메뉴 건너뛰기




Volumn 9, Issue 5, 2013, Pages

Drosophila Functional Elements Are Embedded in Structurally Constrained Sequences

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BASE PAIRING; DROSOPHILA; EPIGENETICS; FUNCTIONAL GENOMICS; GENE FREQUENCY; GENE FUNCTION; GENE SEQUENCE; GENETIC CONSERVATION; MICROSATELLITE MARKER; NONHUMAN; NUCLEOSOME; NUCLEOTIDE SEQUENCE; PROMOTER REGION; REGULATORY MECHANISM; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84878518413     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003512     Document Type: Article
Times cited : (9)

References (73)
  • 1
    • 67149096366 scopus 로고    scopus 로고
    • Widespread Genomic Signatures of Natural Selection in Hominid Evolution
    • doi:10.1371/journal.pgen.1000471
    • McVicker G, Gordon D, Davis C, Green P, (2009) Widespread Genomic Signatures of Natural Selection in Hominid Evolution. PLoS Genet 5: e1000471 doi:10.1371/journal.pgen.1000471.
    • (2009) PLoS Genet , vol.5
    • McVicker, G.1    Gordon, D.2    Davis, C.3    Green, P.4
  • 2
    • 84862984796 scopus 로고    scopus 로고
    • Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast
    • doi:10.1038/ng.2305
    • Raveh-Sadka T, Levo M, Shabi U, Shany B, Keren L, et al. (2012) Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nature genetics 44: 743-750 doi:10.1038/ng.2305.
    • (2012) Nature Genetics , vol.44 , pp. 743-750
    • Raveh-Sadka, T.1    Levo, M.2    Shabi, U.3    Shany, B.4    Keren, L.5
  • 3
    • 33749381311 scopus 로고    scopus 로고
    • Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection
    • doi:10.1101/gr.5655606
    • Liu X, Lee C-K, Granek JA, Clarke ND, Lieb JD, (2006) Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome research 16: 1517-28 doi:10.1101/gr.5655606.
    • (2006) Genome Research , vol.16 , pp. 1517-1528
    • Liu, X.1    Lee, C.-K.2    Granek, J.A.3    Clarke, N.D.4    Lieb, J.D.5
  • 4
    • 62649085538 scopus 로고    scopus 로고
    • The DNA-encoded nucleosome organization of a eukaryotic genome
    • doi:10.1038/nature07667
    • Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, et al. (2008) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458: 362-366 doi:10.1038/nature07667.
    • (2008) Nature , vol.458 , pp. 362-366
    • Kaplan, N.1    Moore, I.K.2    Fondufe-Mittendorf, Y.3    Gossett, A.J.4    Tillo, D.5
  • 5
    • 75149135277 scopus 로고    scopus 로고
    • G+C content dominates intrinsic nucleosome occupancy
    • doi:10.1186/1471-2105-10-442
    • Tillo D, Hughes T, (2009) G+C content dominates intrinsic nucleosome occupancy. BMC bioinformatics 10: 442 doi:10.1186/1471-2105-10-442.
    • (2009) BMC Bioinformatics , vol.10 , pp. 442
    • Tillo, D.1    Hughes, T.2
  • 6
    • 79959557189 scopus 로고    scopus 로고
    • Determinants of nucleosome organization in primary human cells
    • doi:10.1038/nature10002
    • Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, et al. (2011) Determinants of nucleosome organization in primary human cells. Nature 474: 516-20 doi:10.1038/nature10002.
    • (2011) Nature , vol.474 , pp. 516-520
    • Valouev, A.1    Johnson, S.M.2    Boyd, S.D.3    Smith, C.L.4    Fire, A.Z.5
  • 8
    • 84865248380 scopus 로고    scopus 로고
    • Chromatin organization is a major influence on regional mutation rates in human cancer cells
    • doi:10.1038/nature11273
    • Schuster-Böckler B, Lehner B, (2012) Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature 488: 504-7 doi:10.1038/nature11273.
    • (2012) Nature , vol.488 , pp. 504-507
    • Schuster-Böckler, B.1    Lehner, B.2
  • 9
    • 84865777820 scopus 로고    scopus 로고
    • Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
    • doi:10.1101/gr.136366.111
    • Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, et al. (2012) Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Research 22: 1735-1747 doi:10.1101/gr.136366.111.
    • (2012) Genome Research , vol.22 , pp. 1735-1747
    • Kundaje, A.1    Kyriazopoulou-Panagiotopoulou, S.2    Libbrecht, M.3    Smith, C.L.4    Raha, D.5
  • 10
    • 57149100569 scopus 로고    scopus 로고
    • The impact of the nucleosome code on protein-coding sequence evolution in yeast
    • doi:10.1371/journal.pgen.1000250
    • Warnecke T, Batada NN, Hurst LD, (2008) The impact of the nucleosome code on protein-coding sequence evolution in yeast. PLoS Genet 4: e1000250 doi:10.1371/journal.pgen.1000250.
    • (2008) PLoS Genet , vol.4
    • Warnecke, T.1    Batada, N.N.2    Hurst, L.D.3
  • 11
    • 56649089682 scopus 로고    scopus 로고
    • Evolutionary footprints of nucleosome positions in yeast
    • doi:10.1016/j.tig.2008.09.003
    • Washietl S, Machné R, Goldman N, (2008) Evolutionary footprints of nucleosome positions in yeast. Trends in genetics: TIG 24: 583-7 doi:10.1016/j.tig.2008.09.003.
    • (2008) Trends in Genetics: TIG , vol.24 , pp. 583-587
    • Washietl, S.1    Machné, R.2    Goldman, N.3
  • 12
    • 78651240895 scopus 로고    scopus 로고
    • Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast
    • doi:10.1371/journal.pcbi.1001039
    • Kenigsberg E, Bar A, Segal E, Tanay A, (2010) Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast. PLoS Comput Biol 6: e1001039 doi:10.1371/journal.pcbi.1001039.
    • (2010) PLoS Comput Biol , vol.6
    • Kenigsberg, E.1    Bar, A.2    Segal, E.3    Tanay, A.4
  • 13
    • 0034708480 scopus 로고    scopus 로고
    • The Genome Sequence of Drosophila melanogaster
    • doi:10.1126/science.287.5461.2185
    • Adams MD, (2000) The Genome Sequence of Drosophila melanogaster. Science 287: 2185-2195 doi:10.1126/science.287.5461.2185.
    • (2000) Science , vol.287 , pp. 2185-2195
    • Adams, M.D.1
  • 14
    • 78650331647 scopus 로고    scopus 로고
    • Identification of functional elements and regulatory circuits by Drosophila modENCODE
    • doi:10.1126/science.1198374
    • Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, et al. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.) 330: 1787-97 doi:10.1126/science.1198374.
    • (2010) Science (New York, N.Y.) , vol.330 , pp. 1787-1797
    • Roy, S.1    Ernst, J.2    Kharchenko, P.V.3    Kheradpour, P.4    Negre, N.5
  • 15
    • 79953046943 scopus 로고    scopus 로고
    • A cis-regulatory map of the Drosophila genome
    • doi:10.1038/nature09990
    • Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, et al. (2011) A cis-regulatory map of the Drosophila genome. Nature 471: 527-31 doi:10.1038/nature09990.
    • (2011) Nature , vol.471 , pp. 527-531
    • Nègre, N.1    Brown, C.D.2    Ma, L.3    Bristow, C.A.4    Miller, S.W.5
  • 16
    • 84856747483 scopus 로고    scopus 로고
    • Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome
    • doi:10.1016/j.cell.2012.01.010
    • Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, et al. (2012) Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome. Cell 148: 458-72 doi:10.1016/j.cell.2012.01.010.
    • (2012) Cell , vol.148 , pp. 458-472
    • Sexton, T.1    Yaffe, E.2    Kenigsberg, E.3    Bantignies, F.4    Leblanc, B.5
  • 17
    • 27144491328 scopus 로고    scopus 로고
    • Adaptive evolution of non-coding DNA in Drosophila
    • doi:10.1038/nature04107
    • Andolfatto P, (2005) Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-52 doi:10.1038/nature04107.
    • (2005) Nature , vol.437 , pp. 1149-1152
    • Andolfatto, P.1
  • 18
    • 33745612972 scopus 로고    scopus 로고
    • Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
    • doi:10.1101/gr.5022906
    • Halligan DL, Keightley PD, (2006) Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison. Genome research 16: 875-84 doi:10.1101/gr.5022906.
    • (2006) Genome Research , vol.16 , pp. 875-884
    • Halligan, D.L.1    Keightley, P.D.2
  • 19
    • 49749083390 scopus 로고    scopus 로고
    • Positive and negative selection on noncoding DNA in Drosophila simulans
    • doi:10.1093/molbev/msn125
    • Haddrill PR, Bachtrog D, Andolfatto P, (2008) Positive and negative selection on noncoding DNA in Drosophila simulans. Molecular biology and evolution 25: 1825-34 doi:10.1093/molbev/msn125.
    • (2008) Molecular Biology and Evolution , vol.25 , pp. 1825-1834
    • Haddrill, P.R.1    Bachtrog, D.2    Andolfatto, P.3
  • 20
    • 84863012360 scopus 로고    scopus 로고
    • The Drosophila melanogaster Genetic Reference Panel
    • doi:10.1038/nature10811
    • Mackay TFC, Richards S, Stone EA, Barbadilla A, Ayroles JF, et al. (2012) The Drosophila melanogaster Genetic Reference Panel. Nature 482: 173-8 doi:10.1038/nature10811.
    • (2012) Nature , vol.482 , pp. 173-178
    • Mackay, T.F.C.1    Richards, S.2    Stone, E.A.3    Barbadilla, A.4    Ayroles, J.F.5
  • 21
    • 84856806926 scopus 로고    scopus 로고
    • Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner
    • doi:10.1128/MCB.06365-11
    • Moshkin YM, Chalkley GE, Kan TW, Reddy BA, Ozgur Z, et al. (2012) Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner. Molecular and cellular biology 32: 675-88 doi:10.1128/MCB.06365-11.
    • (2012) Molecular and Cellular Biology , vol.32 , pp. 675-688
    • Moshkin, Y.M.1    Chalkley, G.E.2    Kan, T.W.3    Reddy, B.A.4    Ozgur, Z.5
  • 22
    • 43749099875 scopus 로고    scopus 로고
    • Nucleosome organization in the Drosophila genome
    • doi:10.1038/nature06929
    • Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, et al. (2008) Nucleosome organization in the Drosophila genome. Nature 453: 358-62 doi:10.1038/nature06929.
    • (2008) Nature , vol.453 , pp. 358-362
    • Mavrich, T.N.1    Jiang, C.2    Ioshikhes, I.P.3    Li, X.4    Venters, B.J.5
  • 23
    • 84863574768 scopus 로고    scopus 로고
    • Inferring Divergence of Context-Dependent Substitution Rates in Drosophila Genomes with Applications to Comparative Genomics
    • doi:10.1093/molbev/mss056
    • Chachick R, Tanay A, (2012) Inferring Divergence of Context-Dependent Substitution Rates in Drosophila Genomes with Applications to Comparative Genomics. Mol Biol Evol 29: 1769-80 doi: 10.1093/molbev/mss056.
    • (2012) Mol Biol Evol , vol.29 , pp. 1769-1780
    • Chachick, R.1    Tanay, A.2
  • 25
    • 9144242657 scopus 로고    scopus 로고
    • Comprehensive analysis of the base composition around the transcription start site in Metazoa
    • doi:10.1186/1471-2164-5-34
    • Aerts S, Thijs G, Dabrowski M, Moreau Y, Moor B De, (2004) Comprehensive analysis of the base composition around the transcription start site in Metazoa. BMC genomics 5: 34 doi:10.1186/1471-2164-5-34.
    • (2004) BMC Genomics , vol.5 , pp. 34
    • Aerts, S.1    Thijs, G.2    Dabrowski, M.3    Moreau, Y.4    de Moor, B.5
  • 26
    • 38549168437 scopus 로고    scopus 로고
    • Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
    • doi:10.1186/gb-2007-8-6-r101
    • Li L, Zhu Q, He X, Sinha S, Halfon MS, (2007) Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses. Genome biology 8: R101 doi:10.1186/gb-2007-8-6-r101.
    • (2007) Genome Biology , vol.8
    • Li, L.1    Zhu, Q.2    He, X.3    Sinha, S.4    Halfon, M.S.5
  • 27
    • 79955760882 scopus 로고    scopus 로고
    • Dynamic reprogramming of chromatin accessibility during Drosophila embryo development
    • doi:10.1186/gb-2011-12-5-r43
    • Thomas S, Li X-Y, Sabo PJ, Sandstrom R, Thurman RE, et al. (2011) Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome biology 12: R43 doi:10.1186/gb-2011-12-5-r43.
    • (2011) Genome Biology , vol.12
    • Thomas, S.1    Li, X.-Y.2    Sabo, P.J.3    Sandstrom, R.4    Thurman, R.E.5
  • 29
    • 84865708757 scopus 로고    scopus 로고
    • An expansive human regulatory lexicon encoded in transcription factor footprints
    • doi:10.1038/nature11212
    • Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, et al. (2012) An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489: 83-90 doi:10.1038/nature11212.
    • (2012) Nature , vol.489 , pp. 83-90
    • Neph, S.1    Vierstra, J.2    Stergachis, A.B.3    Reynolds, A.P.4    Haugen, E.5
  • 30
    • 84865755978 scopus 로고    scopus 로고
    • The accessible chromatin landscape of the human genome
    • doi:10.1038/nature11232
    • Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, et al. (2012) The accessible chromatin landscape of the human genome. Nature 489: 75-82 doi:10.1038/nature11232.
    • (2012) Nature , vol.489 , pp. 75-82
    • Thurman, R.E.1    Rynes, E.2    Humbert, R.3    Vierstra, J.4    Maurano, M.T.5
  • 32
    • 77949393272 scopus 로고    scopus 로고
    • High nucleosome occupancy is encoded at human regulatory sequences
    • doi:10.1371/journal.pone.0009129
    • Tillo D, Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, et al. (2010) High nucleosome occupancy is encoded at human regulatory sequences. PLoS ONE 5: e9129 doi:10.1371/journal.pone.0009129.
    • (2010) PLoS ONE , vol.5
    • Tillo, D.1    Kaplan, N.2    Moore, I.K.3    Fondufe-Mittendorf, Y.4    Gossett, A.J.5
  • 33
    • 38049024773 scopus 로고    scopus 로고
    • Analysis of sequence conservation at nucleotide resolution
    • doi:10.1371/journal.pcbi.0030254
    • Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S, (2007) Analysis of sequence conservation at nucleotide resolution. PLoS Comput Biol 3: e254 doi:10.1371/journal.pcbi.0030254.
    • (2007) PLoS Comput Biol , vol.3
    • Asthana, S.1    Roytberg, M.2    Stamatoyannopoulos, J.3    Sunyaev, S.4
  • 34
    • 22144494134 scopus 로고    scopus 로고
    • Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences
    • doi:10.1016/j.tig.2005.06.003
    • Walter K, Abnizova I, Elgar G, Gilks WR, (2005) Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences. Trends in genetics: TIG 21: 436-40 doi:10.1016/j.tig.2005.06.003.
    • (2005) Trends in Genetics: TIG , vol.21 , pp. 436-440
    • Walter, K.1    Abnizova, I.2    Elgar, G.3    Gilks, W.R.4
  • 35
    • 34447500684 scopus 로고    scopus 로고
    • Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans
    • doi:10.1186/gb-2007-8-2-r15
    • Vavouri T, Walter K, Gilks WR, Lehner B, Elgar G, (2007) Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans. Genome biology 8: R15 doi:10.1186/gb-2007-8-2-r15.
    • (2007) Genome Biology , vol.8
    • Vavouri, T.1    Walter, K.2    Gilks, W.R.3    Lehner, B.4    Elgar, G.5
  • 36
    • 33749377241 scopus 로고    scopus 로고
    • Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura
    • doi:10.1186/gb-2006-7-7-R67
    • Macdonald SJ, Long AD, (2006) Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura. Genome biology 7: R67 doi:10.1186/gb-2006-7-7-R67.
    • (2006) Genome Biology , vol.7
    • Macdonald, S.J.1    Long, A.D.2
  • 37
    • 58849088872 scopus 로고    scopus 로고
    • Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos
    • doi:10.1371/journal.pbio.1000013
    • Schuettengruber B, Ganapathi M, Leblanc B, Portoso M, Jaschek R, et al. (2009) Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos. PLoS Biol 7: e13 doi:10.1371/journal.pbio.1000013.
    • (2009) PLoS Biol , vol.7
    • Schuettengruber, B.1    Ganapathi, M.2    Leblanc, B.3    Portoso, M.4    Jaschek, R.5
  • 38
    • 33847189172 scopus 로고    scopus 로고
    • Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo
    • doi:10.1101/gad.1509607
    • Zeitlinger J, Zinzen RP, Stark A, Kellis M, Zhang H, et al. (2007) Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes & development 21: 385-90 doi:10.1101/gad.1509607.
    • (2007) Genes & Development , vol.21 , pp. 385-390
    • Zeitlinger, J.1    Zinzen, R.P.2    Stark, A.3    Kellis, M.4    Zhang, H.5
  • 39
    • 25844481290 scopus 로고    scopus 로고
    • Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content
    • doi:10.1186/gb-2005-6-8-r67
    • Haddrill PR, Charlesworth B, Halligan DL, Andolfatto P, (2005) Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. Genome biology 6: R67 doi:10.1186/gb-2005-6-8-r67.
    • (2005) Genome Biology , vol.6
    • Haddrill, P.R.1    Charlesworth, B.2    Halligan, D.L.3    Andolfatto, P.4
  • 40
    • 33644780844 scopus 로고    scopus 로고
    • GC-biased segregation of noncoding polymorphisms in Drosophila
    • doi:10.1534/genetics.105.046524
    • Galtier N, Bazin E, Bierne N, (2006) GC-biased segregation of noncoding polymorphisms in Drosophila. Genetics 172: 221-8 doi:10.1534/genetics.105.046524.
    • (2006) Genetics , vol.172 , pp. 221-228
    • Galtier, N.1    Bazin, E.2    Bierne, N.3
  • 41
    • 44949198268 scopus 로고    scopus 로고
    • The impact of recombination on nucleotide substitutions in the human genome
    • doi:10.1371/journal.pgen.1000071
    • Duret L, Arndt PF, (2008) The impact of recombination on nucleotide substitutions in the human genome. PLoS Genet 4: e1000071 doi:10.1371/journal.pgen.1000071.
    • (2008) PLoS Genet , vol.4
    • Duret, L.1    Arndt, P.F.2
  • 42
    • 58849161775 scopus 로고    scopus 로고
    • Hotspots of biased nucleotide substitutions in human genes
    • doi:10.1371/journal.pbio.1000026
    • Berglund J, Pollard KS, Webster MT, (2009) Hotspots of biased nucleotide substitutions in human genes. PLoS Biol 7: e26 doi:10.1371/journal.pbio.1000026.
    • (2009) PLoS Biol , vol.7
    • Berglund, J.1    Pollard, K.S.2    Webster, M.T.3
  • 43
    • 52449148668 scopus 로고
    • The role of compensatory neutral mutations in molecular evolution
    • doi:10.1007/BF02923549
    • Kimura M, (1985) The role of compensatory neutral mutations in molecular evolution. Journal of Genetics 64: 7-19 doi:10.1007/BF02923549.
    • (1985) Journal of Genetics , vol.64 , pp. 7-19
    • Kimura, M.1
  • 44
    • 34249723155 scopus 로고    scopus 로고
    • Frequent gain and loss of functional transcription factor binding sites
    • doi:10.1371/journal.pcbi.0030099
    • Doniger SW, Fay JC, (2007) Frequent gain and loss of functional transcription factor binding sites. PLoS Comput Biol 3: e99 doi:10.1371/journal.pcbi.0030099.
    • (2007) PLoS Comput Biol , vol.3
    • Doniger, S.W.1    Fay, J.C.2
  • 45
    • 78049323331 scopus 로고    scopus 로고
    • Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants
    • doi:10.1038/ng.680
    • Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T, et al. (2010) Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nature genetics 42: 969-72 doi:10.1038/ng.680.
    • (2010) Nature Genetics , vol.42 , pp. 969-972
    • Li, Y.1    Vinckenbosch, N.2    Tian, G.3    Huerta-Sanchez, E.4    Jiang, T.5
  • 46
    • 84860599674 scopus 로고    scopus 로고
    • Joint genotyping on the fly: Identifying variation among a sequenced panel of inbred lines
    • doi:10.1101/gr.129122.111
    • Stone EA, (2012) Joint genotyping on the fly: Identifying variation among a sequenced panel of inbred lines. Genome Res 22: 966-74 doi:10.1101/gr.129122.111.
    • (2012) Genome Res , vol.22 , pp. 966-974
    • Stone, E.A.1
  • 47
    • 46949087998 scopus 로고    scopus 로고
    • Non-neutral processes drive the nucleotide composition of non-coding sequences in Drosophila
    • doi:10.1098/rsbl.2008.0174
    • Haddrill PR, Charlesworth B, (2008) Non-neutral processes drive the nucleotide composition of non-coding sequences in Drosophila. Biology letters 4: 438-41 doi:10.1098/rsbl.2008.0174.
    • (2008) Biology Letters , vol.4 , pp. 438-441
    • Haddrill, P.R.1    Charlesworth, B.2
  • 48
    • 79953311672 scopus 로고    scopus 로고
    • High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation
    • doi:10.1101/gr.104018.109
    • Ozdemir A, Fisher-Aylor KI, Pepke S, Samanta M, Dunipace L, et al. (2011) High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation. Genome research 21: 566-577 doi:10.1101/gr.104018.109.
    • (2011) Genome Research , vol.21 , pp. 566-577
    • Ozdemir, A.1    Fisher-Aylor, K.I.2    Pepke, S.3    Samanta, M.4    Dunipace, L.5
  • 49
    • 0022448415 scopus 로고
    • Some guidelines for identification of recognition sequences: regulatory sequences frequently contain (T)GTG/CAC(A), TGA/TCA and (T)CTC/GAG(A)
    • Nussinov R, (1986) Some guidelines for identification of recognition sequences: regulatory sequences frequently contain (T)GTG/CAC(A), TGA/TCA and (T)CTC/GAG(A). Biochimica et biophysica acta 866: 93-108.
    • (1986) Biochimica Et Biophysica Acta , vol.866 , pp. 93-108
    • Nussinov, R.1
  • 50
    • 34047230770 scopus 로고    scopus 로고
    • Discovering motifs in ranked lists of DNA sequences
    • doi:10.1371/journal.pcbi.0030039
    • Eden E, Lipson D, Yogev S, Yakhini Z, (2007) Discovering motifs in ranked lists of DNA sequences. PLoS Comput Biol 3: e39 doi:10.1371/journal.pcbi.0030039.
    • (2007) PLoS Comput Biol , vol.3
    • Eden, E.1    Lipson, D.2    Yogev, S.3    Yakhini, Z.4
  • 51
    • 84880306697 scopus 로고    scopus 로고
    • Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers
    • doi:10.1038/ncomms1102
    • Crocker J, Potter N, Erives A, (2010) Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers. Nature communications 1: 99 doi:10.1038/ncomms1102.
    • (2010) Nature Communications , vol.1 , pp. 99
    • Crocker, J.1    Potter, N.2    Erives, A.3
  • 52
    • 0029026719 scopus 로고
    • Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure
    • Iyer V, Struhl K, (1995) Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. The EMBO journal 14: 2570-9.
    • (1995) The EMBO Journal , vol.14 , pp. 2570-2579
    • Iyer, V.1    Struhl, K.2
  • 53
    • 76749088015 scopus 로고    scopus 로고
    • Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers
    • doi:10.1371/journal.pgen.1000829
    • Lusk RW, Eisen MB, (2010) Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers. PLoS Genet 6: e1000829 doi:10.1371/journal.pgen.1000829.
    • (2010) PLoS Genet , vol.6
    • Lusk, R.W.1    Eisen, M.B.2
  • 54
    • 59249100200 scopus 로고    scopus 로고
    • Pervasive hitchhiking at coding and regulatory sites in humans
    • Cai JJ, Macpherson JM, Sella G, Petrov DA, (2009) Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet 5: e1000336.
    • (2009) PLoS Genet , vol.5
    • Cai, J.J.1    Macpherson, J.M.2    Sella, G.3    Petrov, D.A.4
  • 55
    • 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, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, 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    Stamatoyannopoulos, J.A.2    Dutta, A.3    Guigó, R.4    Gingeras, T.R.5
  • 56
    • 80555156662 scopus 로고    scopus 로고
    • Widespread signatures of recent selection linked to nucleosome positioning in the human lineage
    • doi:10.1101/gr.122275.111
    • Prendergast JGD, Semple CAM, (2011) Widespread signatures of recent selection linked to nucleosome positioning in the human lineage. Genome research 21: 1777-87 doi:10.1101/gr.122275.111.
    • (2011) Genome Research , vol.21 , pp. 1777-1787
    • Prendergast, J.G.D.1    Semple, C.A.M.2
  • 57
    • 0034989085 scopus 로고    scopus 로고
    • Local Rates of Recombination Are Positively Correlated with GC Content in the Human Genome
    • Fullerton SM, Bernardo Carvalho A, Clark AG, (2001) Local Rates of Recombination Are Positively Correlated with GC Content in the Human Genome. Molecular Biology and Evolution 18: 1139-1142.
    • (2001) Molecular Biology and Evolution , vol.18 , pp. 1139-1142
    • Fullerton, S.M.1    Bernardo Carvalho, A.2    Clark, A.G.3
  • 59
    • 56849103052 scopus 로고    scopus 로고
    • Evolution acts on enhancer organization to fine-tune gradient threshold readouts
    • doi:10.1371/journal.pbio.0060263
    • Crocker J, Tamori Y, Erives A, (2008) Evolution acts on enhancer organization to fine-tune gradient threshold readouts. PLoS Biol 6: e263 doi:10.1371/journal.pbio.0060263.
    • (2008) PLoS Biol , vol.6
    • Crocker, J.1    Tamori, Y.2    Erives, A.3
  • 61
    • 70349470948 scopus 로고    scopus 로고
    • Structural and functional constraints in the evolution of protein families
    • Worth CL, Gong S, Blundell TL, (2009) Structural and functional constraints in the evolution of protein families. Nature Reviews Molecular Cell Biology 10: 709-720.
    • (2009) Nature Reviews Molecular Cell Biology , vol.10 , pp. 709-720
    • Worth, C.L.1    Gong, S.2    Blundell, T.L.3
  • 62
    • 39749145198 scopus 로고    scopus 로고
    • Dynamic regulation of nucleosome positioning in the human genome
    • doi:10.1016/j.cell.2008.02.022
    • Schones DE, Cui K, Cuddapah S, Roh T-Y, Barski A, et al. (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-98 doi:10.1016/j.cell.2008.02.022.
    • (2008) Cell , vol.132 , pp. 887-898
    • Schones, D.E.1    Cui, K.2    Cuddapah, S.3    Roh, T.-Y.4    Barski, A.5
  • 63
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • doi:10.1126/science.1181369
    • Lieberman-Aiden E, Berkum NL van, Williams L, Imakaev M, Ragoczy T, et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (New York, N.Y.) 326: 289-93 doi:10.1126/science.1181369.
    • (2009) Science (New York, N.Y.) , vol.326 , pp. 289-293
    • Lieberman-Aiden, E.1    van Berkum, N.L.2    Williams, L.3    Imakaev, M.4    Ragoczy, T.5
  • 64
    • 0036923833 scopus 로고    scopus 로고
    • Looping and Interaction between Hypersensitive Sites in the Active β-globin Locus
    • Tolhuis B, Palstra R-J, Splinter E, Grosveld F, Laat W de, (2002) Looping and Interaction between Hypersensitive Sites in the Active β-globin Locus. Molecular Cell 10: 1453-1465.
    • (2002) Molecular Cell , vol.10 , pp. 1453-1465
    • Tolhuis, B.1    Palstra, R.-J.2    Splinter, E.3    Grosveld, F.4    de Laat, W.5
  • 65
    • 77956495708 scopus 로고    scopus 로고
    • Transcriptional enhancers in animal development and evolution
    • doi:10.1016/j.cub.2010.06.070
    • Levine M, (2010) Transcriptional enhancers in animal development and evolution. Current biology: CB 20: R754-63 doi:10.1016/j.cub.2010.06.070.
    • (2010) Current Biology: CB , vol.20
    • Levine, M.1
  • 66
    • 78651514974 scopus 로고    scopus 로고
    • Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila
    • doi:10.1016/j.cell.2010.12.026
    • Bantignies F, Roure V, Comet I, Leblanc B, Schuettengruber B, et al. (2011) Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell 144: 214-26 doi:10.1016/j.cell.2010.12.026.
    • (2011) Cell , vol.144 , pp. 214-226
    • Bantignies, F.1    Roure, V.2    Comet, I.3    Leblanc, B.4    Schuettengruber, B.5
  • 68
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • doi:10.1038/nmeth.1923
    • Langmead B, Salzberg SL, (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods 9: 357-359 doi:10.1038/nmeth.1923.
    • (2012) Nature Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 69
    • 78649884849 scopus 로고    scopus 로고
    • H2A.Z nucleosomes enriched over active genes are homotypic
    • doi:10.1038/nsmb.1926
    • Weber CM, Henikoff JG, Henikoff S, (2010) H2A.Z nucleosomes enriched over active genes are homotypic. Nature structural & molecular biology 17: 1500-7 doi:10.1038/nsmb.1926.
    • (2010) Nature Structural & Molecular Biology , vol.17 , pp. 1500-1507
    • Weber, C.M.1    Henikoff, J.G.2    Henikoff, S.3
  • 70
    • 78651335916 scopus 로고    scopus 로고
    • REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila
    • doi:10.1093/nar/gkq999
    • Gallo SM, Gerrard DT, Miner D, Simich M, Soye BDes, et al. (2011) REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic acids research 39: D118-23 doi:10.1093/nar/gkq999.
    • (2011) Nucleic Acids Research , vol.39
    • Gallo, S.M.1    Gerrard, D.T.2    Miner, D.3    Simich, M.4    Soye, B.D.5
  • 71
    • 79957577720 scopus 로고    scopus 로고
    • Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection
    • Cohen NM, Kenigsberg E, Tanay A, (2011) Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection. Cell 145: 773-786.
    • (2011) Cell , vol.145 , pp. 773-786
    • Cohen, N.M.1    Kenigsberg, E.2    Tanay, A.3
  • 72
    • 79959503826 scopus 로고    scopus 로고
    • The International HapMap Project
    • The International HapMap Project (2003) Nature 426: 789-96.
    • (2003) Nature , vol.426 , pp. 789-796
  • 73
    • 80052851950 scopus 로고    scopus 로고
    • Mouse genomic variation and its effect on phenotypes and gene regulation
    • doi:10.1038/nature10413
    • Keane TM, Goodstadt L, Danecek P, White MA, Wong K, et al. (2011) Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477: 289-94 doi:10.1038/nature10413.
    • (2011) Nature , vol.477 , pp. 289-294
    • Keane, T.M.1    Goodstadt, L.2    Danecek, P.3    White, M.A.4    Wong, K.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.