Aspli: an integrative R package fgor the analysis of alternative splicing using RNA-Seq

ESTEFANIA MANCINI; ARIEL CHERNOMORETZ; MARCELO YANOVSKY

Congreso; 12th Integrative RNA Biology Special Interest Group (IRB-SIG) 2015; 2015

BACKGROUNDAlternative splicing (AS) is a prevalent mechanism of post transcriptional gene regulation in multicellulareukaryotes. It allows a single gene to increase functional and regulatory diversity, through the synthesis of multiplemRNA isoforms encoding structurally and functionally distinct proteins. AS occurs via 4 main events: intronretention (IR), exon skipping (ES) and alternative use of donor and aceptor sites (alt 5' and alt 3'). The developmentof novel high-throughput sequencing methods for RNA (RNA-Seq) provided a very powerful mean to studyalternative splicing under multiple conditions at unprecedented depth. As long as new studies on post-transcriptionalregulation arises, there are an increasing evidence than AS frequency is higher than expected. Despite It has becamethe new standard for studying gene and transcription expression, the use of RNA-seq for the study of transcriptsrepertoire in a given condition is not trivial.RESULTSHere we introduce a very flexible and easy-to-use R package named ASpli. We propose a count based integrativemethod taking into account gene expression, exon and intron differential usage and their relationship with junctionsspanning those features.CONCLUSIONSUsing an annotated transcriptome we are able to classify subgenic features into alternative or not alternative regions.ASpli is intended to facilitate the analysis of RNAseq data for the quantification and discovery of AS events and ithas been used in many recent publications from our lab. Results of the analysis are presented in a user friendlymanner, including plots of the most relevant AS events discovered.