Comprehensive splice-site analysis using comparative genomics

Sheth, N., Roca, X., Hastings, M. L., Roeder, T., Krainer, A. R., Sachidanandam, R. (2006) Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res, 34 (14). pp. 3955-3967. ISSN 1362-4962 (Electronic)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/16914448
DOI: 10.1093/nar/gkl556

Abstract

We have collected over half a million splice sites from five species-Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana-and classified them into four subtypes: U2-type GT-AG and GC-AG and U12-type GT-AG and AT-AC. We have also found new examples of rare splice-site categories, such as U12-type introns without canonical borders, and U2-dependent AT-AC introns. The splice-site sequences and several tools to explore them are available on a public website (SpliceRack). For the U12-type introns, we find several features conserved across species, as well as a clustering of these introns on genes. Using the information content of the splice-site motifs, and the phylogenetic distance between them, we identify: (i) a higher degree of conservation in the exonic portion of the U2-type splice sites in more complex organisms; (ii) conservation of exonic nucleotides for U12-type splice sites; (iii) divergent evolution of C.elegans 3' splice sites (3'ss) and (iv) distinct evolutionary histories of 5' and 3'ss. Our study proves that the identification of broad patterns in naturally-occurring splice sites, through the analysis of genomic datasets, provides mechanistic and evolutionary insights into pre-mRNA splicing.

Item Type: Paper
Uncontrolled Keywords: Animals Arabidopsis genetics Base Sequence Caenorhabditis elegans genetics Conserved Sequence Databases Nucleic Acid Drosophila melanogaster genetics Evolution Molecular Genomics methods Humans Internet Introns Phylogeny RNA Splice Sites Software
Subjects: organism description > plant > Arabidopsis
organism description > animal > C elegans
organism description > animal > insect > Drosophila
bioinformatics > genomics and proteomics > databases > databases
organism description > animal > mammal > primates > hominids > human
organism description > animal > mammal > rodent > mouse
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > splice site
CSHL Authors:
Communities: CSHL labs > Krainer lab
Depositing User: CSHL Librarian
Date: 2006
Date Deposited: 09 Dec 2011 16:00
Last Modified: 09 Apr 2014 15:37
PMCID: PMC1557818
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22898

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