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Volumn 25, Issue 11, 2008, Pages 2431-2437

Alternative splicing and the steady-state ratios of mRNA isoforms generated by it are under strong stabilizing selection in Caenorhabditis elegans

Author keywords

Alternative splicing; Evolution; Microarrays

Indexed keywords

CIS ACTING ELEMENT; MESSENGER RNA; TRANS ACTING FACTOR;

EID: 54149093760     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn181     Document Type: Article
Times cited : (9)

References (40)
  • 1
    • 40149099212 scopus 로고    scopus 로고
    • Barberan-Soler S, Zahler AM. 2008. Alternative splicing regulation during C. elegans development: splicing factors as regulated targets. PLoS Genet. 4:e1000001.
    • Barberan-Soler S, Zahler AM. 2008. Alternative splicing regulation during C. elegans development: splicing factors as regulated targets. PLoS Genet. 4:e1000001.
  • 2
    • 38549152361 scopus 로고    scopus 로고
    • Natural variation and population genetics of Caenorhabditis elegans
    • Barriere A, Felix MA. 2005. Natural variation and population genetics of Caenorhabditis elegans. WormBook. 1-19.
    • (2005) WormBook , pp. 1-19
    • Barriere, A.1    Felix, M.A.2
  • 3
    • 33745899048 scopus 로고    scopus 로고
    • Alternative splicing: New insights from global analyses
    • Blencowe BJ. 2006. Alternative splicing: new insights from global analyses. Cell. 126:37-47.
    • (2006) Cell , vol.126 , pp. 37-47
    • Blencowe, B.J.1
  • 4
    • 0032940802 scopus 로고    scopus 로고
    • smg-7 is required for mRNA surveillance in Caenorhabditis elegans
    • Cali BM, Kuchma SL, Latham J, Anderson P. 1999. smg-7 is required for mRNA surveillance in Caenorhabditis elegans. Genetics. 151:605-616.
    • (1999) Genetics , vol.151 , pp. 605-616
    • Cali, B.M.1    Kuchma, S.L.2    Latham, J.3    Anderson, P.4
  • 5
    • 0028345019 scopus 로고
    • Imprecise excision of the Caenorhabditis elegans transposon Tc1 creates functional 5′ splice sites
    • Carr B, Anderson P. 1994. Imprecise excision of the Caenorhabditis elegans transposon Tc1 creates functional 5′ splice sites. Mol Cell Biol. 14:3426-3433.
    • (1994) Mol Cell Biol , vol.14 , pp. 3426-3433
    • Carr, B.1    Anderson, P.2
  • 6
    • 3943059570 scopus 로고    scopus 로고
    • High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome
    • Denver DR, Morris K, Lynch M, Thomas WK. 2004. High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature. 430:679-682.
    • (2004) Nature , vol.430 , pp. 679-682
    • Denver, D.R.1    Morris, K.2    Lynch, M.3    Thomas, W.K.4
  • 7
    • 18144405733 scopus 로고    scopus 로고
    • The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans
    • Denver DR, Morris K, Streelman JT, Kim SK, Lynch M, Thomas WK. 2005. The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nat Genet. 37:544-548.
    • (2005) Nat Genet , vol.37 , pp. 544-548
    • Denver, D.R.1    Morris, K.2    Streelman, J.T.3    Kim, S.K.4    Lynch, M.5    Thomas, W.K.6
  • 8
    • 0037360525 scopus 로고    scopus 로고
    • Phylogenetics in Caenorhabditis elegans: An analysis of divergence and outcrossing
    • Denver DR, Morris K, Thomas WK. 2003. Phylogenetics in Caenorhabditis elegans: an analysis of divergence and outcrossing. Mol Biol Evol. 20:393-400.
    • (2003) Mol Biol Evol , vol.20 , pp. 393-400
    • Denver, D.R.1    Morris, K.2    Thomas, W.K.3
  • 9
    • 0037336331 scopus 로고    scopus 로고
    • Open source software for the analysis of microarray data
    • March Suppl
    • Dudoit S, Gentleman RC, Quackenbush J. 2003. Open source software for the analysis of microarray data. Biotechniques. March (Suppl):45-51.
    • (2003) Biotechniques , pp. 45-51
    • Dudoit, S.1    Gentleman, R.C.2    Quackenbush, J.3
  • 10
    • 35248901812 scopus 로고    scopus 로고
    • Gene expression, intron density, and splice site strength in Drosophila and Caenorhabditis
    • Fahey ME, Higgins DG. 2007. Gene expression, intron density, and splice site strength in Drosophila and Caenorhabditis. J Mol Evol. 65:349-357.
    • (2007) J Mol Evol , vol.65 , pp. 349-357
    • Fahey, M.E.1    Higgins, D.G.2
  • 11
    • 0030945064 scopus 로고    scopus 로고
    • Natural variation and copulatory plug formation in Caenorhabditis elegans
    • Hodgkin J, Doniach T. 1997. Natural variation and copulatory plug formation in Caenorhabditis elegans. Genetics. 146:149-164.
    • (1997) Genetics , vol.146 , pp. 149-164
    • Hodgkin, J.1    Doniach, T.2
  • 14
    • 0033832676 scopus 로고    scopus 로고
    • Kent WJ, Zahler AM. 2000. Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res. 10:1115-1125.
    • Kent WJ, Zahler AM. 2000. Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res. 10:1115-1125.
  • 15
    • 33846681383 scopus 로고    scopus 로고
    • Different levels of alternative splicing among eukaryotes
    • Kim E, Magen A, Ast G. 2007. Different levels of alternative splicing among eukaryotes. Nucleic Acids Res. 35:125-131.
    • (2007) Nucleic Acids Res , vol.35 , pp. 125-131
    • Kim, E.1    Magen, A.2    Ast, G.3
  • 16
    • 34247330971 scopus 로고    scopus 로고
    • Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements
    • Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE. 2007. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature. 446:926-929.
    • (2007) Nature , vol.446 , pp. 926-929
    • Lareau, L.F.1    Inada, M.2    Green, R.E.3    Wengrod, J.C.4    Brenner, S.E.5
  • 17
    • 34247556560 scopus 로고    scopus 로고
    • Mechanistic insights and identification of two novel factors in the C. elegans NMD pathway
    • Longman D, Plasterk RH, Johnstone IL, Caceres JF. 2007. Mechanistic insights and identification of two novel factors in the C. elegans NMD pathway. Genes Dev. 21:1075-1085.
    • (2007) Genes Dev , vol.21 , pp. 1075-1085
    • Longman, D.1    Plasterk, R.H.2    Johnstone, I.L.3    Caceres, J.F.4
  • 18
    • 33645521073 scopus 로고    scopus 로고
    • Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes
    • Malko DB, Makeev VJ, Mironov AA, Gelfand MS. 2006. Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes. Genome Res. 16:505-509.
    • (2006) Genome Res , vol.16 , pp. 505-509
    • Malko, D.B.1    Makeev, V.J.2    Mironov, A.A.3    Gelfand, M.S.4
  • 19
    • 0035500594 scopus 로고    scopus 로고
    • Stop making nonSense: The C. elegans smg genes
    • Mango SE. 2001. Stop making nonSense: the C. elegans smg genes. Trends Genet. 17:646-653.
    • (2001) Trends Genet , vol.17 , pp. 646-653
    • Mango, S.E.1
  • 20
    • 0037062982 scopus 로고    scopus 로고
    • Alternative pre-mRNA splicing and proteome expansion in metazoans
    • Maniatis T, Tasic B. 2002. Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature. 418:236-243.
    • (2002) Nature , vol.418 , pp. 236-243
    • Maniatis, T.1    Tasic, B.2
  • 22
    • 33846015866 scopus 로고    scopus 로고
    • Functions of the nonsense-mediated mRNA decay pathway in Drosophila development
    • Metzstein MM, Krasnow MA. 2006. Functions of the nonsense-mediated mRNA decay pathway in Drosophila development. PLoS Genet. 2:e180.
    • (2006) PLoS Genet , vol.2
    • Metzstein, M.M.1    Krasnow, M.A.2
  • 23
    • 0038617729 scopus 로고    scopus 로고
    • Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss
    • Modrek B, Lee CJ. 2003. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat Genet. 34:177-180.
    • (2003) Nat Genet , vol.34 , pp. 177-180
    • Modrek, B.1    Lee, C.J.2
  • 24
    • 0030931561 scopus 로고    scopus 로고
    • smg mutants affect the expression of alternatively spliced SR protein mRNAs in Caenorhabditis elegans
    • Morrison M, Harris KS, Roth MB. 1997. smg mutants affect the expression of alternatively spliced SR protein mRNAs in Caenorhabditis elegans. Proc Natl Acad Sci USA. 94:9782-9785.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 9782-9785
    • Morrison, M.1    Harris, K.S.2    Roth, M.B.3
  • 25
    • 33947305594 scopus 로고    scopus 로고
    • Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay
    • Ni JZ, Grate L, Donohue JP, Preston C, Nobida N, O'Brien G, Shiue L, Clark TA, Blume JE, Ares M Jr. 2007. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev. 21:708-718.
    • (2007) Genes Dev , vol.21 , pp. 708-718
    • Ni, J.Z.1    Grate, L.2    Donohue, J.P.3    Preston, C.4    Nobida, N.5    O'Brien, G.6    Shiue, L.7    Clark, T.A.8    Blume, J.E.9    Ares Jr., M.10
  • 26
    • 0027382460 scopus 로고
    • mRNA surveillance by the Caenorhabditis elegans smg genes
    • Pulak R, Anderson P. 1993. mRNA surveillance by the Caenorhabditis elegans smg genes. Genes Dev. 7:1885-1897.
    • (1993) Genes Dev , vol.7 , pp. 1885-1897
    • Pulak, R.1    Anderson, P.2
  • 27
    • 29144512262 scopus 로고    scopus 로고
    • RASE: Recognition of alternatively spliced exons in C. elegans
    • Ratsch G, Sonnenburg S, Scholkopf B. 2005. RASE: recognition of alternatively spliced exons in C. elegans. Bioinformatics. 21(Suppl 1):i369-i377.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Ratsch, G.1    Sonnenburg, S.2    Scholkopf, B.3
  • 28
    • 25844435702 scopus 로고    scopus 로고
    • Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets
    • Rehwinkel J, Letunic I, Raes J, Bork P, Izaurralde E. 2005. Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. RNA. 11:1530-1544.
    • (2005) RNA , vol.11 , pp. 1530-1544
    • Rehwinkel, J.1    Letunic, I.2    Raes, J.3    Bork, P.4    Izaurralde, E.5
  • 29
    • 0037795455 scopus 로고    scopus 로고
    • Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain
    • Roy SW, Fedorov A, Gilbert W. 2003. Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain. Proc Natl Acad Sci USA. 100:7158-7162.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 7158-7162
    • Roy, S.W.1    Fedorov, A.2    Gilbert, W.3
  • 30
    • 34047225575 scopus 로고    scopus 로고
    • High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae
    • Rukov JL, Irimia M, Mork S, Lund VK, Vinther J, Arctander P. 2007. High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae. Mol Biol Evol. 24:909-917.
    • (2007) Mol Biol Evol , vol.24 , pp. 909-917
    • Rukov, J.L.1    Irimia, M.2    Mork, S.3    Lund, V.K.4    Vinther, J.5    Arctander, P.6
  • 31
    • 0029655320 scopus 로고    scopus 로고
    • Splicing removes the Caenorhabditis elegans transposon Tc1 from most mutant pre-mRNAs
    • Rushforth AM, Anderson P. 1996. Splicing removes the Caenorhabditis elegans transposon Tc1 from most mutant pre-mRNAs. Mol Cell Biol. 16:422-429.
    • (1996) Mol Cell Biol , vol.16 , pp. 422-429
    • Rushforth, A.M.1    Anderson, P.2
  • 32
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Article3
    • Smyth GK. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 3(1):Article3.
    • (2004) Stat Appl Genet Mol Biol , vol.3 , Issue.1
    • Smyth, G.K.1
  • 33
    • 0242333835 scopus 로고    scopus 로고
    • Normalization of cDNA microarray data
    • Smyth GK, Speed T. 2003. Normalization of cDNA microarray data. Methods. 31:265-273.
    • (2003) Methods , vol.31 , pp. 265-273
    • Smyth, G.K.1    Speed, T.2
  • 34
    • 0036064148 scopus 로고    scopus 로고
    • Alu-containing exons are alternatively spliced
    • Sorek R, Ast G, Graur D. 2002. Alu-containing exons are alternatively spliced. Genome Res. 12:1060-1067.
    • (2002) Genome Res , vol.12 , pp. 1060-1067
    • Sorek, R.1    Ast, G.2    Graur, D.3
  • 35
    • 1642473041 scopus 로고    scopus 로고
    • How prevalent is functional alternative splicing in the human genome?
    • Sorek R, Shamir R, Ast G. 2004. How prevalent is functional alternative splicing in the human genome? Trends Genet. 20:68-71.
    • (2004) Trends Genet , vol.20 , pp. 68-71
    • Sorek, R.1    Shamir, R.2    Ast, G.3
  • 36
    • 4243088097 scopus 로고    scopus 로고
    • Stein LD, Bao Z, Blasiar D, et al. (36 co-authors). 2003. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 1:E45.
    • Stein LD, Bao Z, Blasiar D, et al. (36 co-authors). 2003. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 1:E45.
  • 38
    • 0033831346 scopus 로고    scopus 로고
    • The fitness effects of spontaneous mutations in Caenorhabditis elegans
    • Vassilieva LL, Hook AM, Lynch M. 2000. The fitness effects of spontaneous mutations in Caenorhabditis elegans. Evol Int J Org Evol. 54:1234-1246.
    • (2000) Evol Int J Org Evol , vol.54 , pp. 1234-1246
    • Vassilieva, L.L.1    Hook, A.M.2    Lynch, M.3
  • 39
    • 42449098125 scopus 로고    scopus 로고
    • Splicing regulation: From a parts list of regulatory elements to an integrated splicing code
    • Wang Z, Burge CB. 2008. Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA. 14:802-813.
    • (2008) RNA , vol.14 , pp. 802-813
    • Wang, Z.1    Burge, C.B.2
  • 40
    • 33846511232 scopus 로고    scopus 로고
    • Modern origin of numerous alternatively spliced human introns from tandem arrays
    • Zhuo D, Madden R, Elela SA, Chabot B. 2007. Modern origin of numerous alternatively spliced human introns from tandem arrays. Proc Natl Acad Sci USA. 104:882-886.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 882-886
    • Zhuo, D.1    Madden, R.2    Elela, S.A.3    Chabot, B.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.