메뉴 건너뛰기




Volumn 33, Issue 7, 2016, Pages 1807-1817

Genomic Locations of Conserved Noncoding Sequences and Their Proximal Protein-Coding Genes in Mammalian Expression Dynamics

Author keywords

Conserved noncoding sequence; Gene expression; Mammalian genome; Physical distance; Regulation

Indexed keywords

LONG UNTRANSLATED RNA; UNTRANSLATED RNA; PROTEIN; SPACER DNA;

EID: 85016147805     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/MOLBEV/MSW058     Document Type: Article
Times cited : (21)

References (49)
  • 1
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • 1000 Genomes Project Consortium 2012. An integrated map of genetic variation from 1,092 human genomes. Nature 491:56–65.
    • (2012) Nature , vol.491 , pp. 56-65
  • 4
    • 0035877648 scopus 로고    scopus 로고
    • Characterization of an evolutionarily conserved far-upstream enhancer in the human alpha 2(I) collagen (COL1A2) gene
    • Antoniv TT, De Val S, Wells D, Denton CP, Rabe C, de Crombrugghe B, Ramirez F, Bou-Gharios G, 2001. Characterization of an evolutionarily conserved far-upstream enhancer in the human alpha 2(I) collagen (COL1A2) gene. J Biol Chem. 276:21754–21764.
    • (2001) J Biol Chem , vol.276 , pp. 21754-21764
    • Antoniv, TT1    De Val, S2    Wells, D3    Denton, CP4    Rabe, C5    de Crombrugghe, B6    Ramirez, F7    Bou-Gharios, G8
  • 5
    • 84892554083 scopus 로고    scopus 로고
    • Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders
    • Babarinde IA, Saitou N. 2013. Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders. Genome Biol Evol. 5:2330–2343.
    • (2013) Genome Biol Evol , vol.5 , pp. 2330-2343
    • Babarinde, IA1    Saitou, N.2
  • 8
    • 84896710720 scopus 로고    scopus 로고
    • A survey of ancient conserved non-coding elements in the PAX6 locus reveals a landscape of interdigitated cis-regulatory archipelagos
    • Bhatia S, Monahan J, Ravi V, Gautier P, Murdoch E, Brenner S, van Heyningen V, Venkatesh B, Kleinjan DA. 2014. A survey of ancient conserved non-coding elements in the PAX6 locus reveals a landscape of interdigitated cis-regulatory archipelagos. Dev Biol. 387:214–228.
    • (2014) Dev Biol , vol.387 , pp. 214-228
    • Bhatia, S1    Monahan, J2    Ravi, V3    Gautier, P4    Murdoch, E5    Brenner, S6    van Heyningen, V7    Venkatesh, B8    Kleinjan, DA.9
  • 9
    • 79955403252 scopus 로고    scopus 로고
    • Gene expression differences among primates are associated with changes in a histone epigenetic modification
    • Cain CE, Blekhman R, Marioni JC, Gilad Y. 2011. Gene expression differences among primates are associated with changes in a histone epigenetic modification. Genetics 187:1225–1234.
    • (2011) Genetics , vol.187 , pp. 1225-1234
    • Cain, CE1    Blekhman, R2    Marioni, JC3    Gilad, Y.4
  • 13
    • 66049090454 scopus 로고    scopus 로고
    • The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome
    • De S, Teichmann SA, Babu MM. 2009. The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome. Genome Res. 19:785–794.
    • (2009) Genome Res , vol.19 , pp. 785-794
    • De, S1    Teichmann, SA2    Babu, MM.3
  • 14
    • 0037083376 scopus 로고    scopus 로고
    • Capturing chromosome conformation
    • Dekker J, Rippe K, Dekker M, Kleckner N. 2002. Capturing chromosome conformation. Science 295:1306–1311.
    • (2002) Science , vol.295 , pp. 1306-1311
    • Dekker, J1    Rippe, K2    Dekker, M3    Kleckner, N.4
  • 15
    • 34248524473 scopus 로고    scopus 로고
    • Mapping networks of physical interactions between genomic elements using 5C technology
    • Dostie J, Dekker J. 2007. Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc. 2:988–1002.
    • (2007) Nat Protoc , vol.2 , pp. 988-1002
    • Dostie, J1    Dekker, J.2
  • 17
    • 0038692119 scopus 로고    scopus 로고
    • Human housekeeping genes are compact
    • Eisenberg E, Levanon EY. 2003. Human housekeeping genes are compact. Trends Genet. 19:362–365.
    • (2003) Trends Genet , vol.19 , pp. 362-365
    • Eisenberg, E1    Levanon, EY.2
  • 18
    • 84884416048 scopus 로고    scopus 로고
    • Human housekeeping genes, revisited
    • Eisenberg E, Levanon EY. 2013. Human housekeeping genes, revisited. Trends Genet. 29:569–574.
    • (2013) Trends Genet , vol.29 , pp. 569-574
    • Eisenberg, E1    Levanon, EY.2
  • 19
    • 0036094107 scopus 로고    scopus 로고
    • Conserved CTCF insulator elements flank the mouse and human b-globin loci
    • Farrell CM, West AG, Felsenfeld G. 2002. Conserved CTCF insulator elements flank the mouse and human b-globin loci. Mol Cell Biol. 22:3820–3831.
    • (2002) Mol Cell Biol , vol.22 , pp. 3820-3831
    • Farrell, CM1    West, AG2    Felsenfeld, G.3
  • 20
    • 0029929793 scopus 로고    scopus 로고
    • An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes
    • Filippova GN, Fagerlie S, Klenova EM, Myers C, Dehner Y, Goodwin G, Neiman PE, Collins SJ, Lobanenkov VV. 1996. An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes. Mol Cell Biol. 16:2802–2813.
    • (1996) Mol Cell Biol , vol.16 , pp. 2802-2813
    • Filippova, GN1    Fagerlie, S2    Klenova, EM3    Myers, C4    Dehner, Y5    Goodwin, G6    Neiman, PE7    Collins, SJ8    Lobanenkov, VV.9
  • 22
    • 84857251182 scopus 로고    scopus 로고
    • CTCF: insights into insulator function during development
    • Herold M, Bartkuhn M, Renkawitz R. 2012. CTCF: insights into insulator function during development. Development 139:1045–1057.
    • (2012) Development , vol.139 , pp. 1045-1057
    • Herold, M1    Bartkuhn, M2    Renkawitz, R.3
  • 23
    • 58149498240 scopus 로고    scopus 로고
    • CTCF-dependent enhancer-blocking by alternative chromatin loop formation
    • Hou C, Zhao H, Tanimoto K, Dean A. 2008. CTCF-dependent enhancer-blocking by alternative chromatin loop formation. Proc Natl Acad Sci U S A. 105:20398–20403.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 20398-20403
    • Hou, C1    Zhao, H2    Tanimoto, K3    Dean, A.4
  • 28
    • 0042810698 scopus 로고    scopus 로고
    • A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly
    • Lettice LA, Heaney SJ, Purdie LA, Li L, de Beer P, Oostra BA, Goode D, Elgar G, Hill RE, de Graaff E. 2003. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet. 12:1725–1735.
    • (2003) Hum Mol Genet , vol.12 , pp. 1725-1735
    • Lettice, LA1    Heaney, SJ2    Purdie, LA3    Li, L4    de Beer, P5    Oostra, BA6    Goode, D7    Elgar, G8    Hill, RE9    de Graaff, E.10
  • 29
    • 84876569149 scopus 로고    scopus 로고
    • Vertebrate paralogous conserved noncoding sequences may be related to gene expressions in brain
    • Matsunami M, Saitou N. 2013. Vertebrate paralogous conserved noncoding sequences may be related to gene expressions in brain. Genome Biol Evol. 5:140–150.
    • (2013) Genome Biol Evol , vol.5 , pp. 140-150
    • Matsunami, M1    Saitou, N.2
  • 30
    • 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, Greg EG. 2009. Early evolution of conserved regulatory sequences associated with development in vertebrates. PLoS Genet. 5(12): e1000762.
    • (2009) PLoS Genet , vol.5 , Issue.12 , pp. e1000762
    • McEwen, GK1    Goode, DK2    Parker, HJ3    Woolfe, A4    Callaway, H5    Greg, EG.6
  • 31
    • 77950529946 scopus 로고    scopus 로고
    • Motif enrichment analysis: a unified framework and an evaluation on ChIP data
    • McLeay RC, Bailey TL. 2010. Motif enrichment analysis: a unified framework and an evaluation on ChIP data. BMC Bioinformatics 11:165.
    • (2010) BMC Bioinformatics , vol.11 , pp. 165
    • McLeay, RC1    Bailey, TL.2
  • 32
    • 0033082237 scopus 로고    scopus 로고
    • Core promoter elements can regulate transcription on a separate chromosome in trans
    • Morris JR, Geyer PK, Wu C. 1999. Core promoter elements can regulate transcription on a separate chromosome in trans. Genes Dev. 13:253–258.
    • (1999) Genes Dev , vol.13 , pp. 253-258
    • Morris, JR1    Geyer, PK2    Wu, C.3
  • 34
    • 77950348678 scopus 로고    scopus 로고
    • Insulators as mediators of intra- and interchromosomal interactions: a common evolutionary theme
    • Ong CT, Corces VG. 2009. Insulators as mediators of intra- and interchromosomal interactions: a common evolutionary theme. J Biol. 8:73.
    • (2009) J Biol , vol.8 , pp. 73
    • Ong, CT1    Corces, VG.2
  • 35
    • 77952077350 scopus 로고    scopus 로고
    • Selection for the compactness of highly expressed genes in Gallus gallus
    • Rao YS, Wang ZF, Chai XW, Wu GZ, Zhou M, Nie QH, Zhang XQ. 2010. Selection for the compactness of highly expressed genes in Gallus gallus. Biol Direct. 5:35.
    • (2010) Biol Direct , vol.5 , pp. 35
    • Rao, YS1    Wang, ZF2    Chai, XW3    Wu, GZ4    Zhou, M5    Nie, QH6    Zhang, XQ.7
  • 36
    • 68549123708 scopus 로고    scopus 로고
    • A cluster of three long-range enhancers directs regional Shh expression in the epithelial linings
    • Sagai T, Amano T, Tamura M, Mizushina Y, Sumiyama K, Shiroishi T. 2009. A cluster of three long-range enhancers directs regional Shh expression in the epithelial linings. Development 136:1665–1674.
    • (2009) Development , vol.136 , pp. 1665-1674
    • Sagai, T1    Amano, T2    Tamura, M3    Mizushina, Y4    Sumiyama, K5    Shiroishi, T.6
  • 38
    • 84931291783 scopus 로고    scopus 로고
    • Functional validation of mouse tyrosinase non-coding regulatory DNA elements by CRISPR-Cas9-mediated mutagenesis
    • Seruggia D, Fernandez A, Cantero M, Pelczar P, Montoliu L. 2015. Functional validation of mouse tyrosinase non-coding regulatory DNA elements by CRISPR-Cas9-mediated mutagenesis. Nucleic Acids Res. 43:4855–4867.
    • (2015) Nucleic Acids Res , vol.43 , pp. 4855-4867
    • Seruggia, D1    Fernandez, A2    Cantero, M3    Pelczar, P4    Montoliu, L.5
  • 41
    • 0037388173 scopus 로고    scopus 로고
    • Regulation of Dlx3 gene expression in visceral arches by evolutionarily conserved enhancer elements
    • Sumiyama K, Ruddle FH. 2003. Regulation of Dlx3 gene expression in visceral arches by evolutionarily conserved enhancer elements. Proc Natl Acad Sci U S A. 100:4030–4034.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 4030-4034
    • Sumiyama, K1    Ruddle, FH.2
  • 42
    • 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, M1    Saitou, N.2
  • 44
    • 29444452159 scopus 로고    scopus 로고
    • Defining a genomic radius for long-range enhancer action: duplicated conserved non-coding elements hold the key
    • Vavouri T, McEwen GK, Woolfe A, Gilks WR, Elgar G. 2006. Defining a genomic radius for long-range enhancer action: duplicated conserved non-coding elements hold the key. Trends Genet. 22:5–10.
    • (2006) Trends Genet , vol.22 , pp. 5-10
    • Vavouri, T1    McEwen, GK2    Woolfe, A3    Gilks, WR4    Elgar, G.5
  • 46
    • 33846112470 scopus 로고    scopus 로고
    • VISTA Enhancer Browser-a database of tissue-specific human enhancers
    • Visel A, Minovitsky S, Dubchak I, Pennacchio LA. 2007. VISTA Enhancer Browser-a database of tissue-specific human enhancers. Nucleic Acids Res. 35:D88–D92.
    • (2007) Nucleic Acids Res , vol.35 , pp. D88-D92
    • Visel, A1    Minovitsky, S2    Dubchak, I3    Pennacchio, LA.4
  • 47
    • 0032509990 scopus 로고    scopus 로고
    • Location of enhancers is essential for the imprinting of H19 and Igf2 genes
    • Webber AL, Ingram RS, Levorse JM, Tilghman SM. 1998. Location of enhancers is essential for the imprinting of H19 and Igf2 genes. Nature 391:711–715.
    • (1998) Nature , vol.391 , pp. 711-715
    • Webber, AL1    Ingram, RS2    Levorse, JM3    Tilghman, SM.4
  • 49
    • 33750203582 scopus 로고    scopus 로고
    • Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions
    • Zhao Z, Tavoosidana G, Sjölinder M, Göndör A, Mariano P, Wang S, Kanduri C, Lezcano M, Sandhu KS, Singh U, et al. 2006. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet. 38:1341–1347.
    • (2006) Nat Genet , vol.38 , pp. 1341-1347
    • Zhao, Z1    Tavoosidana, G2    Sjölinder, M3    Göndör, A4    Mariano, P5    Wang, S6    Kanduri, C7    Lezcano, M8    Sandhu, KS9    Singh, U10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.