102.
    • (2011) PLoS Biol , vol.9 , Issue.7
    • Clark, M.B.1
  • 86
    • 70449953975 scopus 로고    scopus 로고
    • The complex eukaryotic transcriptome: Unexpected pervasive transcription and novel small RNAs
    • Jacquier A (2009) The complex eukaryotic transcriptome: Unexpected pervasive transcription and novel small RNAs. Nat Rev Genet 10(12):833-844.
    • (2009) Nat Rev Genet , vol.10 , Issue.12 , pp. 833-844
    • Jacquier, A.1
  • 87
    • 28644447707 scopus 로고    scopus 로고
    • Genome sequence, comparative analysis and haplotype structure of the domestic dog
    • Lindblad-Toh K, et al. (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438(7069):803-819.
    • (2005) Nature , vol.438 , Issue.7069 , pp. 803-819
    • Lindblad-Toh, K.1
  • 88
    • 65249089637 scopus 로고    scopus 로고
    • Local DNA topography correlates with functional noncoding regions of the human genome
    • Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH (2009) Local DNA topography correlates with functional noncoding regions of the human genome. Science 324(5925):389-392.
    • (2009) Science , vol.324 , Issue.5925 , pp. 389-392
    • Parker, S.C.1    Hansen, L.2    Abaan, H.O.3    Tullius, T.D.4    Margulies, E.H.5
  • 89
    • 78149408021 scopus 로고    scopus 로고
    • Massive turnover of functional sequence in human and other mammalian genomes
    • Meader S, Ponting CP, Lunter G (2010) Massive turnover of functional sequence in human and other mammalian genomes. Genome Res 20(10):1335-1343.
    • (2010) Genome Res , vol.20 , Issue.10 , pp. 1335-1343
    • Meader, S.1    Ponting, C.P.2    Lunter, G.3
  • 90
    • 84866775366 scopus 로고    scopus 로고
    • Evidence of abundant purifying selection in humans for recently acquired regulatory functions
    • Ward LD, Kellis M (2012) Evidence of abundant purifying selection in humans for recently acquired regulatory functions. Science 337(6102):1675-1678.
    • (2012) Science , vol.337 , Issue.6102 , pp. 1675-1678
    • Ward, L.D.1    Kellis, M.2
  • 91
    • 84865856910 scopus 로고    scopus 로고
    • Revising the human mutation rate: Implications for understanding human evolution
    • Scally A, Durbin R (2012) Revising the human mutation rate: Implications for understanding human evolution. Nat Rev Genet 13(10):745-753.
    • (2012) Nat Rev Genet , vol.13 , Issue.10 , pp. 745-753
    • Scally, A.1    Durbin, R.2
  • 92
    • 80055095261 scopus 로고    scopus 로고
    • Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome
    • Lohmueller KE, et al. (2011) Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genet 7(10):e1002326.
    • (2011) PLoS Genet , vol.7 , Issue.10
    • Lohmueller, K.E.1
  • 93
    • 84877601532 scopus 로고    scopus 로고
    • Response to comment on "evidence of abundant purifying selection in humans for recently acquired regulatory functions"
    • Ward LD, Kellis M (2013) Response to comment on "Evidence of abundant purifying selection in humans for recently acquired regulatory functions" Science 340(6133):682.
    • (2013) Science , vol.340 , Issue.6133 , pp. 682
    • Ward, L.D.1    Kellis, M.2
  • 94
    • 69949176863 scopus 로고    scopus 로고
    • Common regulatory variation impacts gene expression in a cell type-dependent manner
    • Dimas AS, et al. (2009) Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 325(5945): 1246-1250.
    • (2009) Science , vol.325 , Issue.5945 , pp. 1246-1250
    • Dimas, A.S.1
  • 95
    • 77950458649 scopus 로고    scopus 로고
    • Transcriptome genetics using second generation sequencing in a Caucasian population
    • Montgomery SB, et al. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464(7289):773-777.
    • (2010) Nature , vol.464 , Issue.7289 , pp. 773-777
    • Montgomery, S.B.1
  • 96
    • 84891685308 scopus 로고    scopus 로고
    • Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals
    • Battle A, et al. (2014) Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res 24(1):14-24.
    • (2014) Genome Res , vol.24 , Issue.1 , pp. 14-24
    • Battle, A.1
  • 97
    • 84857111200 scopus 로고    scopus 로고
    • DNase i sensitivity QTLs are a major determinant of human expression variation
    • Degner JF, et al. (2012) DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482(7385):390-394.
    • (2012) Nature , vol.482 , Issue.7385 , pp. 390-394
    • Degner, J.F.1
  • 98
    • 77950460661 scopus 로고    scopus 로고
    • Understanding mechanisms underlying human gene expression variation with RNA sequencing
    • Pickrell JK, et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464(7289):768-772.
    • (2010) Nature , vol.464 , Issue.7289 , pp. 768-772
    • Pickrell, J.K.1
  • 99
    • 79955564639 scopus 로고    scopus 로고
    • Measuring reproducibility of high-throughput experiments
    • Li Q, Brown JB, Huang H, Bickel PJ (2011) Measuring reproducibility of high-throughput experiments. Ann Appl Stat 5(3):27.
    • (2011) Ann Appl Stat , vol.5 , Issue.3 , pp. 27
    • Li, Q.1    Brown, J.B.2    Huang, H.3    Bickel, P.J.4
  • 100
    • 84868010349 scopus 로고    scopus 로고
    • Revisiting global gene expression analysis
    • Lovén J, et al. (2012) Revisiting global gene expression analysis. Cell 151(3):476-482.
    • (2012) Cell , vol.151 , Issue.3 , pp. 476-482
    • Lovén, J.1
  • 101
    • 79959403670 scopus 로고    scopus 로고
    • Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
    • Islam S, et al. (2011) Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res 21(7):1160-1167.
    • (2011) Genome Res , vol.21 , Issue.7 , pp. 1160-1167
    • Islam, S.1
  • 102
    • 84895562012 scopus 로고    scopus 로고
    • From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing
    • Marinov GK, et al. (2014) From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing. Genome Res.
    • (2014) Genome Res
    • Marinov, G.K.1
  • 104
    • 84865757142 scopus 로고    scopus 로고
    • Landscape of transcription in human cells
    • Djebali S, et al. (2012) Landscape of transcription in human cells. Nature 489(7414):101-108.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 101-108
    • Djebali, S.1
  • 105
    • 33748805480 scopus 로고    scopus 로고
    • Spreading of silent chromatin: Inaction at a distance
    • Talbert PB, Henikoff S (2006) Spreading of silent chromatin: Inaction at a distance. Nat Rev Genet 7(10):793-803.
    • (2006) Nat Rev Genet , vol.7 , Issue.10 , pp. 793-803
    • Talbert, P.B.1    Henikoff, S.2
  • 106
    • 23744493161 scopus 로고    scopus 로고
    • Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
    • King DC, et al. (2005) Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res 15(8): 1051-1060.
    • (2005) Genome Res , vol.15 , Issue.8 , pp. 1051-1060
    • King, D.C.1
  • 107
    • 0024591610 scopus 로고
    • An erythroid-specific, developmental-stage-independent enhancer far upstream of the human "beta-like globin" genes
    • Tuan DY, Solomon WB, London IM, Lee DP (1989) An erythroid-specific, developmental-stage-independent enhancer far upstream of the human "beta-like globin" genes. Proc Natl Acad Sci USA 86(8):2554-2558.
    • (1989) Proc Natl Acad Sci USA , vol.86 , Issue.8 , pp. 2554-2558
    • Tuan, D.Y.1    Solomon, W.B.2    London, I.M.3    Lee, D.P.4
  • 108
    • 0023430030 scopus 로고
    • An enhancer element lies 3' to the human A gamma globin gene
    • Bodine DM, Ley TJ (1987) An enhancer element lies 3' to the human A gamma globin gene. EMBO J 6(10):2997-3004.
    • (1987) EMBO J , vol.6 , Issue.10 , pp. 2997-3004
    • Bodine, D.M.1    Ley, T.J.2
  • 109
    • 77950930726 scopus 로고    scopus 로고
    • Transcriptional silencing of gamma-globin by BCL11A involves long-range interactions and cooperation with SOX6
    • Xu J, et al. (2010) Transcriptional silencing of gamma-globin by BCL11A involves long-range interactions and cooperation with SOX6. Genes Dev 24(8):783-798.
    • (2010) Genes Dev , vol.24 , Issue.8 , pp. 783-798
    • Xu, J.1
  • 110
    • 80052439730 scopus 로고    scopus 로고
    • A functional element necessary for fetal hemoglobin silencing
    • Sankaran VG, et al. (2011) A functional element necessary for fetal hemoglobin silencing. N Engl J Med 365(9):807-814.
    • (2011) N Engl J Med , vol.365 , Issue.9 , pp. 807-814
    • Sankaran, V.G.1
  • 111
    • 84865739425 scopus 로고    scopus 로고
    • Architecture of the human regulatory network derived from ENCODE data
    • Gerstein MB, et al. (2012) Architecture of the human regulatory network derived from ENCODE data. Nature 489(7414):91-100.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 91-100
    • Gerstein, M.B.1
  • 112
    • 84873086126 scopus 로고    scopus 로고
    • Chromatin marks identify critical cell types for fine mapping complex trait variants
    • Trynka G, et al. (2013) Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat Genet 45(2): 124-130.
    • (2013) Nat Genet , vol.45 , Issue.2 , pp. 124-130
    • Trynka, G.1
  • 113
    • 84884288934 scopus 로고    scopus 로고
    • Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity
    • Ran FA, et al. (2013) Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154(6): 1380-1389.
    • (2013) Cell , vol.154 , Issue.6 , pp. 1380-1389
    • Ran, F.A.1
  • 114
    • 71849115077 scopus 로고    scopus 로고
    • Genome engineering
    • Carr PA, Church GM (2009) Genome engineering. Nat Biotechnol 27(12):1151-1162.
    • (2009) Nat Biotechnol , vol.27 , Issue.12 , pp. 1151-1162
    • Carr, P.A.1    Church, G.M.2
  • 115
    • 78651237647 scopus 로고    scopus 로고
    • Identifying a high fraction of the human genome to be under selective constraint using GERP++
    • Davydov EV, et al. (2010) Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLOS Comput Biol 6(12):e1001025.
    • (2010) PLOS Comput Biol , vol.6 , Issue.12
    • Davydov, E.V.1
  • 116
    • 63849308888 scopus 로고    scopus 로고
    • Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
    • Hesselberth JR, et al. (2009) Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 6(4):283-289.
    • (2009) Nat Methods , vol.6 , Issue.4 , pp. 283-289
    • Hesselberth, J.R.1


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