Cargando…

A General Definition and Nomenclature for Alternative Splicing Events

Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells is one of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) is a key phenomenon contributing to the production of different mature transcr...

Descripción completa

Detalles Bibliográficos
Autores principales: Sammeth, Michael, Foissac, Sylvain, Guigó, Roderic
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2467475/
https://www.ncbi.nlm.nih.gov/pubmed/18688268
http://dx.doi.org/10.1371/journal.pcbi.1000147
_version_ 1782157461486043136
author Sammeth, Michael
Foissac, Sylvain
Guigó, Roderic
author_facet Sammeth, Michael
Foissac, Sylvain
Guigó, Roderic
author_sort Sammeth, Michael
collection PubMed
description Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells is one of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) is a key phenomenon contributing to the production of different mature transcripts from the same primary RNA sequence. As a plethora of different transcript forms is available in databases, a first step to uncover the biology that drives AS is to identify the different types of reflected splicing variation. In this work, we present a general definition of the AS event along with a notation system that involves the relative positions of the splice sites. This nomenclature univocally and dynamically assigns a specific “AS code” to every possible pattern of splicing variation. On the basis of this definition and the corresponding codes, we have developed a computational tool (AStalavista) that automatically characterizes the complete landscape of AS events in a given transcript annotation of a genome, thus providing a platform to investigate the transcriptome diversity across genes, chromosomes, and species. Our analysis reveals that a substantial part—in human more than a quarter—of the observed splicing variations are ignored in common classification pipelines. We have used AStalavista to investigate and to compare the AS landscape of different reference annotation sets in human and in other metazoan species and found that proportions of AS events change substantially depending on the annotation protocol, species-specific attributes, and coding constraints acting on the transcripts. The AStalavista system therefore provides a general framework to conduct specific studies investigating the occurrence, impact, and regulation of AS.
format Text
id pubmed-2467475
institution National Center for Biotechnology Information
language English
publishDate 2008
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-24674752008-08-08 A General Definition and Nomenclature for Alternative Splicing Events Sammeth, Michael Foissac, Sylvain Guigó, Roderic PLoS Comput Biol Research Article Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells is one of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) is a key phenomenon contributing to the production of different mature transcripts from the same primary RNA sequence. As a plethora of different transcript forms is available in databases, a first step to uncover the biology that drives AS is to identify the different types of reflected splicing variation. In this work, we present a general definition of the AS event along with a notation system that involves the relative positions of the splice sites. This nomenclature univocally and dynamically assigns a specific “AS code” to every possible pattern of splicing variation. On the basis of this definition and the corresponding codes, we have developed a computational tool (AStalavista) that automatically characterizes the complete landscape of AS events in a given transcript annotation of a genome, thus providing a platform to investigate the transcriptome diversity across genes, chromosomes, and species. Our analysis reveals that a substantial part—in human more than a quarter—of the observed splicing variations are ignored in common classification pipelines. We have used AStalavista to investigate and to compare the AS landscape of different reference annotation sets in human and in other metazoan species and found that proportions of AS events change substantially depending on the annotation protocol, species-specific attributes, and coding constraints acting on the transcripts. The AStalavista system therefore provides a general framework to conduct specific studies investigating the occurrence, impact, and regulation of AS. Public Library of Science 2008-08-08 /pmc/articles/PMC2467475/ /pubmed/18688268 http://dx.doi.org/10.1371/journal.pcbi.1000147 Text en Sammeth 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
Sammeth, Michael
Foissac, Sylvain
Guigó, Roderic
A General Definition and Nomenclature for Alternative Splicing Events
title A General Definition and Nomenclature for Alternative Splicing Events
title_full A General Definition and Nomenclature for Alternative Splicing Events
title_fullStr A General Definition and Nomenclature for Alternative Splicing Events
title_full_unstemmed A General Definition and Nomenclature for Alternative Splicing Events
title_short A General Definition and Nomenclature for Alternative Splicing Events
title_sort general definition and nomenclature for alternative splicing events
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2467475/
https://www.ncbi.nlm.nih.gov/pubmed/18688268
http://dx.doi.org/10.1371/journal.pcbi.1000147
work_keys_str_mv AT sammethmichael ageneraldefinitionandnomenclatureforalternativesplicingevents
AT foissacsylvain ageneraldefinitionandnomenclatureforalternativesplicingevents
AT guigoroderic ageneraldefinitionandnomenclatureforalternativesplicingevents
AT sammethmichael generaldefinitionandnomenclatureforalternativesplicingevents
AT foissacsylvain generaldefinitionandnomenclatureforalternativesplicingevents
AT guigoroderic generaldefinitionandnomenclatureforalternativesplicingevents