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Volumn 38, Issue 4, 2009, Pages 1071-1085

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DEVELOPMENTAL BIOLOGY; EXON; GENE ACTIVITY; GENE CONTROL; GENE DUPLICATION; GENE FUNCTION; GENE SEQUENCE; GENETIC CODE; GENETIC CONSERVATION; GENETIC REGULATION; GENOMICS; MAMMAL; PRIORITY JOURNAL; VERTEBRATE; ANIMAL; BINDING SITE; CHEMISTRY; CHROMATIN; ENHANCER REGION; GENETICS; GENOME; HUMAN; METABOLISM; MOLECULAR EVOLUTION; MOUSE; PROTEIN TERTIARY STRUCTURE; ZEBRA FISH;

EID: 77950352433     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1124     Document Type: Article
Times cited : (40)

References (63)
  • 6
    • 38949097100 scopus 로고    scopus 로고
    • Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock
    • Stephen, S., Pheasant, M., Makunin, I.V. and Mattick, J.S. (2008) Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock. Mol. Biol. Evol., 25, 402-408.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 402-408
    • Stephen, S.1    Pheasant, M.2    Makunin, I.V.3    Mattick, J.S.4
  • 7
    • 34249937354 scopus 로고    scopus 로고
    • Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
    • Lowe, C.B., Bejerano, G. and Haussler, D. (2007) Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc. Natl Acad. Sci. USA, 104, 8005-8010.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 8005-8010
    • Lowe, C.B.1    Bejerano, G.2    Haussler, D.3
  • 8
    • 33745620751 scopus 로고    scopus 로고
    • Functional noncoding sequences derived from SINEs in the mammalian genome
    • Nishihara, H., Smit, A.F. and Okada, N. (2006) Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res., 16, 864-874.
    • (2006) Genome Res. , vol.16 , pp. 864-874
    • Nishihara, H.1    Smit, A.F.2    Okada, N.3
  • 9
    • 33746801653 scopus 로고    scopus 로고
    • A family of conserved noncoding elements derived from an ancient transposable element
    • Xie, X., Kamal, M. and Lander, E.S. (2006) A family of conserved noncoding elements derived from an ancient transposable element. Proc. Natl Acad. Sci. USA, 103, 11659-11664.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 11659-11664
    • Xie, X.1    Kamal, M.2    Lander, E.S.3
  • 10
    • 45549100203 scopus 로고    scopus 로고
    • An ultraconserved Hox-Pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4
    • Lampe, X., Samad, O.A., Guiguen, A., Matis, C., Remacle, S., Picard, J.J., Rijli, F.M. and Rezsohazy, R. (2008) An ultraconserved Hox-Pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4. Nucleic Acids Res., 36, 3214-3225.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 3214-3225
    • Lampe, X.1    Samad, O.A.2    Guiguen, A.3    Matis, C.4    Remacle, S.5    Picard, J.J.6    Rijli, F.M.7    Rezsohazy, R.8
  • 11
    • 58149512003 scopus 로고    scopus 로고
    • A regulatory module embedded in the coding region of Hoxa2 controls expression in rhombomere 2
    • Tumpel, S., Cambronero, F., Sims, C., Krumlauf, R. and Wiedemann, L.M. (2008) A regulatory module embedded in the coding region of Hoxa2 controls expression in rhombomere 2. Proc. Natl Acad. Sci. USA, 105, 20077-20082.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 20077-20082
    • Tumpel, S.1    Cambronero, F.2    Sims, C.3    Krumlauf, R.4    Wiedemann, L.M.5
  • 12
    • 0035678575 scopus 로고    scopus 로고
    • Multiple snoRNA gene clusters from Arabidopsis
    • Brown, J.W., Clark, G.P., Leader, D.J., Simpson, C.G. and Lowe, T. (2001) Multiple snoRNA gene clusters from Arabidopsis. RNA, 7, 1817-1832.
    • (2001) RNA , vol.7 , pp. 1817-1832
    • Brown, J.W.1    Clark, G.P.2    Leader, D.J.3    Simpson, C.G.4    Lowe, T.5
  • 13
    • 52049094401 scopus 로고    scopus 로고
    • Genomewide analysis of box C/D and box H/ACA snoRNAs in Chlamydomonas reinhardtii reveals an extensive organization into intronic gene clusters
    • Chen, C.L., Chen, C.J., Vallon, O., Huang, Z.P., Zhou, H. and Qu, L.H. (2008) Genomewide analysis of box C/D and box H/ACA snoRNAs in Chlamydomonas reinhardtii reveals an extensive organization into intronic gene clusters. Genetics, 179, 21-30.
    • (2008) Genetics , vol.179 , pp. 21-30
    • Chen, C.L.1    Chen, C.J.2    Vallon, O.3    Huang, Z.P.4    Zhou, H.5    Qu, L.H.6
  • 14
    • 0030033546 scopus 로고    scopus 로고
    • A mammalian gene with introns instead of exons generating stable RNA products
    • Tycowski, K.T., Shu, M.D. and Steitz, J.A. (1996) A mammalian gene with introns instead of exons generating stable RNA products. Nature, 379, 464-466.
    • (1996) Nature , vol.379 , pp. 464-466
    • Tycowski, K.T.1    Shu, M.D.2    Steitz, J.A.3
  • 17
    • 43549106605 scopus 로고    scopus 로고
    • Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes
    • Engstrom, 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
    • Engstrom, P.G.1    Fredman, D.2    Lenhard, B.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
  • 19
    • 34248213721 scopus 로고    scopus 로고
    • Detecting non-coding selective pressure in coding regions
    • Chen, H. and Blanchette, M. (2007) Detecting non-coding selective pressure in coding regions. BMC Evol. Biol., 7(Suppl 1), S9.
    • (2007) BMC Evol. Biol. , vol.7 , Issue.SUPPL 1
    • Chen, H.1    Blanchette, M.2
  • 23
    • 0036677662 scopus 로고    scopus 로고
    • TFBS: Computational framework for transcription factor binding site analysis
    • Lenhard, B. and Wasserman, W.W. (2002) TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics, 18, 1135-1136.
    • (2002) Bioinformatics , vol.18 , pp. 1135-1136
    • Lenhard, B.1    Wasserman, W.W.2
  • 26
    • 0030958773 scopus 로고    scopus 로고
    • Promoter analysis in living zebrafish embryos identifies a cis-acting motif required for neuronal expression of GATA-2
    • Meng, A., Tang, H., Ong, B.A., Farrell, M.J. and Lin, S. (1997) Promoter analysis in living zebrafish embryos identifies a cis-acting motif required for neuronal expression of GATA-2. Proc. Natl Acad. Sci. USA, 94, 6267-6272.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 6267-6272
    • Meng, A.1    Tang, H.2    Ong, B.A.3    Farrell, M.J.4    Lin, S.5
  • 27
    • 60549097668 scopus 로고    scopus 로고
    • Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes
    • Navratilova, P., Fredman, D., Hawkins, T.A., Turner, K., Lenhard, B. and Becker, T.S. (2009) Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Dev. Biol., 327, 526-540.
    • (2009) Dev. Biol. , vol.327 , pp. 526-540
    • Navratilova, P.1    Fredman, D.2    Hawkins, T.A.3    Turner, K.4    Lenhard, B.5    Becker, T.S.6
  • 28
    • 70349619801 scopus 로고    scopus 로고
    • Web-based tools and approaches to study long-range gene regulation in Metazoa
    • Fredman, D., Engstrom, P.G. and Lenhard, B. (2009) Web-based tools and approaches to study long-range gene regulation in Metazoa. Brief Funct. Genomic Proteomic, 8, 231-42.
    • (2009) Brief Funct. Genomic Proteomic , vol.8 , pp. 231-242
    • Fredman, D.1    Engstrom, P.G.2    Lenhard, B.3
  • 29
    • 55549128249 scopus 로고    scopus 로고
    • Dispensability of mammalian DNA
    • McLean, C. and Bejerano, G. (2008) Dispensability of mammalian DNA. Genome Res., 18, 1743-1751.
    • (2008) Genome Res. , vol.18 , pp. 1743-1751
    • McLean, C.1    Bejerano, G.2
  • 33
    • 3142739466 scopus 로고    scopus 로고
    • Detecting selection in noncoding regions of nucleotide sequences
    • Wong, W.S. and Nielsen, R. (2004) Detecting selection in noncoding regions of nucleotide sequences. Genetics, 167, 949-958.
    • (2004) Genetics , vol.167 , pp. 949-958
    • Wong, W.S.1    Nielsen, R.2
  • 34
    • 33745772571 scopus 로고    scopus 로고
    • New methods for detecting lineage-specific selection
    • Siepel, A., Pollard, K. and Haussler, D. (2006) New methods for detecting lineage-specific selection. Res. Comput. Mol. Biol., 3909, 190-205.
    • (2006) Res. Comput. Mol. Biol. , vol.3909 , pp. 190-205
    • Siepel, A.1    Pollard, K.2    Haussler, D.3
  • 35
    • 1842505125 scopus 로고    scopus 로고
    • Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics
    • Sandelin, A. and Wasserman, W.W (2004) Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J. Mol. Biol., 338, 207-215.
    • (2004) J. Mol. Biol. , vol.338 , pp. 207-215
    • Sandelin, A.1    Wasserman, W.W.2
  • 36
    • 0003421005 scopus 로고    scopus 로고
    • Sinauer Associates, Sunderland, Mass
    • Li, W.-H. (1997) Molecular Evolution. Sinauer Associates, Sunderland, Mass.
    • (1997) Molecular Evolution
    • Li, W.-H.1
  • 37
    • 0036720020 scopus 로고    scopus 로고
    • The Ka/Ks ratio: diagnosing the form of sequence evolution
    • Hurst, L.D. (2002) The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet., 18, 486.
    • (2002) Trends Genet , vol.18 , pp. 486
    • Hurst, L.D.1
  • 38
    • 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, W.R., Lehner, B. and 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
  • 45
    • 26444603772 scopus 로고    scopus 로고
    • Two rounds of whole genome duplication in the ancestral vertebrate
    • Dehal, P. and Boore, J.L. (2005) Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol., 3, e314.
    • (2005) PLoS Biol. , vol.3
    • Dehal, P.1    Boore, J.L.2
  • 46
    • 23744493161 scopus 로고    scopus 로고
    • Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
    • King, D.C., Taylor, J., Elnitski, L., Chiaromonte, F., Miller, W. and Hardison, R.C. (2005) Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res., 15, 1051-1060.
    • (2005) Genome Res. , vol.15 , pp. 1051-1060
    • King, D.C.1    Taylor, J.2    Elnitski, L.3    Chiaromonte, F.4    Miller, W.5    Hardison, R.C.6
  • 47
    • 33644853819 scopus 로고    scopus 로고
    • Can RNA selection pressure distort the measurement of Ka/Ks?
    • Xing, Y. and Lee, C. (2006) Can RNA selection pressure distort the measurement of Ka/Ks? Gene, 370, 1-5.
    • (2006) Gene , vol.370 , pp. 1-5
    • Xing, Y.1    Lee, C.2
  • 48
    • 33745394130 scopus 로고    scopus 로고
    • Alternative splicing and RNA selection pressure-evolutionary consequences for eukaryotic genomes
    • Xing, Y. and Lee, C. (2006) Alternative splicing and RNA selection pressure-evolutionary consequences for eukaryotic genomes. Nat. Rev. Genet., 7, 499-509.
    • (2006) Nat. Rev. Genet. , vol.7 , pp. 499-509
    • Xing, Y.1    Lee, C.2
  • 50
    • 27544498768 scopus 로고    scopus 로고
    • Assessing the application of Ka/Ks ratio test to alternatively spliced exons
    • Xing, Y. and Lee, C. (2005) Assessing the application of Ka/Ks ratio test to alternatively spliced exons. Bioinformatics, 21, 3701-3703.
    • (2005) Bioinformatics , vol.21 , pp. 3701-3703
    • Xing, Y.1    Lee, C.2
  • 53
    • 37549020292 scopus 로고    scopus 로고
    • Essential elements in the coding region of mRNA for translation of ColE2 Rep protein
    • Nagase, T., Nishio, S. and Itoh, T. (2008) Essential elements in the coding region of mRNA for translation of ColE2 Rep protein. Plasmid, 59, 36-44.
    • (2008) Plasmid , vol.59 , pp. 36-44
    • Nagase, T.1    Nishio, S.2    Itoh, T.3
  • 54
    • 0025324535 scopus 로고
    • Identification and characterization of an enhancer in the coding region of the genome of human immunodeficiency virus type 1
    • Verdin, E., Becker, N., Bex, F., Droogmans, L. and Burny, A. (1990) Identification and characterization of an enhancer in the coding region of the genome of human immunodeficiency virus type 1. Proc. Natl Acad. Sci. USA, 87, 4874-4878.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 4874-4878
    • Verdin, E.1    Becker, N.2    Bex, F.3    Droogmans, L.4    Burny, A.5
  • 55
    • 0031883264 scopus 로고    scopus 로고
    • mRNA instability elements in the human papillomavirus type 16 L2 coding region
    • Sokolowski, M., Tan, W., Jellne, M. and Schwartz, S. (1998) mRNA instability elements in the human papillomavirus type 16 L2 coding region. J. Virol., 72, 1504-1515.
    • (1998) J. Virol. , vol.72 , pp. 1504-1515
    • Sokolowski, M.1    Tan, W.2    Jellne, M.3    Schwartz, S.4
  • 56
    • 0142060844 scopus 로고    scopus 로고
    • Mutational inactivation of two distinct negative RNA elements in the human papillomavirus type 16 L2 coding region induces production of high levels of L2 in human cells
    • Oberg, D., Collier, B., Zhao, X. and Schwartz, S. (2003) Mutational inactivation of two distinct negative RNA elements in the human papillomavirus type 16 L2 coding region induces production of high levels of L2 in human cells. J. Virol., 77, 11674-11684
    • (2003) J. Virol. , vol.77 , pp. 11674-11684
    • Oberg, D.1    Collier, B.2    Zhao, X.3    Schwartz, S.4
  • 57
    • 2942659655 scopus 로고    scopus 로고
    • Characterization of regulatory elements within the coat protein (CP) coding region of Tobacco mosaic virus affecting subgenomic transcription and green fluorescent protein expression from the CP subgenomic RNA promoter
    • Man, M. and Epel, B.L. (2004) Characterization of regulatory elements within the coat protein (CP) coding region of Tobacco mosaic virus affecting subgenomic transcription and green fluorescent protein expression from the CP subgenomic RNA promoter. J. Gen. Virol., 85, 1727-1738.
    • (2004) J. Gen. Virol. , vol.85 , pp. 1727-1738
    • Man, M.1    Epel, B.L.2
  • 58
    • 11144294108 scopus 로고    scopus 로고
    • A transcriptional regulatory element in the coding sequence of the human Bcl-2 gene
    • Lang, G., Gombert, W.M. and Gould, H.J. (2005) A transcriptional regulatory element in the coding sequence of the human Bcl-2 gene. Immunology, 114, 25-36.
    • (2005) Immunology , vol.114 , pp. 25-36
    • Lang, G.1    Gombert, W.M.2    Gould, H.J.3
  • 59
    • 48249144806 scopus 로고    scopus 로고
    • A transcriptional enhancer from the coding region of ADAMTS5
    • Barthel, K.K. and Liu, X. (2008) A transcriptional enhancer from the coding region of ADAMTS5. PLoS ONE, 3, e2184.
    • (2008) PLoS ONE , vol.3
    • Barthel, K.K.1    Liu, X.2
  • 60
    • 53649103358 scopus 로고    scopus 로고
    • Screening reveals conserved and nonconserved transcriptional regulatory elements including an E3/E4 allele-dependent APOE coding region enhancer
    • Chen, H.P., Lin, A., Bloom, J.S., Khan, A.H., Park, C.C. and Smith, D.J. (2008) Screening reveals conserved and nonconserved transcriptional regulatory elements including an E3/E4 allele-dependent APOE coding region enhancer. Genomics, 92, 292-300.
    • (2008) Genomics , vol.92 , pp. 292-300
    • Chen, H.P.1    Lin, A.2    Bloom, J.S.3    Khan, A.H.4    Park, C.C.5    Smith, D.J.6
  • 61
    • 54449097149 scopus 로고    scopus 로고
    • A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence
    • Forman, J.J., Legesse-Miller, A. and Coller, H.A. (2008) A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc. Natl Acad. Sci. USA, 105, 14879-14884.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 14879-14884
    • Forman, J.J.1    Legesse-Miller, A.2    Coller, H.A.3
  • 63
    • 37449026431 scopus 로고    scopus 로고
    • Comprehensive characterization of the cis-regulatory code responsible for the spatio-temporal expression of olSix3 2 in the developing medaka forebrain
    • Conte, I. and Bovolenta, P. (2007) Comprehensive characterization of the cis-regulatory code responsible for the spatio-temporal expression of olSix3.2 in the developing medaka forebrain. Genome Biol., 8, R137.
    • (2007) Genome Biol. , vol.8
    • Conte, I.1    Bovolenta, P.2


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