Cross-kingdom patterns of alternative splicing and splice recognition

McGuire, Abigail M.; Pearson, Matthew D.; Neafsey, Daniel E.; Galagan, James E.

doi:10.1186/gb-2008-9-3-r50

Cross-kingdom patterns of alternative splicing and splice recognition

Journal Article · Wed Mar 05 00:00:00 EST 2008 · GenomeBiology.com

DOI:https://doi.org/10.1186/gb-2008-9-3-r50· OSTI ID:1626726

McGuire, Abigail M. ^[1]; Pearson, Matthew D. ^[2]; Neafsey, Daniel E. ^[2]; Galagan, James E. ^[2]

The Broad Institute of MIT and Harvard, Cambridge, MA (United States); DOE/OSTI
The Broad Institute of MIT and Harvard, Cambridge, MA (United States)

Variations in transcript splicing can reveal how eukaryotes recognize intronic splice sites. Retained introns (RIs) commonly appear when the intron definition (ID) mechanism of splice site recognition inconsistently identifies intron-exon boundaries, and cassette exons (CEs) are often caused by variable recognition of splice junctions by the exon definition (ED) mechanism. We have performed a comprehensive survey of alternative splicing across 42 eukaryotes to gain insight into how spliceosomal introns are recognized. All eukaryotes we studied exhibit RIs, which appear more frequently than previously thought. CEs are also present in all kingdoms and most of the organisms in our analysis. We observe that the ratio of CEs to RIs varies substantially among kingdoms, while the ratio of competing 3' acceptor and competing 5' donor sites remains nearly constant. In addition, we find the ratio of CEs to RIs in each organism correlates with the length of its introns. In all 14 fungi we examined, as well as in most of the 9 protists, RIs far outnumber CEs. This differs from the trend seen in 13 multicellular animals, where CEs occur much more frequently than RIs. The six plants we analyzed exhibit intermediate proportions of CEs and RIs. Our results suggest that most extant eukaryotes are capable of recognizing splice sites via both ID and ED, although ED is most common in multicellular animals and ID predominates in fungi and most protists.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); The Broad Institute of MIT and Harvard, Cambridge, MA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626726

Journal Information:: GenomeBiology.com, Journal Name: GenomeBiology.com Journal Issue: 3 Vol. 9; ISSN 1465-6906

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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