A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current l...

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Detalles Bibliográficos
Autores: Zhang, Runxuan, Calixto, Cristiane P. G., Márquez, Yamile, Venhuizen, Peter, Tzioutziou, Nikoleta A., Guo, Wenbin, Spensley, Mark, Entizne, Juan Carlos, Lewandowska, Dominika, Have, Sara Ten, Frey, Nicolas Freidit, Hirt, Heribert, James, Allan B., Nimmo, Hugh G., Barta, Andrea, Kalyna, Maria, Brown, John W. S.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2017
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/34992
Acceso en línea:http://hdl.handle.net/10230/34992
http://dx.doi.org/10.1093/nar/gkx267
Access Level:acceso abierto
Palabra clave:Alternative splicing
Arabidopsis
Sequence analysis
Proteomics
Descripción
Sumario:Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.

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