Comparative analysis of information contents relevant to recognition of introns in many species

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Iwata, Hiroaki ^a   Gotoh, Osamu ^a,b  

^a KYOTO UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; OLIGOMER;

ALGORITHM; ARTICLE; CHORDATA; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA BINDING MOTIF; EUKARYOTE; FUNGUS; GENE CLUSTER; GENETIC CODE; HUMAN; INTRON; MAMMAL; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PLANT; PREDICTION; PROTIST LIFE CYCLE STAGE; RNA SPLICING; SIGNAL TRANSDUCTION; ANIMAL; DNA BASE COMPOSITION; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY;

EUKARYOTA; MAMMALIA;

ANIMALS; BASE COMPOSITION; EVOLUTION, MOLECULAR; HUMANS; INTRONS; PHYLOGENY; RNA SPLICING;

EID: 78651503221     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-45     Document Type: Article

References (55)

1. Black DL. Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 2003, 72:291-336. 10.1146/annurev.biochem.72.121801.161720, 12626338.
2. Douris V, Telford MJ, Averof M. Evidence for multiple independent origins of trans-splicing in Metazoa. Mol Biol Evol 2009, 27:684-693. 10.1093/molbev/msp286, 19942614.
3. Ast G. How did alternative splicing evolve?. Nat Rev Genet 2004, 5:773-782. 10.1038/nrg1451, 15510168.
4. Berglund JA, Chua K, Abovich N, Reed R, Rosbash M. The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC. Cell 1997, 89:781-787. 10.1016/S0092-8674(00)80261-5, 9182766.
5. Lim LP, Burge CB. A computational analysis of sequence features involved in recognition of short introns. Proc Natl Acad Sci USA 2001, 98:11193-11198. 10.1073/pnas.201407298, 58706, 11572975.
6. Kaufer NF, Potashkin J. Analysis of the splicing machinery in fission yeast: a comparison with budding yeast and mammals. Nucleic Acids Res 2000, 28:3003-3010. 10.1093/nar/28.16.3003, 108416, 10931913.
7. Anantharaman V, Koonin EV, Aravind L. Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res 2002, 30:1427-1464. 10.1093/nar/30.7.1427, 101826, 11917006.
8. Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol 2004, 5:R7. 10.1186/gb-2004-5-2-r7, 395751, 14759257.
9. Collins L, Penny D. Complex spliceosomal organization ancestral to extant eukaryotes. Mol Biol Evol 2005, 22:1053-1066. 10.1093/molbev/msi091, 15659557.
10. Burge CB, Padgett RA, Sharp PA. Evolutionary fates and origins of U12-type introns. Mol Cell 1998, 2:773-785. 10.1016/S1097-2765(00)80292-0, 9885565.
11. Sheth N, Roca X, Hastings ML, Roeder T, Krainer AR, Sachidanandam R. Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res 2006, 34:3955-3967. 10.1093/nar/gkl556, 1557818, 16914448.
12. Schwartz SH, Silva J, Burstein D, Pupko T, Eyras E, Ast G. Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res 2008, 18:88-103. 10.1101/gr.6818908, 2134773, 18032728.
13. Wiebauer K, Herrero JJ, Filipowicz W. Nuclear pre-mRNA processing in plants: distinct modes of 3'-splice-site selection in plants and animals. Mol Cell Biol 1988, 8:2042-2051. 363383, 3386632.
14. Goodall GJ, Filipowicz W. The AU-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing. Cell 1989, 58:473-483. 10.1016/0092-8674(89)90428-5, 2758463.
15. Beggs JD, van den Berg J, van Ooyen A, Weissmann C. Abnormal expression of chromosomal rabbit beta-globin gene in Saccharomyces cerevisiae. Nature 1980, 283:835-840. 10.1038/283835a0, 6987524.
16. Langford CJ, Gallwitz D. Evidence for an intron-contained sequence required for the splicing of yeast RNA polymerase II transcripts. Cell 1983, 33:519-527. 10.1016/0092-8674(83)90433-6, 6305513.
17. Banerjee H, Rahn A, Gawande B, Guth S, Valcarcel J, Singh R. The conserved RNA recognition motif 3 of U2 snRNA auxiliary factor (U2AF 65) is essential in vivo but dispensable for activity in vitro. RNA 2004, 10:240-253. 10.1261/rna.5153204, 1370536, 14730023.
18. Izquierdo JM, Valcarcel J. A simple principle to explain the evolution of pre-mRNA splicing. Genes Dev 2006, 20:1679-1684. 10.1101/gad.1449106, 16818600.
19. Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268:78-94. 10.1006/jmbi.1997.0951, 9149143.
20. Salamov AA, Solovyev VV. Ab initio gene finding in Drosophila genomic DNA. Genome Res 2000, 10:516-522. 10.1101/gr.10.4.516, 310882, 10779491.
21. Borodovsky M, McIninch J. GENMARK: parallel gene recognition for both DNA strands. Comp Chem 1993, 17:123-133.
22. Kol G, Lev-Maor G, Ast G. Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation. Hum Mol Genet 2005, 14:1559-1568. 10.1093/hmg/ddi164, 15857856.
23. Marz M, Kirsten T, Stadler PF. Evolution of spliceosomal snRNA genes in metazoan animals. J Mol Evol 2008, 67:594-607. 10.1007/s00239-008-9149-6, 19030770.
24. Vinogradov AE. Intron-genome size relationship on a large evolutionary scale. J Mol Evol 1999, 49:376-384. 10.1007/PL00006561, 10473779.
25. Lynch M, Conery JS. The origins of genome complexity. Science 2003, 302:1401-1404. 10.1126/science.1089370, 14631042.
26. Gregory TR. Synergy between sequence and size in large-scale genomics. Nat Rev Genet 2005, 6:699-708. 10.1038/nrg1674, 16151375.
27. Gotoh O. Direct mapping and alignment of protein sequences onto genomic sequence. Bioinformatics 2008b, 24:2438-2444.
28. Sharp PA, Burge CB. Classification of introns: U2-type or U12-type. Cell 1997, 91:875-879. 10.1016/S0092-8674(00)80479-1, 9428511.
29. Patel AA, Steitz JA. Splicing double: insights from the second spliceosome. Nat Rev Mol Cell Biol 2003, 4:960-970. 10.1038/nrm1259, 14685174.
30. Chen M, Manley JL. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol 2009, 10:741-754. 2958924, 19773805.
31. Fox-Walsh KL, Dou Y, Lam BJ, Hung SP, Baldi PF, Hertel KJ. The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc Natl Acad Sci USA 2005, 102:16176-16181. 10.1073/pnas.0508489102, 1283478, 16260721.
32. Gotoh O. A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence. Nucleic Acids Res 2008a, 36:2630-2638.
33. Lu DV, Brown RH, Arumugam M, Brent MR. Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner. Bioinformatics 2009, 25:1587-1593. 10.1093/bioinformatics/btp273, 2732315, 19414532.
34. Kapustin Y, Souvorov A, Tatusova T, Lipman D. Splign: algorithms for computing spliced alignments with identification of paralogs. Biol Direct 2008, 3:20. 10.1186/1745-6150-3-20, 2440734, 18495041.
35. Slater GS, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 2005, 6:31. 10.1186/1471-2105-6-31, 553969, 15713233.
36. Davila Lopez M, Rosenblad MA, Samuelsson T. Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components. Nucleic Acids Res 2008, 36:3001-3010. 10.1093/nar/gkn142, 2396436, 18390578.
37. Levine A, Durbin R. A computational scan for U12-dependent introns in the human genome sequence. Nucleic Acids Res 2001, 29:4006-4013. 10.1093/nar/29.1.300, 60238, 11574683.
38. Zhu W, Brendel V. Identification, characterization and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome. Nucleic Acids Res 2003, 31:4561-4572. 10.1093/nar/gkg492, 169882, 12888517.
39. Guthrie C, Patterson B. Spliceosomal snRNAs. Annu Rev Genet 1988, 22:387-419. 10.1146/annurev.ge.22.120188.002131, 2977088.
40. Salzberg SL. A method for identifying splice sites and translational start sites in eukaryotic mRNA. Comput Appl Biosci 1997, 13:365-376.
41. Brendel V, Kleffe J. Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA. Nucleic Acids Res 1998, 26:4748-4757. 10.1093/nar/26.20.4748, 147908, 9753745.
42. Majoros WH. Methods for Computational Gene Prediction 2007, New York: Cambridge University Press.
43. Pontius JU, Wagner L, Schuler GD. UniGene: a unified view of the transcriptome 2003, Bethesda, MD: National Center for Biotechnology Information.
44. Harris NL, Senapathy P. Distribution and consensus of branch point signals in eukaryotic genes: a computerized statistical analysis. Nucleic Acids Res 1990, 18:3015-3019. 10.1093/nar/18.10.3015, 330832, 2349097.
45. Kullback S. Information Theory and Statistics. Wiley, New York 1959,
46. Kullback S, Leibler RA. On information and sufficiency. Ann Math Statist 1951, 22:79-86.
47. Sneath PHA, Sokal RR. Numerical taxonomy. Freeman San Francisco 1973,
48. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6 [computer program]. 2004,
49. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007, 35:7188-7196. 10.1093/nar/gkm864, 2175337, 17947321.
50. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A. Rfam: updates to the RNA families database. Nucleic Acids Res 2009, 37:D136-140. 10.1093/nar/gkn766, 2686503, 18953034.
51. Katoh K, Toh H. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics 2008, 9:212. 10.1186/1471-2105-9-212, 2387179, 18439255.
52. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002, 30:3059-3066. 10.1093/nar/gkf436, 135756, 12136088.
53. Puigbo P, Garcia-Vallve S, McInerney JO. TOPD/FMTS: a new software to compare phylogenetic trees. Bioinformatics 2007, 23:1556-1558. 10.1093/bioinformatics/btm135, 17459965.
54. MacQueen J. Some methods for classification and analysis of multivariate observations. Proc 5th Berkeley Symposium 1967, 281-297.
55. Lloyd SP. Least square quantization in PCM. Bell Telephone Laboratories Paper, Murray Hill 1957,