메뉴 건너뛰기




Volumn 5, Issue 1, 2013, Pages 140-150

Vertebrate paralogous conserved noncoding sequences may be related to gene expressions in brain

Author keywords

Gene regulation; Genome duplication; Noncoding sequences; Vertebrates

Indexed keywords

VERTEBRATA;

EID: 84876569149     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evs128     Document Type: Article
Times cited : (13)

References (46)
  • 1
    • 34547561588 scopus 로고    scopus 로고
    • FatiGO+: A functional profiling tool for genomic data. Integration of functional annotation, regulatorymotifs and interaction data with microarray experiments
    • Al-Shahrour F, et al. 2007. FatiGO+: a functional profiling tool for genomic data. Integration of functional annotation, regulatorymotifs and interaction data with microarray experiments. Nucleic Acids Res. 35: W91-W96.
    • (2007) Nucleic Acids Res. , vol.35
    • Al-Shahrour, F.1
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 3
    • 35248882434 scopus 로고    scopus 로고
    • The random versus fragile breakage models of chromosome evolution: A matter of resolution
    • Becker TS, Lenhard B. 2007. The random versus fragile breakage models of chromosome evolution: a matter of resolution. Mol Genet Genomics. 278:487-491.
    • (2007) Mol Genet Genomics. , vol.278 , pp. 487-491
    • Becker, T.S.1    Lenhard, B.2
  • 4
    • 2542542256 scopus 로고    scopus 로고
    • Ultra conserved elements in the human genome
    • Bejerano G, et al. 2004. Ultra conserved elements in the human genome. Science 304:1321-1325.
    • (2004) Science , vol.304 , pp. 1321-1325
    • Bejerano, G.1
  • 5
    • 33745067419 scopus 로고    scopus 로고
    • The gain and loss of genes during 600 million years of vertebrate evolution
    • Blomme T, et al. 2007. The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol. 7:R43.
    • (2007) Genome Biol. , vol.7
    • Blomme, T.1
  • 6
    • 0033519674 scopus 로고    scopus 로고
    • Developmental basis of limblessness and axial patterning in snakes
    • Cohn MJ, Tickle C. 1999. Developmental basis of limblessness and axial patterning in snakes. Nature 399:474-479.
    • (1999) Nature , vol.399 , pp. 474-479
    • Cohn, M.J.1    Tickle, C.2
  • 7
    • 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 U S A. 107:21931-21936.
    • (2010) Proc Natl Acad Sci U S A. , vol.107 , pp. 21931-21936
    • Creyghton, M.P.1
  • 8
    • 26444603772 scopus 로고    scopus 로고
    • Two rounds of whole genome duplication in the ancestral vertebrate
    • Dehal P, Boore JL. 2005. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 3:1700-1708.
    • (2005) PLoS Biol. , vol.3 , pp. 1700-1708
    • Dehal, P.1    Boore, J.L.2
  • 9
    • 23744502709 scopus 로고    scopus 로고
    • A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts
    • de la Calle-Mustienes E, et al. 2005. A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts. Genome Res. 15:1061-1072.
    • (2005) Genome Res. , vol.15 , pp. 1061-1072
    • De La Calle-Mustienes, E.1
  • 10
    • 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 489:57-74.
    • (2012) Nature , vol.489 , pp. 57-74
  • 11
    • 0032893932 scopus 로고    scopus 로고
    • Preservation of duplicate genes by complementary, degenerative mutations
    • Force A, Lynch M, Pickett FB, Amores A, Yan YL. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545.
    • (1999) Genetics , vol.151 , pp. 1531-1545
    • Force, A.1    Lynch, M.2    Pickett, F.B.3    Amores, A.4    Yan, Y.L.5
  • 12
    • 28844477866 scopus 로고    scopus 로고
    • The genesis and evolution of homeobox gene clusters
    • Garcia-Fernández J. 2005. The genesis and evolution of homeobox gene clusters. Nat Rev Genet. 6:881-892.
    • (2005) Nat Rev Genet. , vol.6 , pp. 881-892
    • Garcia-Fernández, J.1
  • 13
    • 22344454794 scopus 로고    scopus 로고
    • Ultra conserved elements in insect genomes: A highly conserved intronic sequence implicated in the control of homothorax mRNA splicing
    • Glazov EA, Pheasant M, McGraw EA, Bejerano G, Mattick JS. 2005. Ultra conserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Res. 15:800-808.
    • (2005) Genome Res. , vol.15 , pp. 800-808
    • Glazov, E.A.1    Pheasant, M.2    McGraw, E.A.3    Bejerano, G.4    Mattick, J.S.5
  • 14
    • 33847334699 scopus 로고    scopus 로고
    • Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
    • Heintzman ND, et al. 2007. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 39:311-318.
    • (2007) Nat Genet. , vol.39 , pp. 311-318
    • Heintzman, N.D.1
  • 15
    • 65549104157 scopus 로고    scopus 로고
    • Histone modifications at human enhancers reflect global cell-type-specific gene expression
    • Heintzman ND, et al. 2009. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459:108-112.
    • (2009) Nature , vol.459 , pp. 108-112
    • Heintzman, N.D.1
  • 16
    • 46449117597 scopus 로고    scopus 로고
    • The amphioxus genome illuminates vertebrate origins and cephalochordate biology
    • Holland LZ, et al. 2008. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res. 18:1100-1111.
    • (2008) Genome Res. , vol.18 , pp. 1100-1111
    • Holland, L.Z.1
  • 17
    • 70350741353 scopus 로고    scopus 로고
    • Deeply conserved chordate noncoding sequences preserve genome synteny but not drive gene duplication retention
    • Hufton AL, et al. 2009. Deeply conserved chordate noncoding sequences preserve genome synteny but not drive gene duplication retention. Genome Res. 19:2036-2051.
    • (2009) Genome Res. , vol.19 , pp. 2036-2051
    • Hufton, A.L.1
  • 18
    • 0038817774 scopus 로고    scopus 로고
    • EVOC: A controlled vocabulary for unifying gene expression data
    • Kelso J, et al. 2003. eVOC: a controlled vocabulary for unifying gene expression data. Genome Res. 13:1222-1230.
    • (2003) Genome Res. , vol.13 , pp. 1222-1230
    • Kelso, J.1
  • 19
    • 38449118642 scopus 로고    scopus 로고
    • Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - A fundamental feature of vertebrate genomes
    • Kikuta H, Fredman D, Rinkwitz S, Lenhard B, Becker TS. 2007. Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes. Genome Biol. 8(1 Suppl):S4.
    • (2007) Genome Biol. , vol.8 , Issue.1 SUPPL.
    • Kikuta, H.1    Fredman, D.2    Rinkwitz, S.3    Lenhard, B.4    Becker, T.S.5
  • 20
    • 23844519339 scopus 로고    scopus 로고
    • A high-resolution map of active promoters in the human genome
    • Kim TH, et al. 2005. A high-resolution map of active promoters in the human genome. Nature 436:876-880.
    • (2005) Nature , vol.436 , pp. 876-880
    • Kim, T.H.1
  • 21
    • 33947201809 scopus 로고    scopus 로고
    • Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
    • Kim TH, et al. 2007. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128:1231-1245.
    • (2007) Cell , vol.128 , pp. 1231-1245
    • Kim, T.H.1
  • 22
    • 57749184792 scopus 로고    scopus 로고
    • Timing of genome duplications relative to the origin of the vertebrates: Did cyclostomes diverge before or after?
    • Kuraku S, Meyer A, Kuratani S. 2009. Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after? Mol Biol Evol. 26:47-59.
    • (2009) Mol Biol Evol. , vol.26 , pp. 47-59
    • Kuraku, S.1    Meyer, A.2    Kuratani, S.3
  • 23
    • 79952163548 scopus 로고    scopus 로고
    • Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes
    • Lee AP, Kerk SY, Tan YY, Brenner S, Venkatesh B. 2011. Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes. Mol Biol Evol. 28:1205-1215.
    • (2011) Mol Biol Evol. , vol.28 , pp. 1205-1215
    • Lee, A.P.1    Kerk, S.Y.2    Tan, Y.Y.3    Brenner, S.4    Venkatesh, B.5
  • 24
    • 9344246836 scopus 로고    scopus 로고
    • Conserved expression domains for genes upstream and within the HoxA and HoxD clusters suggests a long-range enhancer existed before cluster duplication
    • Lehoczky JA, Williams ME, Innis JW. 2004. Conserved expression domains for genes upstream and within the HoxA and HoxD clusters suggests a long-range enhancer existed before cluster duplication. Evol Dev. 6: 423-430.
    • (2004) Evol Dev. , vol.6 , pp. 423-430
    • Lehoczky, J.A.1    Williams, M.E.2    Innis, J.W.3
  • 25
    • 0037263482 scopus 로고    scopus 로고
    • Numerous groups of chromosomal regional paralogies strongly indicate two genome doublings at the root of the vertebrates
    • Lundin LG, Larhammar D, Hallböök F. 2003. Numerous groups of chromosomal regional paralogies strongly indicate two genome doublings at the root of the vertebrates. J Struct Funct Genomics. 3:53-63.
    • (2003) J Struct Funct Genomics. , vol.3 , pp. 53-63
    • Lundin, L.G.1    Larhammar, D.2    Hallböök, F.3
  • 26
    • 77952679366 scopus 로고    scopus 로고
    • Ohnologs in the human genome are dosage balanced and frequently associated with disease
    • Makino T, McLysaght A. 2010. Ohnologs in the human genome are dosage balanced and frequently associated with disease. Proc Natl Acad Sci U S A. 107:9270-9274.
    • (2010) Proc Natl Acad Sci U S A. , vol.107 , pp. 9270-9274
    • Makino, T.1    McLysaght, A.2
  • 27
    • 78650005339 scopus 로고    scopus 로고
    • Evolution of conserved non-coding sequences within the vertebrate Hox clusters through the two-round whole duplications revealed by phylogenetic footprinting analysis
    • Matsunami M, Sumiyama K, Saitou N. 2010. Evolution of conserved non-coding sequences within the vertebrate Hox clusters through the two-round whole duplications revealed by phylogenetic footprinting analysis. J Mol Evol. 71:427-436.
    • (2010) J Mol Evol. , vol.71 , pp. 427-436
    • Matsunami, M.1    Sumiyama, K.2    Saitou, N.3
  • 28
    • 33645519275 scopus 로고    scopus 로고
    • Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis
    • McEwen GK, et al. 2006. Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis. Genome Res. 16:451-465.
    • (2006) Genome Res. , vol.16 , pp. 451-465
    • McEwen, G.K.1
  • 29
    • 74249085481 scopus 로고    scopus 로고
    • Early evolution of conserved regulatory sequences associated with development in vertebrates
    • McEwen GK, Goode DK, Parker HJ, Woolfe A, Callaway H, et al. 2009. Early evolution of conserved regulatory sequences associated with development in vertebrates. PLoS Genet. 12:e1000762.
    • (2009) PLoS Genet. , vol.12
    • McEwen, G.K.1    Goode, D.K.2    Parker, H.J.3    Woolfe, A.4    Callaway, H.5
  • 30
    • 34548420992 scopus 로고    scopus 로고
    • Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates
    • Nakatani Y, Takeda H, Kohara Y, Morishita S. 2007. Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res. 17:1254-1265.
    • (2007) Genome Res. , vol.17 , pp. 1254-1265
    • Nakatani, Y.1    Takeda, H.2    Kohara, Y.3    Morishita, S.4
  • 32
    • 77957243921 scopus 로고    scopus 로고
    • Long noncoding RNAs with enhancer-like function in human cells
    • Ørom UA, et al. 2010. Long noncoding RNAs with enhancer-like function in human cells. Cell 43:46-58.
    • (2010) Cell , vol.43 , pp. 46-58
    • Ørom, U.A.1
  • 33
    • 0038157152 scopus 로고    scopus 로고
    • Dosage sensitivity and the evolution of gene families in yeast
    • Papp B, Pál C, Hurst LD. 2003. Dosage sensitivity and the evolution of gene families in yeast. Nature 424:194-197.
    • (2003) Nature , vol.424 , pp. 194-197
    • Papp, B.1    Pál, C.2    Hurst, L.D.3
  • 34
    • 33751316959 scopus 로고    scopus 로고
    • In vivo enhancer analysis of human conserved non-coding sequences
    • Pennacchio LA, et al. 2006. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444:499-502.
    • (2006) Nature , vol.444 , pp. 499-502
    • Pennacchio, L.A.1
  • 35
    • 45749086679 scopus 로고    scopus 로고
    • The amphioxus genome and the evolution of the chordate karyotype
    • Putnam NH, et al. 2008. The amphioxus genome and the evolution of the chordate karyotype. Nature 453:1064-1071.
    • (2008) Nature , vol.453 , pp. 1064-1071
    • Putnam, N.H.1
  • 36
    • 79959412621 scopus 로고    scopus 로고
    • Unresolved orthology and peculiar coding sequence properties of lamprey genes: The KCNA gene family as test case
    • Qiu H, Hildebrand F, Kuraku S, Meyer A. 2011. Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case. BMC Genomics 12:325.
    • (2011) BMC Genomics , vol.12 , pp. 325
    • Qiu, H.1    Hildebrand, F.2    Kuraku, S.3    Meyer, A.4
  • 37
    • 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 470:279-283.
    • (2011) Nature , vol.470 , pp. 279-283
    • Rada-Iglesias, A.1
  • 38
    • 34250729138 scopus 로고    scopus 로고
    • Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
    • Rinn JL, et al. 2007. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129:1311-1323.
    • (2007) Cell , vol.129 , pp. 1311-1323
    • Rinn, J.L.1
  • 39
    • 84864462544 scopus 로고    scopus 로고
    • A map of the cis-regulatory sequences in the mouse genome
    • Shen Y, et al. 2012. A map of the cis-regulatory sequences in the mouse genome. Nature 488:116-20.
    • (2012) Nature , vol.488 , pp. 116-120
    • Shen, Y.1
  • 40
    • 0038613098 scopus 로고    scopus 로고
    • A global control region defines a chromosomal regulatory landscape containing the HoxD cluster
    • Spitz F, Gonzalez F, Duboule D. 2003. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113:405-417.
    • (2003) Cell , vol.113 , pp. 405-417
    • Spitz, F.1    Gonzalez, F.2    Duboule, D.3
  • 41
    • 84865416771 scopus 로고    scopus 로고
    • Identification and characterization of lineage-specific highly conserved noncoding sequences in mammalian genomes
    • Takahashi M, Saitou N. 2012. Identification and characterization of lineage-specific highly conserved noncoding sequences in mammalian genomes. Genome Biol Evol. 4:641-657.
    • (2012) Genome Biol Evol. , vol.4 , pp. 641-657
    • Takahashi, M.1    Saitou, N.2
  • 42
    • 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
    • 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 Biol. 8:R15.
    • (2007) Genome Biol. , vol.8
    • Vavouri, T.1    Walter, K.2    Gilks, W.R.3    Lehner, B.4    Elgar, G.5
  • 44
    • 33646377321 scopus 로고    scopus 로고
    • Highly conserved non-coding sequences are associated with vertebrate development
    • Woolfe A, et al. 2005. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3:116-130.
    • (2005) PLoS Biol. , vol.3 , pp. 116-130
    • Woolfe, A.1
  • 45
    • 35248843126 scopus 로고    scopus 로고
    • CONDOR: A database resource of developmentally- associated conserved non-coding elements
    • Woolfe A, et al. 2007. CONDOR: a database resource of developmentally- associated conserved non-coding elements. BMC Dev Biol. 7: 100.
    • (2007) BMC Dev Biol. , vol.7 , pp. 100
    • Woolfe, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.