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Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data.

ABSTRACT:

Background

Alternative RNA splicing allows cells to produce multiple protein isoforms from one gene. These isoforms may have specialized functions, and may be tissue- or stage-specific. Our aim was to use computational analysis of SAGE and genomic data to predict alternatively spliced transcripts expressed in C. elegans.

Results

We predicted novel alternatively spliced variants and confirmed five of eighteen candidates selected for experimental validation by RT-PCR tests and DNA sequencing.

Conclusion

We show that SAGE data can be efficiently used to discover alternative mRNA isoforms, including those with skipped exons or retained introns. Our results also imply that C. elegans may produce a larger number of alternatively spliced transcripts than initially estimated.

SUBMITTER: Ruzanov P

PROVIDER: S-EPMC2216036 | biostudies-literature | 2007 Nov

REPOSITORIES: biostudies-literature

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Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data.

Ruzanov Peter P Jones Steven J SJ Riddle Donald L DL

BMC genomics 20071130

<h4>Background</h4>Alternative RNA splicing allows cells to produce multiple protein isoforms from one gene. These isoforms may have specialized functions, and may be tissue- or stage-specific. Our aim was to use computational analysis of SAGE and genomic data to predict alternatively spliced transcripts expressed in C. elegans.<h4>Results</h4>We predicted novel alternatively spliced variants and confirmed five of eighteen candidates selected for experimental validation by RT-PCR tests and DNA s ...[more]

PMID: 18053145

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