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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...

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Autores principales: Song, Shiqin, Huang, Qianli, Guo, Jiaming, Li-Ling, Jesse, Chen, Xueping, Ma, Fei
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2009
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.
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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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