IntSplice: Prediction of the splicing consequences of intronic single-nucleotide variations in the human genome

Journal of Human Genetics

Volumn 61, Issue 7, 2016, Pages 633-640

  Shibata, Akihide ^a   Okuno, Tatsuya ^a   Rahman, Mohammad Alinoor ^a   Azuma, Yoshiteru ^a   Takeda, Jun Ichi ^a   Masuda, Akio ^a   Selcen, Duygu ^b   Engel, Andrew G ^b   Ohno, Kinji ^a  

^a NAGOYA UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^b MAYO CLINIC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; RNA;

ADULT; ALTERNATIVE RNA SPLICING; ARTICLE; CASE REPORT; CONGENITAL MYASTHENIC SYNDROME; EFFECT SIZE; GENE DOSAGE; GENE FREQUENCY; GENE MUTATION; HELA CELL LINE; HUMAN; HUMAN CELL; HUMAN GENOME; HUMAN TISSUE; MALE; PREDICTION; REVERSE TRANSCRIPTION; RNA SEQUENCE; SINGLE NUCLEOTIDE VARIATION; SUPPORT VECTOR MACHINE; ANTIBODY SPECIFICITY; BIOLOGY; CELL LINE; GENE EXPRESSION; GENETICS; INTRON; MUTATION; MYASTHENIC SYNDROMES, CONGENITAL; NUCLEIC ACID DATABASE; PROCEDURES; RNA SPLICING; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; SOFTWARE; WEB BROWSER;

ADULT; CELL LINE; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; GENE EXPRESSION; GENOME, HUMAN; HUMANS; INTRONS; MUTATION; MYASTHENIC SYNDROMES, CONGENITAL; ORGAN SPECIFICITY; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA SPLICING; SENSITIVITY AND SPECIFICITY; SOFTWARE; SUPPORT VECTOR MACHINE; WEB BROWSER;

EID: 84979633655     PISSN: 14345161     EISSN: 1435232X     Source Type: Journal    
DOI: 10.1038/jhg.2016.23     Document Type: Article

References (43)

1. Black, D. L. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72, 291-336 (2003
2. Jurica, M. S., & Moore, M. J. Pre-mRNA splicing: awash in a sea of proteins. Mol. Cell. 12, 5-14 (2003
3. Reed, R. Initial splice-site recognition and pairing during pre-mRNA splicing. Curr. Opin. Genet. Dev. 6, 215-220 (1996
4. Gooding, C., Edge, C., Lorenz, M., Coelho, M. B., Winters, M., Kaminski, C. F., et al. MBNL1 and PTB cooperate to repress splicing of Tpm1 exon 3. Nucleic Acids Res. 41, 4765-4782 (2013
5. Krawczak, M., Thomas, N. S., Hundrieser, B., Mort, M., Wittig, M., Hampe, J., et al. Single base-pair substitutions in exon-intron junctions of human genes: nature, distribution, and consequences for mRNA splicing. Hum. Mutat. 28, 150-158 (2007
6. Sterne-Weiler, T., Howard, J., Mort, M., Cooper, D. N., & Sanford, J. R. Loss of exon identity is a common mechanism of human inherited disease. Genome Res. 21, 1563-1571 (2011
7. Cartegni, L., Wang, J., Zhu, Z., Zhang, M. Q., & Krainer, A. R. ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Res. 31, 3568-3571 (2003
8. Goren, A., Ram, O., Amit, M., Keren, H., Lev-Maor, G., Vig, I., et al. Comparative analysis identifies exonic splicing regulatory sequences-The complex definition of enhancers and silencers. Mol. Cell 22, 769-781 (2006
9. Wang, Z., Rolish, M. E., Yeo, G., Tung, V., Mawson, M., & Burge, C. B. Systematic identification and analysis of exonic splicing silencers. Cell 119, 831-845 (2004
10. Zhang, Z., & Krainer, A. R. Involvement of SR proteins in mRNA surveillance. Mol. Cell 16, 597-607 (2004
11. Zhang, X. H., Kangsamaksin, T., Chao, M. S., Banerjee, J. K., & Chasin, L. A. Exon inclusion is dependent on predictable exonic splicing enhancers. Mol. Cell. Biol. 25, 7323-7332 (2005
12. Fairbrother, W. G., Yeh, R. F., Sharp, P. A., & Burge, C. B. Predictive identification of exonic splicing enhancers in human genes. Science 297, 1007-1013 (2002
13. Desmet, F. O., Hamroun, D., Lalande, M., Collod-Beroud, G., Claustres, M.& Beroud, C. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res. 37, e67 (2009
14. Piva, F., Giulietti, M., Nocchi, L., & Principato, G. SpliceAid: a database of experimental RNA target motifs bound by splicing proteins in humans. Bioinformatics 25, 1211-1213 (2009
15. Piva, F., Giulietti, M., Burini, A. B., & Principato, G. SpliceAid 2: a database of human splicing factors expression data and RNA target motifs. Hum. Mutat. 33, 81-85 (2012
16. Divina, P., Kvitkovicova, A., Buratti, E., & Vorechovsky, I. Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping.. Eur. J. Hum. Genet. 17, 759-765 (2009
17. Lim, K. H., Ferraris, L., Filloux, M. E., Raphael, B. J., & Fairbrother, W. G. Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes. Proc. Natl. Acad. Sci. USA 108, 11093-11098 (2011
18. Chang, T. H., Huang, H. Y., Hsu, J. B., Weng, S. L., Horng, J. T., & Huang, H. D. An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. BMC Bioinformatics 14 (), S4 (2013
19. Shapiro, M. B., & Senapathy, P. RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res. 15, 7155-7174 (1987
20. Yeo, G., & Burge, C. B. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J. Comput. Biol. 11, 377-394 (2004
21. Gao, K., Masuda, A., Matsuura, T., & Ohno, K. Human branch point consensus sequence is yUnAy. Nucleic Acids Res. 36, 2257-2267 (2008
22. Corvelo, A., Hallegger, M., Smith, C. W., & Eyras, E. Genome-wide association between branch point properties and alternative splicing. PLoS Comput. Biol. 6, e1001016 (2010
23. Taggart, A. J., DeSimone, A. M., Shih, J. S., Filloux, M. E., & Fairbrother, W. G. Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo. Nat. Struct. Mol. Biol. 19, 719-721 (2012
24. Bitton, D. A., Rallis, C., Jeffares, D. C., Smith, G. C., Chen, Y. Y., Codlin, S., et al. LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq. Genome Res. 24, 1169-1179 (2014
25. Fu, Y., Masuda, A., Ito, M., Shinmi, J., & Ohno, K. AG-dependent 3'-splice sites are predisposed to aberrant splicing due to a mutation at the first nucleotide of an exon. Nucleic Acids Res. 39, 4396-4404 (2011
26. Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476 (2008
27. Pan, Q., Shai, O., Lee, L. J., Frey, B. J., & Blencowe, B. J. Deep surveying of alternative splicing complexity in the human transcriptome by high-Throughput sequencing. Nat. Genet. 40, 1413-1415 (2008
28. Trapnell, C., Pachter, L., & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009
29. Katz, Y., Wang, E. T., Airoldi, E. M., & Burge, C. B. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods 7, 1009-1015 (2010
30. Chang, C. C., & Lin, C. J. LIBSVM: A Library for Support Vector Machines. ACM T Intel Syst Tec. 2, Article 27 (2011
31. Rahman, M. A., Masuda, A., Ohe, K., Ito, M., Hutchinson, D. O., Mayeda, A., et al. HnRNP L and hnRNP LL antagonistically modulate PTB-mediated splicing suppression of CHRNA1 pre-mRNA. Sci. Rep. 3, 2931 (2013
32. Ohno, K., Anlar, B., Ozdirim, E., Brengman, J. M., DeBleecker, J. L., & Engel, A. G. Myasthenic syndromes in Turkish kinships due to mutations in the acetylcholine receptor. Ann. Neurol. 44, 234-241 (1998
33. Das, R., Zhou, Z., & Reed, R. Functional association of U2 snRNP with the ATP-independent spliceosomal complex E. Mol. Cell 5, 779-787 (2000
34. Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415 (2003
35. Gahura, O., Hammann, C., Valentova, A., Puta, F., & Folk, P. Secondary structure is required for 3' splice site recognition in yeast. Nucleic Acids Res. 39, 9759-9767 (2011
36. Plass, M., Codony-Servat, C., Ferreira, P. G., Vilardell, J., & Eyras, E. RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae. RNA 18, 1103-1115 (2012
37. Pervouchine, D. D., Khrameeva, E. E., Pichugina, M. Y., Nikolaienko, O. V., Gelfand, M. S., Rubtsov, P. M., et al. Evidence for widespread association of mammalian splicing and conserved long-range RNA structures. RNA 18, 1-15 (2012
38. Ohno, K., Engel, A. G., Shen, X. M., Selcen, D., Brengman, J., Harper, C. M., et al. Rapsyn mutations in humans cause endplate acetylcholine-receptor deficiency and myasthenic syndrome. Am J Hum Genet. 70, 875-885 (2002
39. Milone, M., Shen, X. M., Selcen, D., Ohno, K., Brengman, J., Iannaccone, S. T., et al. Myasthenic syndrome due to defects in rapsyn: clinical and molecular findings in 39 patients. Neurology 73, 228-235 (2009
40. Kornblihtt, A. R., Schor, I. E., Allo, M., Dujardin, G., Petrillo, E., & Munoz, M. J. Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat. Rev. Mol. Cell Biol. 14, 153-165 (2013
41. Giulietti, M., Piva, F., D'Antonio, M., D'Onorio De, M. P., Paoletti, D., Castrignano, T., et al. SpliceAid-F: a database of human splicing factors and their RNA-binding sites. Nucleic Acids Res. 41, D125-D131 (2013
42. Rahman, M. A., Nasrin, F., Masuda, A., & Ohno, K. Decoding abnormal splicing code in human diseases. J. Invest. Genomics 2, 00016 (2015
43. Rieder, L. E., & Reenan, R. A. The intricate relationship between RNA structure, editing, and splicing. Semin. Cell Dev. Biol. 23, 281-288 (2012