Cross-kingdom patterns of alternative splicing and splice recognition
Background: 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 ca...
| Main Authors: | , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
BioMed Central Ltd
2010
|
| Online Access: | http://hdl.handle.net/1721.1/58763 |
| _version_ | 1811085641698508800 |
|---|---|
| author | McGuire, Abigail Manson Pearson, Matthew D. Neafsey, Daniel E. Galagan, James E. |
| author2 | Broad Institute of MIT and Harvard |
| author_facet | Broad Institute of MIT and Harvard McGuire, Abigail Manson Pearson, Matthew D. Neafsey, Daniel E. Galagan, James E. |
| author_sort | McGuire, Abigail Manson |
| collection | MIT |
| description | Background: 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. Results: 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. Conclusion 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. |
| first_indexed | 2024-09-23T13:12:55Z |
| format | Article |
| id | mit-1721.1/58763 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T13:12:55Z |
| publishDate | 2010 |
| publisher | BioMed Central Ltd |
| record_format | dspace |
| spelling | mit-1721.1/587632024-07-19T20:03:00Z Cross-kingdom patterns of alternative splicing and splice recognition McGuire, Abigail Manson Pearson, Matthew D. Neafsey, Daniel E. Galagan, James E. Broad Institute of MIT and Harvard Neafsey, Daniel E. McGuire, Abigail Manson Pearson, Matthew D. Galagan, James E. Background: 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. Results: 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. Conclusion 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. National Science Foundation (U.S.) (Comparative Fungal Genomics grant MCB-0450812) National Institute of Allergy and Infectious Diseases (U.S.) (Contract for Microbial Gene Centers HHSN26620040001C) 2010-09-29T18:48:10Z 2010-09-29T18:48:10Z 2008-03 2007-10 2010-09-03T16:22:39Z Article http://purl.org/eprint/type/JournalArticle 1474-760X 1474-7596 http://hdl.handle.net/1721.1/58763 Genome Biology. 2008 Mar 05;9(3):R50 18321378 en http://dx.doi.org/10.1186/gb-2008-9-3-r50 Genome Biology Creative Commons Attribution http://creativecommons.org/licenses/by/2.0 McGuire et al.; licensee BioMed Central Ltd. application/pdf BioMed Central Ltd BioMed Central Ltd |
| spellingShingle | McGuire, Abigail Manson Pearson, Matthew D. Neafsey, Daniel E. Galagan, James E. Cross-kingdom patterns of alternative splicing and splice recognition |
| title | Cross-kingdom patterns of alternative splicing and splice recognition |
| title_full | Cross-kingdom patterns of alternative splicing and splice recognition |
| title_fullStr | Cross-kingdom patterns of alternative splicing and splice recognition |
| title_full_unstemmed | Cross-kingdom patterns of alternative splicing and splice recognition |
| title_short | Cross-kingdom patterns of alternative splicing and splice recognition |
| title_sort | cross kingdom patterns of alternative splicing and splice recognition |
| url | http://hdl.handle.net/1721.1/58763 |
| work_keys_str_mv | AT mcguireabigailmanson crosskingdompatternsofalternativesplicingandsplicerecognition AT pearsonmatthewd crosskingdompatternsofalternativesplicingandsplicerecognition AT neafseydaniele crosskingdompatternsofalternativesplicingandsplicerecognition AT galaganjamese crosskingdompatternsofalternativesplicingandsplicerecognition |