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Comparative Component Analysis of Exons with Different Splicing Frequencies
Transcriptional isoforms are not just random combinations of exons. What has caused exons to be differentially spliced and whether exons with different splicing frequencies are subjected to divergent regulation by potential elements or splicing signals? Beyond the conventional classification for alt...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2671145/ https://www.ncbi.nlm.nih.gov/pubmed/19404386 http://dx.doi.org/10.1371/journal.pone.0005387 |
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author | Song, Shiqin Huang, Qianli Guo, Jiaming Li-Ling, Jesse Chen, Xueping Ma, Fei |
author_facet | Song, Shiqin Huang, Qianli Guo, Jiaming Li-Ling, Jesse Chen, Xueping Ma, Fei |
author_sort | Song, Shiqin |
collection | PubMed |
description | Transcriptional isoforms are not just random combinations of exons. What has caused exons to be differentially spliced and whether exons with different splicing frequencies are subjected to divergent regulation by potential elements or splicing signals? Beyond the conventional classification for alternatively spliced exons (ASEs) and constitutively spliced exons (CSEs), we have classified exons from alternatively spliced human genes and their mouse orthologs (12,314 and 5,464, respectively) into four types based on their splicing frequencies. Analysis has indicated that different groups of exons presented divergent compositional and regulatory properties. Interestingly, with the decrease of splicing frequency, exons tend to have greater lengths, higher GC content, and contain more splicing elements and repetitive elements, which seem to imply that the splicing frequency is influenced by such factors. Comparison of non-alternatively spliced (NAS) mouse genes with alternatively spliced human orthologs also suggested that exons with lower splicing frequencies may be newly evolved ones which gained functions with splicing frequencies altered through the evolution. Our findings have revealed for the first time that certain factors may have critical influence on the splicing frequency, suggesting that exons with lower splicing frequencies may originate from old repetitive sequences, with splicing sites altered by mutation, gaining novel functions and become more frequently spliced. |
format | Text |
id | pubmed-2671145 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-26711452009-04-30 Comparative Component Analysis of Exons with Different Splicing Frequencies Song, Shiqin Huang, Qianli Guo, Jiaming Li-Ling, Jesse Chen, Xueping Ma, Fei PLoS One Research Article Transcriptional isoforms are not just random combinations of exons. What has caused exons to be differentially spliced and whether exons with different splicing frequencies are subjected to divergent regulation by potential elements or splicing signals? Beyond the conventional classification for alternatively spliced exons (ASEs) and constitutively spliced exons (CSEs), we have classified exons from alternatively spliced human genes and their mouse orthologs (12,314 and 5,464, respectively) into four types based on their splicing frequencies. Analysis has indicated that different groups of exons presented divergent compositional and regulatory properties. Interestingly, with the decrease of splicing frequency, exons tend to have greater lengths, higher GC content, and contain more splicing elements and repetitive elements, which seem to imply that the splicing frequency is influenced by such factors. Comparison of non-alternatively spliced (NAS) mouse genes with alternatively spliced human orthologs also suggested that exons with lower splicing frequencies may be newly evolved ones which gained functions with splicing frequencies altered through the evolution. Our findings have revealed for the first time that certain factors may have critical influence on the splicing frequency, suggesting that exons with lower splicing frequencies may originate from old repetitive sequences, with splicing sites altered by mutation, gaining novel functions and become more frequently spliced. Public Library of Science 2009-04-30 /pmc/articles/PMC2671145/ /pubmed/19404386 http://dx.doi.org/10.1371/journal.pone.0005387 Text en Song et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Song, Shiqin Huang, Qianli Guo, Jiaming Li-Ling, Jesse Chen, Xueping Ma, Fei Comparative Component Analysis of Exons with Different Splicing Frequencies |
title | Comparative Component Analysis of Exons with Different Splicing Frequencies |
title_full | Comparative Component Analysis of Exons with Different Splicing Frequencies |
title_fullStr | Comparative Component Analysis of Exons with Different Splicing Frequencies |
title_full_unstemmed | Comparative Component Analysis of Exons with Different Splicing Frequencies |
title_short | Comparative Component Analysis of Exons with Different Splicing Frequencies |
title_sort | comparative component analysis of exons with different splicing frequencies |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2671145/ https://www.ncbi.nlm.nih.gov/pubmed/19404386 http://dx.doi.org/10.1371/journal.pone.0005387 |
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