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Volumn 13, Issue 1, 2012, Pages

Evolution of cis-regulatory elements in yeast de novo and duplicated new genes

Author keywords

De novo gene; Promoter architecture; Regulatory evolution; TFBS turnover

Indexed keywords

TATA BINDING PROTEIN; TRANSCRIPTION FACTOR;

EID: 84871367915     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-717     Document Type: Article
Times cited : (8)

References (79)
  • 1
    • 78649231644 scopus 로고    scopus 로고
    • Origins, evolution, and phenotypic impact of new genes
    • 10.1101/gr.101386.109, 2945180, 20651121
    • Kaessmann H. Origins, evolution, and phenotypic impact of new genes. Genome Res 2010, 20:1313-1326. 10.1101/gr.101386.109, 2945180, 20651121.
    • (2010) Genome Res , vol.20 , pp. 1313-1326
    • Kaessmann, H.1
  • 2
    • 0242354129 scopus 로고    scopus 로고
    • The origin of new genes: glimpses from the young and old
    • Long M, Betrán E, Thornton K, Wang W. The origin of new genes: glimpses from the young and old. Nat Rev Genet 2003, 4:865-875.
    • (2003) Nat Rev Genet , vol.4 , pp. 865-875
    • Long, M.1    Betrán, E.2    Thornton, K.3    Wang, W.4
  • 3
    • 50649090652 scopus 로고    scopus 로고
    • De novo origination of a new protein-coding gene in Saccharomyces cerevisiae
    • 10.1534/genetics.107.084491, 2390625, 18493065
    • Cai J, Zhao R, Jiang H, Wang W. De novo origination of a new protein-coding gene in Saccharomyces cerevisiae. Genetics 2008, 179:487-496. 10.1534/genetics.107.084491, 2390625, 18493065.
    • (2008) Genetics , vol.179 , pp. 487-496
    • Cai, J.1    Zhao, R.2    Jiang, H.3    Wang, W.4
  • 4
    • 0142124263 scopus 로고    scopus 로고
    • Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
    • 10.1101/gr.1589103, 403683, 14525925
    • Krylov DM, Wolf YI, Rogozin IB, Koonin EV. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res 2003, 13:2229-2235. 10.1101/gr.1589103, 403683, 14525925.
    • (2003) Genome Res , vol.13 , pp. 2229-2235
    • Krylov, D.M.1    Wolf, Y.I.2    Rogozin, I.B.3    Koonin, E.V.4
  • 5
    • 56549119570 scopus 로고    scopus 로고
    • Turning a hobby into a job: how duplicated genes find new functions
    • 10.1038/nrg2482, 19015656
    • Conant GC, Wolfe KH. Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 2008, 9:938-950. 10.1038/nrg2482, 19015656.
    • (2008) Nat Rev Genet , vol.9 , pp. 938-950
    • Conant, G.C.1    Wolfe, K.H.2
  • 6
    • 59849091566 scopus 로고    scopus 로고
    • The life and death of gene families
    • 10.1002/bies.080085, 19153999
    • Demuth JP, Hahn MW. The life and death of gene families. BioEssays 2009, 31:29-39. 10.1002/bies.080085, 19153999.
    • (2009) BioEssays , vol.31 , pp. 29-39
    • Demuth, J.P.1    Hahn, M.W.2
  • 7
    • 0037387007 scopus 로고    scopus 로고
    • Comparison of the genomes of human and mouse lays the foundation of genome zoology
    • 10.1093/hmg/ddg078, 12651866
    • Emes RD. Comparison of the genomes of human and mouse lays the foundation of genome zoology. Hum Mol Genet 2003, 12:701-709. 10.1093/hmg/ddg078, 12651866.
    • (2003) Hum Mol Genet , vol.12 , pp. 701-709
    • Emes, R.D.1
  • 8
    • 78650385315 scopus 로고    scopus 로고
    • New genes in Drosophila quickly become essential
    • 10.1126/science.1196380, 21164016
    • Chen S, Zhang YE, Long M. New genes in Drosophila quickly become essential. Science 2010, 330:1682-1685. 10.1126/science.1196380, 21164016.
    • (2010) Science , vol.330 , pp. 1682-1685
    • Chen, S.1    Zhang, Y.E.2    Long, M.3
  • 9
    • 0035697435 scopus 로고    scopus 로고
    • The probability of preservation of a newly arisen gene duplicate
    • 1461922, 11779815
    • Lynch M, O'Hely M, Walsh B, Force A. The probability of preservation of a newly arisen gene duplicate. Genetics 2001, 159:1789-1804. 1461922, 11779815.
    • (2001) Genetics , vol.159 , pp. 1789-1804
    • Lynch, M.1    O'Hely, M.2    Walsh, B.3    Force, A.4
  • 10
    • 77950395160 scopus 로고    scopus 로고
    • Gene duplication and the evolution of ribosomal protein gene regulation in yeast
    • 10.1073/pnas.0911905107, 2851827, 20212107
    • Wapinski I, Pfiffner J, French C, Socha A, Thompson DA, Regev A. Gene duplication and the evolution of ribosomal protein gene regulation in yeast. Proc Natl Acad Sci USA 2010, 107:5505-5510. 10.1073/pnas.0911905107, 2851827, 20212107.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 5505-5510
    • Wapinski, I.1    Pfiffner, J.2    French, C.3    Socha, A.4    Thompson, D.A.5    Regev, A.6
  • 11
    • 38649142412 scopus 로고    scopus 로고
    • The limits of subfunctionalization
    • 10.1186/1471-2148-7-213, 2213666, 17988397
    • MacCarthy T, Bergman A. The limits of subfunctionalization. BMC Evol Biol 2007, 7:213. 10.1186/1471-2148-7-213, 2213666, 17988397.
    • (2007) BMC Evol Biol , vol.7 , pp. 213
    • MacCarthy, T.1    Bergman, A.2
  • 12
    • 0041704531 scopus 로고    scopus 로고
    • Evolution of cis-regulatory elements in duplicated genes of yeast
    • 10.1016/S0168-9525(03)00174-4, 12902158
    • Papp B, Pal C, Hurst LD. Evolution of cis-regulatory elements in duplicated genes of yeast. Trends Genet 2003, 19:417-422. 10.1016/S0168-9525(03)00174-4, 12902158.
    • (2003) Trends Genet , vol.19 , pp. 417-422
    • Papp, B.1    Pal, C.2    Hurst, L.D.3
  • 14
    • 0017771466 scopus 로고
    • Evolution and tinkering
    • 10.1126/science.860134, 860134
    • Jacob F. Evolution and tinkering. Science 1977, 196:1161-1166. 10.1126/science.860134, 860134.
    • (1977) Science , vol.196 , pp. 1161-1166
    • Jacob, F.1
  • 15
    • 0035807336 scopus 로고    scopus 로고
    • Positive selection of a gene family during the emergence of humans and African apes
    • 10.1038/35097067, 11586358, Bailey J a
    • Johnson ME, Viggiano L, Abdul-Rauf M, Goodwin G, Rocchi M, Eichler EE, . Bailey J a Positive selection of a gene family during the emergence of humans and African apes. Nature 2001, 413:514-519. 10.1038/35097067, 11586358, Bailey J a.
    • (2001) Nature , vol.413 , pp. 514-519
    • Johnson, M.E.1    Viggiano, L.2    Abdul-Rauf, M.3    Goodwin, G.4    Rocchi, M.5    Eichler, E.E.6
  • 16
    • 33745585334 scopus 로고    scopus 로고
    • Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression
    • 10.1073/pnas.0509809103, 1502557, 16777968, Lindfors H a
    • Levine MT, Jones CD, Kern AD, Begun DJ, . Lindfors H a Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proc Natl Acad Sci USA 2006, 103:9935-9939. 10.1073/pnas.0509809103, 1502557, 16777968, Lindfors H a.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 9935-9939
    • Levine, M.T.1    Jones, C.D.2    Kern, A.D.3    Begun, D.J.4
  • 17
    • 70349270547 scopus 로고    scopus 로고
    • Emergence of a new gene from an intergenic region
    • 10.1016/j.cub.2009.07.049, 19733073, Heinen TJ a J
    • Staubach F, Häming D, Tautz D, . Heinen TJ a J Emergence of a new gene from an intergenic region. Curr Biol 2009, 19:1527-1531. 10.1016/j.cub.2009.07.049, 19733073, Heinen TJ a J.
    • (2009) Curr Biol , vol.19 , pp. 1527-1531
    • Staubach, F.1    Häming, D.2    Tautz, D.3
  • 18
    • 70349645640 scopus 로고    scopus 로고
    • Recent de novo origin of human protein-coding genes
    • 10.1101/gr.095026.109, 2765279, 19726446
    • Knowles DG, McLysaght A. Recent de novo origin of human protein-coding genes. Genome Res 2009, 19:1752-1759. 10.1101/gr.095026.109, 2765279, 19726446.
    • (2009) Genome Res , vol.19 , pp. 1752-1759
    • Knowles, D.G.1    McLysaght, A.2
  • 20
    • 77950521826 scopus 로고    scopus 로고
    • A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand
    • 10.1038/cr.2010.31, 20195295
    • Li D, Dong Y, Jiang Y, Jiang H, Cai J, Wang W. A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand. Cell Res 2010, 20:408-420. 10.1038/cr.2010.31, 20195295.
    • (2010) Cell Res , vol.20 , pp. 408-420
    • Li, D.1    Dong, Y.2    Jiang, Y.3    Jiang, H.4    Cai, J.5    Wang, W.6
  • 21
    • 84887212396 scopus 로고    scopus 로고
    • A rice gene of de novo origin negatively regulates pathogen-induced defense response
    • 10.1371/journal.pone.0004603, 2643483, 19240804
    • Xiao W, Liu H, Li Y, Li X, Xu C, Long M, Wang S. A rice gene of de novo origin negatively regulates pathogen-induced defense response. PLoS One 2009, 4:e4603. 10.1371/journal.pone.0004603, 2643483, 19240804.
    • (2009) PLoS One , vol.4
    • Xiao, W.1    Liu, H.2    Li, Y.3    Li, X.4    Xu, C.5    Long, M.6    Wang, S.7
  • 22
    • 79957554358 scopus 로고    scopus 로고
    • Intron retention in the Drosophila melanogaster Rieske Iron Sulphur Protein gene generated a new protein
    • 3113295, 21610726
    • Gontijo AM, Miguela V, Whiting MF, Woodruff RC, Dominguez M. Intron retention in the Drosophila melanogaster Rieske Iron Sulphur Protein gene generated a new protein. Nat Commun 2011, 2:323. 3113295, 21610726.
    • (2011) Nat Commun , vol.2 , pp. 323
    • Gontijo, A.M.1    Miguela, V.2    Whiting, M.F.3    Woodruff, R.C.4    Dominguez, M.5
  • 23
    • 34250748633 scopus 로고    scopus 로고
    • Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade
    • 1894579, 17435230, Lindfors H a
    • Begun DJ, Kern AD, Jones CD, . Lindfors H a Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics 2007, 176:1131-1137. 1894579, 17435230, Lindfors H a.
    • (2007) Genetics , vol.176 , pp. 1131-1137
    • Begun, D.J.1    Kern, A.D.2    Jones, C.D.3
  • 26
    • 77449140452 scopus 로고    scopus 로고
    • Identifying and quantifying orphan protein sequences in fungi
    • 10.1016/j.jmb.2009.11.053, 19944701
    • Ekman D, Elofsson A. Identifying and quantifying orphan protein sequences in fungi. J Mol Biol 2010, 396:396-405. 10.1016/j.jmb.2009.11.053, 19944701.
    • (2010) J Mol Biol , vol.396 , pp. 396-405
    • Ekman, D.1    Elofsson, A.2
  • 27
    • 81755187310 scopus 로고    scopus 로고
    • De Novo Origin of Human Protein-Coding Genes
    • 10.1371/journal.pgen.1002379, 3213175, 22102831
    • Wu D-D, Irwin DM, Zhang Y-P. De Novo Origin of Human Protein-Coding Genes. PLoS Genet 2011, 7:e1002379. 10.1371/journal.pgen.1002379, 3213175, 22102831.
    • (2011) PLoS Genet , vol.7
    • Wu, D.-D.1    Irwin, D.M.2    Zhang, Y.-P.3
  • 28
    • 79951580190 scopus 로고    scopus 로고
    • De novo origin of new genes with introns in Plasmodium vivax
    • 10.1016/j.febslet.2011.01.017, 21241695
    • Yang Z, Huang J. De novo origin of new genes with introns in Plasmodium vivax. FEBS Lett 2011, 585:641-644. 10.1016/j.febslet.2011.01.017, 21241695.
    • (2011) FEBS Lett , vol.585 , pp. 641-644
    • Yang, Z.1    Huang, J.2
  • 29
    • 80052969570 scopus 로고    scopus 로고
    • The evolutionary origin of orphan genes
    • Tautz D, Domazet-Lošo T. The evolutionary origin of orphan genes. Nat Rev Genet 2011, 12:692-702.
    • (2011) Nat Rev Genet , vol.12 , pp. 692-702
    • Tautz, D.1    Domazet-Lošo, T.2
  • 30
    • 0035986888 scopus 로고    scopus 로고
    • Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover
    • 10.1093/oxfordjournals.molbev.a004169, 12082130
    • Dermitzakis ET, Clark AG. Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover. Mol Biol Evol 2002, 19:1114-1121. 10.1093/oxfordjournals.molbev.a004169, 12082130.
    • (2002) Mol Biol Evol , vol.19 , pp. 1114-1121
    • Dermitzakis, E.T.1    Clark, A.G.2
  • 32
    • 34249723155 scopus 로고    scopus 로고
    • Frequent gain and loss of functional transcription factor binding sites
    • 10.1371/journal.pcbi.0030099, 1876492, 17530920
    • Doniger SW, Fay JC. Frequent gain and loss of functional transcription factor binding sites. PLoS Comput Biol 2007, 3:e99. 10.1371/journal.pcbi.0030099, 1876492, 17530920.
    • (2007) PLoS Comput Biol , vol.3
    • Doniger, S.W.1    Fay, J.C.2
  • 33
    • 79952276786 scopus 로고    scopus 로고
    • Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence?
    • 10.1093/gbe/evq066, 2997565, 21068212
    • Venkataram S, Fay JC. Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence?. Genome Biol Evol 2010, 2:851-858. 10.1093/gbe/evq066, 2997565, 21068212.
    • (2010) Genome Biol Evol , vol.2 , pp. 851-858
    • Venkataram, S.1    Fay, J.C.2
  • 34
    • 79955623470 scopus 로고    scopus 로고
    • Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules
    • 10.1371/journal.pgen.1002053, 3084208, 21572512
    • He BZ, Holloway AK, Maerkl SJ, Kreitman M. Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules. PLoS Genet 2011, 7:e1002053. 10.1371/journal.pgen.1002053, 3084208, 21572512.
    • (2011) PLoS Genet , vol.7
    • He, B.Z.1    Holloway, A.K.2    Maerkl, S.J.3    Kreitman, M.4
  • 35
    • 2442537233 scopus 로고    scopus 로고
    • Gene regulatory network growth by duplication
    • 10.1038/ng1340, 15107850, Teichmann S a
    • Babu MM, . Teichmann S a Gene regulatory network growth by duplication. Nat Genet 2004, 36:492-496. 10.1038/ng1340, 15107850, Teichmann S a.
    • (2004) Nat Genet , vol.36 , pp. 492-496
    • Babu, M.M.1
  • 36
    • 57749177443 scopus 로고    scopus 로고
    • RNA-based gene duplication: mechanistic and evolutionary insights
    • Kaessmann H, Vinckenbosch N, Long M. RNA-based gene duplication: mechanistic and evolutionary insights. Nat Rev Genet 2009, 10:19-31.
    • (2009) Nat Rev Genet , vol.10 , pp. 19-31
    • Kaessmann, H.1    Vinckenbosch, N.2    Long, M.3
  • 37
    • 4444242626 scopus 로고    scopus 로고
    • Cis-Regulatory and protein evolution in orthologous and duplicate genes
    • 10.1101/gr.2662504, 509261, 15256508
    • Castillo-Davis CI, Hartl DL, Achaz G. cis-Regulatory and protein evolution in orthologous and duplicate genes. Genome Res 2004, 14:1530-1536. 10.1101/gr.2662504, 509261, 15256508.
    • (2004) Genome Res , vol.14 , pp. 1530-1536
    • Castillo-Davis, C.I.1    Hartl, D.L.2    Achaz, G.3
  • 38
    • 78650509490 scopus 로고    scopus 로고
    • Novel genes exhibit distinct patterns of function acquisition and network integration
    • 10.1186/gb-2010-11-12-r127, 3046487, 21187012, Capra J a
    • Pollard KS, Singh M, . Capra J a Novel genes exhibit distinct patterns of function acquisition and network integration. Genome Biol 2010, 11:R127. 10.1186/gb-2010-11-12-r127, 3046487, 21187012, Capra J a.
    • (2010) Genome Biol , vol.11
    • Pollard, K.S.1    Singh, M.2
  • 39
    • 79957636947 scopus 로고    scopus 로고
    • Evidence of association between Nucleosome Occupancy and the Evolution of Transcription Factor Binding Sites in Yeast
    • 10.1186/1471-2148-11-150, 3124427, 21627806
    • Swamy KBS, Chu W-Y, Wang C-Y, Tsai H-K, Wang D. Evidence of association between Nucleosome Occupancy and the Evolution of Transcription Factor Binding Sites in Yeast. BMC Evol Biol 2011, 11:150. 10.1186/1471-2148-11-150, 3124427, 21627806.
    • (2011) BMC Evol Biol , vol.11 , pp. 150
    • Swamy, K.B.S.1    Chu, W.-Y.2    Wang, C.-Y.3    Tsai, H.-K.4    Wang, D.5
  • 40
    • 84855306788 scopus 로고    scopus 로고
    • A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast
    • 10.1101/gr.124099.111, 3246209, 21930892
    • Zaugg JB, Luscombe NM. A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast. Genome Res 2012, 22:84-94. 10.1101/gr.124099.111, 3246209, 21930892.
    • (2012) Genome Res , vol.22 , pp. 84-94
    • Zaugg, J.B.1    Luscombe, N.M.2
  • 41
    • 77955045449 scopus 로고    scopus 로고
    • The role of nucleosome positioning in the evolution of gene regulation
    • 10.1371/journal.pbio.1000414, 2897762, 20625544
    • Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ. The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 2010, 8:e1000414. 10.1371/journal.pbio.1000414, 2897762, 20625544.
    • (2010) PLoS Biol , vol.8
    • Tsankov, A.M.1    Thompson, D.A.2    Socha, A.3    Regev, A.4    Rando, O.J.5
  • 42
    • 57149100569 scopus 로고    scopus 로고
    • The impact of the nucleosome code on protein-coding sequence evolution in yeast
    • 10.1371/journal.pgen.1000250, 2570795, 18989456
    • Warnecke T, Batada NN, Hurst LD. The impact of the nucleosome code on protein-coding sequence evolution in yeast. PLoS Genet 2008, 4:e1000250. 10.1371/journal.pgen.1000250, 2570795, 18989456.
    • (2008) PLoS Genet , vol.4
    • Warnecke, T.1    Batada, N.N.2    Hurst, L.D.3
  • 43
    • 56649089682 scopus 로고    scopus 로고
    • Evolutionary footprints of nucleosome positions in yeast
    • 10.1016/j.tig.2008.09.003, 18951646
    • Washietl S, Machné R, Goldman N. Evolutionary footprints of nucleosome positions in yeast. Trends Genet 2008, 24:583-587. 10.1016/j.tig.2008.09.003, 18951646.
    • (2008) Trends Genet , vol.24 , pp. 583-587
    • Washietl, S.1    Machné, R.2    Goldman, N.3
  • 44
    • 76749122797 scopus 로고    scopus 로고
    • The enrichment of TATA box and the scarcity of depleted proximal nucleosome in the promoters of duplicated yeast genes
    • 10.1007/s00239-009-9309-3, 20013336, Babbitt G a
    • Kim Y, Lee JH, . Babbitt G a The enrichment of TATA box and the scarcity of depleted proximal nucleosome in the promoters of duplicated yeast genes. J Mol Evol 2010, 70:69-73. 10.1007/s00239-009-9309-3, 20013336, Babbitt G a.
    • (2010) J Mol Evol , vol.70 , pp. 69-73
    • Kim, Y.1    Lee, J.H.2
  • 45
    • 43749088127 scopus 로고    scopus 로고
    • Two strategies for gene regulation by promoter nucleosomes
    • 10.1101/gr.076059.108, 2493397, 18448704
    • Tirosh I, Barkai N. Two strategies for gene regulation by promoter nucleosomes. Genome Res 2008, 18:1084-1091. 10.1101/gr.076059.108, 2493397, 18448704.
    • (2008) Genome Res , vol.18 , pp. 1084-1091
    • Tirosh, I.1    Barkai, N.2
  • 48
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the Universal Protein Resource (UniProt)
    • 3245120, 22102590
    • Uniprot T. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 2012, 40:D71-D75. 3245120, 22102590.
    • (2012) Nucleic Acids Res , vol.40
    • Uniprot, T.1
  • 49
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • 10.1126/science.1158441, 2951732, 18451266
    • Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320:1344-1349. 10.1126/science.1158441, 2951732, 18451266.
    • (2008) Science , vol.320 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6    Snyder, M.7
  • 50
    • 84055187690 scopus 로고    scopus 로고
    • Evolutionary erosion of yeast sex chromosomes by mating-type switching accidents
    • 10.1073/pnas.1112808108, 3250169, 22123960
    • Gordon JL, Armisén D, Proux-Wéra E, Óhéigeartaigh SS, Byrne KP, Wolfe KH. Evolutionary erosion of yeast sex chromosomes by mating-type switching accidents. Proc Natl Acad Sci USA 2011, 108:20024-20029. 10.1073/pnas.1112808108, 3250169, 22123960.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 20024-20029
    • Gordon, J.L.1    Armisén, D.2    Proux-Wéra, E.3    Óhéigeartaigh, S.S.4    Byrne, K.P.5    Wolfe, K.H.6
  • 51
    • 33644787447 scopus 로고    scopus 로고
    • OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
    • 10.1093/nar/gkj123, 1347485, 16381887
    • Chen F, Mackey AJ, Stoeckert CJ, Roos DS. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 2006, 34:D363-D368. 10.1093/nar/gkj123, 1347485, 16381887.
    • (2006) Nucleic Acids Res , vol.34
    • Chen, F.1    Mackey, A.J.2    Stoeckert, C.J.3    Roos, D.S.4
  • 53
    • 34547557480 scopus 로고    scopus 로고
    • MYBS: a comprehensive web server for mining transcription factor binding sites in yeast
    • 10.1093/nar/gkm379, 1933147, 17537814
    • Tsai H-K, Chou M-Y, Shih C-H, Huang GT-W, Chang T-H, Li W-H. MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. Nucleic Acids Res 2007, 35:W221-W226. 10.1093/nar/gkm379, 1933147, 17537814.
    • (2007) Nucleic Acids Res , vol.35
    • Tsai, H.-K.1    Chou, M.-Y.2    Shih, C.-H.3    Huang, G.T.-W.4    Chang, T.-H.5    Li, W.-H.6
  • 54
    • 34547569191 scopus 로고    scopus 로고
    • STAMP: a web tool for exploring DNA-binding motif similarities
    • 10.1093/nar/gkm272, 1933206, 17478497
    • Mahony S, Benos PV. STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 2007, 35:W253-W258. 10.1093/nar/gkm272, 1933206, 17478497.
    • (2007) Nucleic Acids Res , vol.35
    • Mahony, S.1    Benos, P.V.2
  • 56
    • 52749097035 scopus 로고    scopus 로고
    • Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules
    • 10.1038/nprot.2008.97, 18802439
    • Turatsinze J-V, Thomas-Chollier M, Defrance M, van Helden J. Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat Protoc 2008, 3:1578-1588. 10.1038/nprot.2008.97, 18802439.
    • (2008) Nat Protoc , vol.3 , pp. 1578-1588
    • Turatsinze, J.-V.1    Thomas-Chollier, M.2    Defrance, M.3    van Helden, J.4
  • 58
    • 75349098018 scopus 로고    scopus 로고
    • A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome
    • 10.1186/gb-2009-10-10-r109, 2784324, 19814794
    • Jiang C, Pugh BF. A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biol 2009, 10:R109. 10.1186/gb-2009-10-10-r109, 2784324, 19814794.
    • (2009) Genome Biol , vol.10
    • Jiang, C.1    Pugh, B.F.2
  • 59
    • 35748950713 scopus 로고    scopus 로고
    • Exploring the functional landscape of gene expression: directed search of large microarray compendia
    • 10.1093/bioinformatics/btm403, 17724061, Hibbs M a
    • Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG, . Hibbs M a Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics 2007, 23:2692-2699. 10.1093/bioinformatics/btm403, 17724061, Hibbs M a.
    • (2007) Bioinformatics , vol.23 , pp. 2692-2699
    • Hess, D.C.1    Myers, C.L.2    Huttenhower, C.3    Li, K.4    Troyanskaya, O.G.5
  • 60
    • 72449210454 scopus 로고    scopus 로고
    • Detecting positive selection in the budding yeast genome
    • 10.1111/j.1420-9101.2009.01851.x, 19878412
    • Li Y-D, Liang H, Gu Z, Lin Z, Guan W, Zhou L, Li Y-Q, Li W-H. Detecting positive selection in the budding yeast genome. J Evol Biol 2009, 22:2430-2437. 10.1111/j.1420-9101.2009.01851.x, 19878412.
    • (2009) J Evol Biol , vol.22 , pp. 2430-2437
    • Li, Y.-D.1    Liang, H.2    Gu, Z.3    Lin, Z.4    Guan, W.5    Zhou, L.6    Li, Y.-Q.7    Li, W.-H.8
  • 61
    • 80052877875 scopus 로고    scopus 로고
    • Inferring regulatory mechanisms from patterns of evolutionary divergence
    • Tirosh I, Barkai N. Inferring regulatory mechanisms from patterns of evolutionary divergence. Mol Syst Biol 2011, 7:1-10.
    • (2011) Mol Syst Biol , vol.7 , pp. 1-10
    • Tirosh, I.1    Barkai, N.2
  • 62
    • 33745583768 scopus 로고    scopus 로고
    • A genetic signature of interspecies variations in gene expression
    • 10.1038/ng1819, 16783381
    • Tirosh I, Weinberger A, Carmi M, Barkai N. A genetic signature of interspecies variations in gene expression. Nat Genet 2006, 38:830-834. 10.1038/ng1819, 16783381.
    • (2006) Nat Genet , vol.38 , pp. 830-834
    • Tirosh, I.1    Weinberger, A.2    Carmi, M.3    Barkai, N.4
  • 63
    • 1542328960 scopus 로고    scopus 로고
    • Identification and distinct regulation of yeast TATA box-containing genes
    • 10.1016/S0092-8674(04)00205-3, 15006352
    • Basehoar AD, Zanton SJ, Pugh BF. Identification and distinct regulation of yeast TATA box-containing genes. Cell 2004, 116:699-709. 10.1016/S0092-8674(04)00205-3, 15006352.
    • (2004) Cell , vol.116 , pp. 699-709
    • Basehoar, A.D.1    Zanton, S.J.2    Pugh, B.F.3
  • 65
    • 0027197504 scopus 로고
    • Transcription factors are required for the meiotic recombination hotspot at the HIS4 locus in Saccharomyces cerevisiae
    • 10.1073/pnas.90.14.6621, 46984, 8341678, White M a
    • Dominska M, Petes TD, . White M a Transcription factors are required for the meiotic recombination hotspot at the HIS4 locus in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 1993, 90:6621-6625. 10.1073/pnas.90.14.6621, 46984, 8341678, White M a.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 6621-6625
    • Dominska, M.1    Petes, T.D.2
  • 66
    • 31344463434 scopus 로고    scopus 로고
    • Global Analysis of the Relationship between the Binding of the Bas1p Transcription Factor and Meiosis-Specific Double-Strand DNA Breaks in Saccharomyces cerevisiae
    • 10.1128/MCB.26.3.1014-1027.2006, 1347019, 16428454
    • Mieczkowski PA, Dominska M, Buck MJ, Gerton JL, Lieb JD, Petes TD. Global Analysis of the Relationship between the Binding of the Bas1p Transcription Factor and Meiosis-Specific Double-Strand DNA Breaks in Saccharomyces cerevisiae. Mol Cell Biol 2006, 26:1014-1027. 10.1128/MCB.26.3.1014-1027.2006, 1347019, 16428454.
    • (2006) Mol Cell Biol , vol.26 , pp. 1014-1027
    • Mieczkowski, P.A.1    Dominska, M.2    Buck, M.J.3    Gerton, J.L.4    Lieb, J.D.5    Petes, T.D.6
  • 67
    • 0035807880 scopus 로고    scopus 로고
    • Meiotic recombination frequencies are affected by nutritional states in Saccharomyces cerevisiae
    • 10.1073/pnas.201529598, 64715, 11724920
    • Abdullah MF, Borts RH. Meiotic recombination frequencies are affected by nutritional states in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2001, 98:14524-14529. 10.1073/pnas.201529598, 64715, 11724920.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 14524-14529
    • Abdullah, M.F.1    Borts, R.H.2
  • 68
    • 0036161403 scopus 로고    scopus 로고
    • Phylogenetic footprinting reveals multiple regulatory elements involved in control of the meiotic recombination gene, REC102
    • 10.1002/yea.800, 11788965
    • Jiao K, Nau JJ, Cool M, Gray WM, Fassler JS, Malone RE. Phylogenetic footprinting reveals multiple regulatory elements involved in control of the meiotic recombination gene, REC102. Yeast 2002, 19:99-114. 10.1002/yea.800, 11788965.
    • (2002) Yeast , vol.19 , pp. 99-114
    • Jiao, K.1    Nau, J.J.2    Cool, M.3    Gray, W.M.4    Fassler, J.S.5    Malone, R.E.6
  • 69
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • 10.1038/nature01644, 12748633
    • Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423:241-254. 10.1038/nature01644, 12748633.
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 70
    • 77950339177 scopus 로고    scopus 로고
    • Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites
    • 10.1016/j.ygeno.2010.01.002, 2848887, 20079828, Jaeger S a
    • Chan ET, Berger MF, Stottmann R, Hughes TR, Bulyk ML, . Jaeger S a Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites. Genomics 2010, 95:185-195. 10.1016/j.ygeno.2010.01.002, 2848887, 20079828, Jaeger S a.
    • (2010) Genomics , vol.95 , pp. 185-195
    • Chan, E.T.1    Berger, M.F.2    Stottmann, R.3    Hughes, T.R.4    Bulyk, M.L.5
  • 71
    • 1842584947 scopus 로고    scopus 로고
    • Applied bioinformatics for the identification of regulatory elements
    • 10.1038/nrg1315, 15131651
    • Wasserman WW, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 2004, 5:276-287. 10.1038/nrg1315, 15131651.
    • (2004) Nat Rev Genet , vol.5 , pp. 276-287
    • Wasserman, W.W.1    Sandelin, A.2
  • 72
    • 80052605861 scopus 로고    scopus 로고
    • Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters
    • 10.1371/journal.pone.0024279, 3170328, 21931670
    • Erb I, van Nimwegen E. Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters. PLoS One 2011, 6:e24279. 10.1371/journal.pone.0024279, 3170328, 21931670.
    • (2011) PLoS One , vol.6
    • Erb, I.1    van Nimwegen, E.2
  • 73
    • 80053215814 scopus 로고    scopus 로고
    • Predominant gain of promoter TATA box after gene duplication associated with stress responses
    • 10.1093/molbev/msr116, 21515810
    • Zou Y, Huang W, Gu Z, Gu X. Predominant gain of promoter TATA box after gene duplication associated with stress responses. Mol Biol Evol 2011, 28:2893-2904. 10.1093/molbev/msr116, 21515810.
    • (2011) Mol Biol Evol , vol.28 , pp. 2893-2904
    • Zou, Y.1    Huang, W.2    Gu, Z.3    Gu, X.4
  • 74
    • 57149119464 scopus 로고    scopus 로고
    • Distinct modes of regulation by chromatin encoded through nucleosome positioning signals
    • 10.1371/journal.pcbi.1000216, 2570626, 18989395
    • Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol 2008, 4:e1000216. 10.1371/journal.pcbi.1000216, 2570626, 18989395.
    • (2008) PLoS Comput Biol , vol.4
    • Field, Y.1    Kaplan, N.2    Fondufe-Mittendorf, Y.3    Moore, I.K.4    Sharon, E.5    Lubling, Y.6    Widom, J.7    Segal, E.8
  • 75
    • 33846214719 scopus 로고    scopus 로고
    • Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters
    • 10.1016/j.gene.2006.09.029, 1955227, 17123746
    • Yang C, Bolotin E, Jiang T, Sladek FM, Martinez E. Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene 2007, 389:52-65. 10.1016/j.gene.2006.09.029, 1955227, 17123746.
    • (2007) Gene , vol.389 , pp. 52-65
    • Yang, C.1    Bolotin, E.2    Jiang, T.3    Sladek, F.M.4    Martinez, E.5
  • 76
    • 1542285166 scopus 로고    scopus 로고
    • A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae
    • 10.1016/S1097-2765(04)00087-5, 14992726
    • Huisinga KL, Pugh BF. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol Cell 2004, 13:573-585. 10.1016/S1097-2765(04)00087-5, 14992726.
    • (2004) Mol Cell , vol.13 , pp. 573-585
    • Huisinga, K.L.1    Pugh, B.F.2
  • 77
    • 77954309914 scopus 로고    scopus 로고
    • Sporulation patterning and invasive growth in wild and domesticated yeast colonies
    • 10.1016/j.resmic.2010.04.001, 2897909, 20420901
    • Piccirillo S, Honigberg SM. Sporulation patterning and invasive growth in wild and domesticated yeast colonies. Res Microbiol 2010, 161:390-398. 10.1016/j.resmic.2010.04.001, 2897909, 20420901.
    • (2010) Res Microbiol , vol.161 , pp. 390-398
    • Piccirillo, S.1    Honigberg, S.M.2
  • 78
    • 39749159114 scopus 로고    scopus 로고
    • Prezygotic reproductive isolation between Saccharomyces cerevisiae and Saccharomyces paradoxus
    • 10.1186/1471-2148-8-1, 2249576, 18179683
    • Maclean CJ, Greig D. Prezygotic reproductive isolation between Saccharomyces cerevisiae and Saccharomyces paradoxus. BMC Evol Biol 2008, 8:1. 10.1186/1471-2148-8-1, 2249576, 18179683.
    • (2008) BMC Evol Biol , vol.8 , pp. 1
    • Maclean, C.J.1    Greig, D.2
  • 79
    • 84876692585 scopus 로고    scopus 로고
    • Developmental cycle and pharmaceutically relevant compounds of Salinispora actinobacteria isolated from Great Barrier Reef marine sponges
    • E-pub ahead of print, Fuerst J a
    • Ng YK, Hewavitharana AK, Webb R, Shaw PN, . Fuerst J a Developmental cycle and pharmaceutically relevant compounds of Salinispora actinobacteria isolated from Great Barrier Reef marine sponges. Appl Microbiol Biotechnol 2012, E-pub ahead of print, Fuerst J a.
    • (2012) Appl Microbiol Biotechnol
    • Ng, Y.K.1    Hewavitharana, A.K.2    Webb, R.3    Shaw, P.N.4


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