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A general definition and nomenclature for alternative splicing events
Guigó Serra, Roderic; Sammeth, Michael; Foissac, Sylvain
Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells isone of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) is a key phenomenoncontributing to the production of different mature transcripts from the same primary RNA sequence. As a plethora ofdifferent transcript forms is available in databases, a first step to uncover the biology that drives AS is to identify thedifferent types of reflected splicing variation. In this work, we present a general definition of the AS event along with anotation system that involves the relative positions of the splice sites. This nomenclature univocally and dynamically assignsa specific ‘‘AS code’’ to every possible pattern of splicing variation. On the basis of this definition and the correspondingcodes, we have developed a computational tool (AStalavista) that automatically characterizes the complete landscape of ASevents in a given transcript annotation of a genome, thus providing a platform to investigate the transcriptome diversityacross genes, chromosomes, and species. Our analysis reveals that a substantial part—in human more than a quarter—ofthe observed splicing variations are ignored in common classification pipelines. We have used AStalavista to investigate andto compare the AS landscape of different reference annotation sets in human and in other metazoan species and found thatproportions of AS events change substantially depending on the annotation protocol, species-specific attributes, andcoding constraints acting on the transcripts. The AStalavista system therefore provides a general framework to conductspecific studies investigating the occurrence, impact, and regulation of AS.
This work has been funded by a DAAD (German Academic Exchange Service) postdoctoral fellowship to MS. Further support has been provided by grants from the NHGRI Encode project, the European Union ATD project, and the Spanish Plan Nacional de I+D.
2013-07-02
Factors de transcripció
Cèl·lules eucariotes -- Aspectes genètics
Animals
Bees
Caenorhabditis elegans
Cattle
Chickens
Classification
Cluster analysis
Databases
Genetic
Dogs
Drosophila melanogaster
Gene expression profiling
Genomics
Humans
Mice
Pan troglodytes
Rats
RNA Splice Sites
Sequence analysis
RNA
Species specificity
Terminology as topic
Zebrafish
Xenopus
(c) 2008 Sammeth et al. 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 credited.
http://creativecommons.org/licenses/by/2.5/
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info:eu-repo/semantics/publishedVersion
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