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Volumn 18, Issue 9, 2011, Pages 1115-1130

Mapping association between long-range cis-regulatory regions and their target genes using synteny

Author keywords

Evolution; genomic rearrangements; genomics; multiple alignment; phylogenetic analyses; regulatory regions

Indexed keywords

HISTONE;

EID: 80052612784     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0088     Document Type: Conference Paper
Times cited : (3)

References (77)
  • 1
    • 27544443178 scopus 로고    scopus 로고
    • Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny
    • DOI 10.1093/hmg/ddi338
    • Ahituv, N., Prabhakar, S., Poulin, F., et al. 2005. Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny. Hum. Mol. Genet. 14, 3057-3063. (Pubitemid 41535470)
    • (2005) Human Molecular Genetics , vol.14 , Issue.20 , pp. 3057-3063
    • Ahituv, N.1    Prabhakar, S.2    Poulin, F.3    Rubin, E.M.4    Couronne, O.5
  • 2
    • 65149092197 scopus 로고    scopus 로고
    • Transcriptional features ofgenomic regulatory blocks
    • Akalin, A., Fredman, D., Arner, E., et al. 2009. Transcriptional features ofgenomic regulatory blocks. Genome Biol. 10, R38.
    • (2009) Genome Biol. , vol.10
    • Akalin, A.1    Fredman, D.2    Arner, E.3
  • 3
    • 48449104742 scopus 로고    scopus 로고
    • Babelomics: Advanced functional profiling of transcriptomics, proteomics and genomics experiments
    • Al-Shahrour, F., Carbonell, J., Minguez, P., et al. 2008. Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. Nucleic Acids Res. 36, 341-346.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 341-346
    • Al-Shahrour, F.1    Carbonell, J.2    Minguez, P.3
  • 5
    • 0024146931 scopus 로고
    • Enhancers: Mechanisms of action and cell specificity
    • Atchison, M.L. 1988. Enhancers: mechanisms of action and cell specificity. Annu. Rev. Cell Biol. 4, 127-153. (Pubitemid 19139254)
    • (1988) Annual Review of Cell Biology , vol.4 , pp. 127-153
    • Atchison, M.L.1
  • 6
    • 0034756824 scopus 로고    scopus 로고
    • Comparative genomics of the SOX9 region in human and Fugu rubripes: Conservation of short regulatory sequence elements within large intergenic regions
    • DOI 10.1006/geno.2001.6648
    • Bagheri-Fam, S., Ferraz, C., Demaille, J., et al. 2001. Comparative genomics of the SOX9 region in human and Fugurubripes: conservation of short regulatory sequence elements within large intergenic regions. Genomics 78, 73-82. (Pubitemid 33043661)
    • (2001) Genomics , vol.78 , Issue.1-2 , pp. 73-82
    • Bagheri-Fam, S.1    Ferraz, C.2    Demaille, J.3    Scherer, G.4    Pfeifer, D.5
  • 7
    • 35248882434 scopus 로고    scopus 로고
    • The random versus fragile breakage models of chromosome evolution: A matter of resolution
    • DOI 10.1007/s00438-007-0287-0
    • Becker, T.S., and Lenhard, B. 2007. The random versus fragile breakage models of chromosome evolution: a matter of resolution. Mol. Genet. Genomics 278, 487-491. (Pubitemid 47568710)
    • (2007) Molecular Genetics and Genomics , vol.278 , Issue.5 , pp. 487-491
    • Becker, T.S.1    Lenhard, B.2
  • 10
    • 33847032960 scopus 로고    scopus 로고
    • The mammalian epigenome
    • DOI 10.1016/j.cell.2007.01.033, PII S0092867407001286
    • Bernstein, B.E., Meissner, A., and Lander, E.S. 2007. The mammalian epigenome. Cell 128, 669-681. (Pubitemid 46273573)
    • (2007) Cell , vol.128 , Issue.4 , pp. 669-681
    • Bernstein, B.E.1    Meissner, A.2    Lander, E.S.3
  • 11
    • 33745152719 scopus 로고    scopus 로고
    • Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression
    • Blanchette, M., Bataille, A., Chen, X., et al. 2006. Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res. 16, 656-668.
    • (2006) Genome Res. , vol.16 , pp. 656-668
    • Blanchette, M.1    Bataille, A.2    Chen, X.3
  • 13
    • 33745067419 scopus 로고    scopus 로고
    • The gain and loss of genes during 600 million years of vertebrate evolution
    • Blomme, T., Vandepoele, K., Bodt, S.D., et al. 2006. The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol. 7, R43.
    • (2006) Genome Biol. , vol.7
    • Blomme, T.1    Vandepoele, K.2    Bodt, S.D.3
  • 18
    • 70350029560 scopus 로고    scopus 로고
    • Synorth: Exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes
    • Dong, X., Fredman, D., and Lenhard, B. 2009. Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. Genome Biol. 10, R86.
    • (2009) Genome Biol. , vol.10
    • Dong, X.1    Fredman, D.2    Lenhard, B.3
  • 20
    • 77951621301 scopus 로고    scopus 로고
    • The genome sequence of taurine cattle: A window to ruminant biology and evolution
    • Elsik, C.G., Tellam, R.L., Worley, K.C., et al. 2009. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324, 522-528.
    • (2009) Science , vol.324 , pp. 522-528
    • Elsik, C.G.1    Tellam, R.L.2    Worley, K.C.3
  • 21
    • 43549106605 scopus 로고    scopus 로고
    • Ancora: A web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes
    • Engström, P.G., Fredman, D., and Lenhard, B. 2008. Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. Genome Biol. 9, R34.
    • (2008) Genome Biol. , vol.9
    • Engström, P.G.1    Fredman, D.2    Lenhard, B.3
  • 22
    • 0035282698 scopus 로고    scopus 로고
    • Prediction of operons in microbial genomes
    • Ermolaeva, M.D., White, O., and Salzberg, S.L. 2001. Prediction of operons in microbial genomes. Nucleic Acids Res. 29, 1216-1221. (Pubitemid 32186208)
    • (2001) Nucleic Acids Research , vol.29 , Issue.5 , pp. 1216-1221
    • Ermolaeva, M.D.1    White, O.2    Salzberg, S.L.3
  • 23
    • 39749149956 scopus 로고    scopus 로고
    • Housekeeping genes tend to show reduced upstream sequence conservation
    • Farré, D., Bellora, N., Mularoni, L., et al. 2007. Housekeeping genes tend to show reduced upstream sequence conservation. Genome Biol. 8, R140.
    • (2007) Genome Biol. , vol.8
    • Farré, D.1    Bellora, N.2    Mularoni, L.3
  • 24
    • 37049246982 scopus 로고
    • Construction of phylogenetic trees
    • Fitch, W.M. and Margoliash, E. 1967. Construction of phylogenetic trees. Science 155, 279-284.
    • (1967) Science , vol.155 , pp. 279-284
    • Fitch, W.M.1    Margoliash, E.2
  • 26
    • 65149100263 scopus 로고    scopus 로고
    • Chromatin conformation signatures of cellular differentiation
    • Fraser, J., Rousseau, M., Shenker, S., et al. 2009. Chromatin conformation signatures of cellular differentiation. Genome Biol. 10, R37.
    • (2009) Genome Biol. , vol.10
    • Fraser, J.1    Rousseau, M.2    Shenker, S.3
  • 27
    • 63849091245 scopus 로고    scopus 로고
    • Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
    • Fullwood, M.J., Wei, C.-L., Liu, E.T., et al. 2009. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 19, 521-532.
    • (2009) Genome Res. , vol.19 , pp. 521-532
    • Fullwood, M.J.1    Wei, C.-L.2    Liu, E.T.3
  • 28
    • 70350651269 scopus 로고    scopus 로고
    • Global patterns of cis-variation in human cells revealed by high-density allelic expression analysis
    • Ge, B., Pokholok, D.K., Kwan, T., et al. 2009. Global patterns of cis-variation in human cells revealed by high-density allelic expression analysis. Nat. Genet. 41, 1216-1222.
    • (2009) Nat. Genet. , vol.41 , pp. 1216-1222
    • Ge, B.1    Pokholok, D.K.2    Kwan, T.3
  • 29
    • 1842684068 scopus 로고    scopus 로고
    • Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    • Gibbs, R., Weinstock, G., Metzker, M., et al. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428, 493-521.
    • (2004) Nature , vol.428 , pp. 493-521
    • Gibbs, R.1    Weinstock, G.2    Metzker, M.3
  • 31
    • 10644283823 scopus 로고    scopus 로고
    • Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
    • Hillier, L., Miller, W., Birney, E., et al. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695-716.
    • (2004) Nature , vol.432 , pp. 695-716
    • Hillier, L.1    Miller, W.2    Birney, E.3
  • 32
    • 2942517813 scopus 로고    scopus 로고
    • Cis-Regulatory control circuits in development
    • DOI 10.1016/j.ydbio.2004.03.031, PII S001216060400243X
    • Howard, M.L., and Davidson, E.H. 2004. cis-regulatory control circuits in development. Dev. Biol. 271, 109-118. (Pubitemid 38757779)
    • (2004) Developmental Biology , vol.271 , Issue.1 , pp. 109-118
    • Howard, M.L.1    Davidson, E.H.2
  • 38
    • 0034782502 scopus 로고    scopus 로고
    • Aniridia-associated translocations, DNase hypersensitivity, sequence comparison and transgenic analysis redefine the functional domain of PAX6
    • Kleinjan, D.A., Seawright, A., Schedl, A., et al. 2001. Aniridia-associated translocations, DNase hypersensitivity, sequence comparison and transgenic analysis redefine the functional domain of PAX6. Hum. Mol. Genet. 10, 2049-2059. (Pubitemid 32998817)
    • (2001) Human Molecular Genetics , vol.10 , Issue.19 , pp. 2049-2059
    • Kleinjan, D.A.1    Seawright, A.2    Schedl, A.3    Quinlan, R.A.4    Danes, S.5    Van Heyningen, V.6
  • 39
    • 11144339384 scopus 로고    scopus 로고
    • Long-range control of gene expression: Emerging mechanisms and disruption in disease
    • DOI 10.1086/426833
    • Kleinjan, D.A., and van Heyningen, V. 2005. Long-range control of gene expression: emerging mechanisms and disruption in disease. Am. J. Hum. Genet. 76, 8-32. (Pubitemid 40023762)
    • (2005) American Journal of Human Genetics , vol.76 , Issue.1 , pp. 8-32
    • Kleinjan, D.A.1    Van Heyningen, V.2
  • 40
    • 33748928159 scopus 로고    scopus 로고
    • The diverse functions of MicroRNAs in animal development and disease
    • DOI 10.1016/j.devcel.2006.09.009, PII S1534580706004023
    • Kloosterman, W.P., and Plasterk, R.HA. 2006. The diverse functions of micrornas in animal development and disease. Dev. Cell. 11, 441-450. (Pubitemid 44430905)
    • (2006) Developmental Cell , vol.11 , Issue.4 , pp. 441-450
    • Kloosterman, W.P.1    Plasterk, R.H.A.2
  • 41
    • 33847076849 scopus 로고    scopus 로고
    • Chromatin modifications and their function
    • DOI 10.1016/j.cell.2007.02.005, PII S0092867407001845
    • Kouzarides, T. 2007. Chromatin modifications and their function. Cell 128, 693-705. (Pubitemid 46273577)
    • (2007) Cell , vol.128 , Issue.4 , pp. 693-705
    • Kouzarides, T.1
  • 43
    • 66049138940 scopus 로고    scopus 로고
    • Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories
    • Larkin, D.M., Pape, G., Donthu, R., et al. 2009. Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. Genome Res. 19, 770-777.
    • (2009) Genome Res. , vol.19 , pp. 770-777
    • Larkin, D.M.1    Pape, G.2    Donthu, R.3
  • 50
    • 70349160409 scopus 로고    scopus 로고
    • Long-range regulation is a major driving force in maintaining genome integrity
    • Mongin, E., Dewar, K., and Blanchette, M. 2009. Long-range regulation is a major driving force in maintaining genome integrity. BMC Evol. Biol. 9, 203.
    • (2009) BMC Evol. Biol. , vol.9 , pp. 203
    • Mongin, E.1    Dewar, K.2    Blanchette, M.3
  • 53
    • 4944260940 scopus 로고    scopus 로고
    • The regulatory content of intergenic DNA shapes genome archi-tecture
    • Nelson, C.E., Hersh, B.M., and Carroll, S.B. 2004. The regulatory content of intergenic DNA shapes genome archi-tecture. Genome Biol. 5, R25.
    • (2004) Genome Biol. , vol.5
    • Nelson, C.E.1    Hersh, B.M.2    Carroll, S.B.3
  • 54
    • 0142084743 scopus 로고    scopus 로고
    • Scanning human gene deserts for long-range enhancers
    • DOI 10.1126/science.1088328
    • Nobrega, MA., Ovcharenko, I., Afzal, V., et al. 2003. Scanning human gene deserts for long-range enhancers. Science 302, 413. (Pubitemid 37296259)
    • (2003) Science , vol.302 , Issue.5644 , pp. 413
    • Nobrega, M.A.1    Ovcharenko, I.2    Afzal, V.3    Rubin, E.M.4
  • 55
    • 12744261452 scopus 로고    scopus 로고
    • Evolution and functional classification of vertebrate gene deserts
    • Ovcharenko, I., Loots, G.G., Nobrega, MA., et al. 2005. Evolution and functional classification of vertebrate gene deserts. Genome Res. 15, 137-145.
    • (2005) Genome Res. , vol.15 , pp. 137-145
    • Ovcharenko, I.1    Loots, G.G.2    Nobrega, M.A.3
  • 56
    • 54949108148 scopus 로고    scopus 로고
    • Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
    • Paten, B., Herrero, J., Beal, K., et al. 2008. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res. 18, 1814-1828.
    • (2008) Genome Res. , vol.18 , pp. 1814-1828
    • Paten, B.1    Herrero, J.2    Beal, K.3
  • 57
    • 33645766047 scopus 로고    scopus 로고
    • The fragile breakage versus random breakage models of chromosome evolution
    • Peng, Q., Pevzner, PA., and Tesler, G. 2006. The fragile breakage versus random breakage models of chromosome evolution. PLo S Comput. Biol. 2, e14.
    • (2006) PLo S Comput. Biol. , vol.2
    • Peng, Q.1    Pevzner, P.A.2    Tesler, G.3
  • 60
    • 0030960672 scopus 로고    scopus 로고
    • Transcriptional activation by recruitment
    • DOI 10.1038/386569a0
    • Ptashne, M., and Gann, A. 1997. Transcriptional activation by recruitment. Nature 386, 569-577. (Pubitemid 27175417)
    • (1997) Nature , vol.386 , Issue.6625 , pp. 569-577
    • Ptashne, M.1    Gann, A.2
  • 61
    • 76249098866 scopus 로고    scopus 로고
    • Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX SOX4, and IRX3
    • Ragvin, A., Moro, E., Fredman, D., et al. 2010. Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3. Proc. Natl. Acad. Sci. USA 107, 775-780.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 775-780
    • Ragvin, A.1    Moro, E.2    Fredman, D.3
  • 62
    • 75549089967 scopus 로고    scopus 로고
    • The UCSC genome browser database: Update 2010
    • Rhead, B., Karolchik, D., Kuhn, R.M., et al. 2010. The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 38, D613-D619.
    • (2010) Nucleic Acids Res. , vol.38
    • Rhead, B.1    Karolchik, D.2    Kuhn, R.M.3
  • 63
    • 71049155308 scopus 로고    scopus 로고
    • Cpg-depleted promoters harbor tissue-specific transcription factor binding signals\-implications for motif overrepresentation analyses
    • Roider, H.G., Lenhard, B., Kanhere, A., et al. 2009. Cpg-depleted promoters harbor tissue-specific transcription factor binding signals\-implications for motif overrepresentation analyses. Nucleic Acids Res. 37, 6305-6315.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 6305-6315
    • Roider, H.G.1    Lenhard, B.2    Kanhere, A.3
  • 64
    • 22144473057 scopus 로고    scopus 로고
    • Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
    • Sandelin, A., Bailey, P., Bruce, S., et al. 2004. Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 5, 99.
    • (2004) BMC Genomics , vol.5 , pp. 99
    • Sandelin, A.1    Bailey, P.2    Bruce, S.3
  • 65
    • 19344375742 scopus 로고    scopus 로고
    • Transcriptional control in the segmentation gene network of Dro-sophila
    • Schroeder, M.D., Pearce, M., Fak, J., et al. 2004. Transcriptional control in the segmentation gene network of Dro-sophila. PLo S Biol. 2, E271.
    • (2004) PLo S Biol. , vol.2
    • Schroeder, M.D.1    Pearce, M.2    Fak, J.3
  • 66
    • 0037267806 scopus 로고    scopus 로고
    • Human-mouse alignments with BLASTZ
    • Schwartz, S., Kent, W., Smit, A., et al. 2003. Human-mouse alignments with BLASTZ. Genome Res. 13, 103-107.
    • (2003) Genome Res. , vol.13 , pp. 103-107
    • Schwartz, S.1    Kent, W.2    Smit, A.3
  • 68
    • 0038613098 scopus 로고    scopus 로고
    • A global control region defines a chromosomal regulatory landscape containing the HoxD cluster
    • DOI 10.1016/S0092-8674(03)00310-6
    • Spitz, F., Gonzalez, F., and Duboule, D. 2003. A global control region defines a chromosomal regulatory landscape containing the hoxd cluster. Cell 113, 405-417. (Pubitemid 36556121)
    • (2003) Cell , vol.113 , Issue.3 , pp. 405-417
    • Spitz, F.1    Gonzalez, F.2    Duboule, D.3
  • 69
    • 56649106344 scopus 로고    scopus 로고
    • Structural relationships between highly conserved elements and genes in vertebrate genomes
    • Sun, H., Skogerbø, G., Wang, Z., et al. 2008. Structural relationships between highly conserved elements and genes in vertebrate genomes. PLo S ONE 3, e3727.
    • (2008) PLo S ONE , vol.3
    • Sun, H.1    Skogerbø, G.2    Wang, Z.3
  • 71
    • 29444452159 scopus 로고    scopus 로고
    • Defining a genomic radius for long-range enhancer action: Duplicated conserved non-coding elements hold the key
    • DOI 10.1016/j.tig.2005.10.005, PII S0168952505003203
    • Vavouri, T., Mc Ewen, G. K., Woolfe, A., et al. 2006. Defining a genomic radius for long-range enhancer action: duplicated conserved non-coding elements hold the key. Trends Genet. 22, 5-10. (Pubitemid 43011991)
    • (2006) Trends in Genetics , vol.22 , Issue.1 , pp. 5-10
    • Vavouri, T.1    McEwen, G.K.2    Woolfe, A.3    Gilks, W.R.4    Elgar, G.5
  • 73
    • 33846112470 scopus 로고    scopus 로고
    • VISTA Enhancer Browser - A database of tissue-specific human enhancers
    • DOI 10.1093/nar/gkl822
    • Visel, A., Minovitsky, S., Dubchak, I., et al. 2006. Vista enhancer browser\-a database of tissue-specific human enhancers. Nucleic Acids Res. 35, D88-D92. (Pubitemid 46056176)
    • (2007) Nucleic Acids Research , vol.35 , Issue.SUPPL. 1
    • Visel, A.1    Minovitsky, S.2    Dubchak, I.3    Pennacchio, L.A.4
  • 76
    • 20044366725 scopus 로고    scopus 로고
    • Highly conserved non-coding sequences are associated with ver-tebrate development
    • Woolfe, A., Goodson, M., Goode, D., et al. 2005. Highly conserved non-coding sequences are associated with ver-tebrate development. PLo S Biol. 3, e7.
    • (2005) PLo S Biol. , vol.3
    • Woolfe, A.1    Goodson, M.2    Goode, D.3
  • 77
    • 19344368143 scopus 로고    scopus 로고
    • Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity
    • DOI 10.1016/j.gene.2005.01.012, PII S0378111905000405
    • Yamashita, R., Suzuki, Y., Sugano, S., et al. 2005. Genome-wide analysis reveals strong correlation between cpg islands with nearby transcription start sites of genes and their tissue specificity. Gene 350, 129-136. (Pubitemid 40719057)
    • (2005) Gene , vol.350 , Issue.2 , pp. 129-136
    • Yamashita, R.1    Suzuki, Y.2    Sugano, S.3    Nakai, K.4


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