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

Zhang, R. et al. (2017) A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Research, 45(9), pp. 5061-5073. (doi: 10.1093/nar/gkx267) (PMID:28402429) (PMCID:PMC5435985)

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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.

Item Type:Articles
Glasgow Author(s) Enlighten ID:Nimmo, Professor Hugh and James, Dr Allan
Authors: Zhang, R., Calixto, C. P.G., Marquez, Y., Venhuizen, P., Tzioutziou, N. A., Guo, W., Spensley, M., Entizne, J. C., Lewandowska, D., ten Have, S., Frei dit Frey, N., Hirt, H., James, A. B., Nimmo, H. G., Barta, A., Kalyna, M., and Brown, J. W.S.
College/School:College of Medical Veterinary and Life Sciences > School of Molecular Biosciences
Journal Name:Nucleic Acids Research
Publisher:Oxford University Press
ISSN (Online):1362-4962
Published Online:11 April 2017
Copyright Holders:Copyright © 2017 The Authors
First Published:First published in Nucleic Acids Research 45(9):5061-5073
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
607041Mechanisms and function of alternative splicing in the plant circadian clockHugh NimmoBiotechnology and Biological Sciences Research Council (BBSRC)BB/K006835/1RI MOLECULAR CELL & SYSTEMS BIOLOGY