title: Detection of generic differential RNA processing events from RNA-seq data.
abstract: RNA-seq data analysis has revealed abundant alternative splicing in eukaryotic mRNAs. However, splicing is only one of many processing events that transcripts may undergo during their lifetime. We present here RNAprof (RNA profile analysis), a program for the detection of differential processing events from the comparison of RNA-seq experiments. RNAprof implements a specific gene-level normalization procedure and compares RNA-seq coverage profiles at nucleotide resolution to detect regions of significant coverage differences, independently of splice sites or other gene features. We used RNAprof to analyze the effect of alternative-splicing regulators NSRa and NSRb on the Arabidopsis thaliana transcriptome. A number of intron retention events and alternative transcript structures were specifically detected by RNAprof and confirmed by qRT-PCR. Further tests using a public Mus musculus RNA-seq dataset and comparisons with other RNA isoform predictors showed that RNAprof uniquely identified sets of highly significant processing events as well as other relevant library-specific differences in RNA-seq profiles. This highlights an important layer of variation that remains undetected by current protocols for RNA-seq analysis.
authors: a I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud , 1 avenue de la terrasse, 91198 Gif sur Yvette , France.|b Swiss Institute of Bioinformatics, Quartier Sorge , bâtiment Génopode - 1015 Lausanne , Switzerland.
authors: Van Du T
authors: Vdu T
authors: Tran
authors: a I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud , 1 avenue de la terrasse, 91198 Gif sur Yvette , France.
authors: Oussema
authors: O
authors: Souiai
authors: c Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité , Bâtiment 630, 91405 Orsay , France.
authors: Natali
authors: N
authors: Romero-Barrios
authors: c Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité , Bâtiment 630, 91405 Orsay , France.
authors: Martin
authors: M
authors: Crespi
authors: a I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud , 1 avenue de la terrasse, 91198 Gif sur Yvette , France.
authors: Daniel
authors: D
authors: Gautheret
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000378:metabolism; D019295:Computational Biology / Q000379:methods* / Q000592:standards; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods / Q000592:standards; D051379:Mice; D012313:RNA / Q000235:genetics*; D012323:RNA Processing, Post-Transcriptional; D017423:Sequence Analysis, RNA / Q000379:methods* / Q000592:standards
chemical_list: D029681:Arabidopsis Proteins; D012313:RNA
keywords: Alternative polyadenylation; RNA processing; RNA-seq; alternative splicing; alternative transcripts