Analysis of alternative splicing in timecourse experiments using Aspli R/Bioconductor package

ISERTE JAVIER; ESTEFANIA MANCINI; ROMANOWSKI ANDRES; A. CHERNOMORETZ

Congreso; IV International Society for Computational Biology-Latin America Bioinformatics Conference; 2016

International Society for Computational Biology

Alternative splicing (AS) is amechanism of post transcriptional gene regulation in eukaryotes. It allows asingle gene to increase functional and regulatory diversity, through thesynthesis of multiple mRNA isoforms encoding distinct proteins. AS occurs via 4main events: intron retention (IR), exon skipping (ES) and alternative use ofdonor and acceptor splicing sites (Alt5´SS and Alt3´SS). The development ofnovel high-throughput sequencing methods for RNA (RNA-Seq) provided a verypowerful means to study AS under multiple conditions at unprecedented depth. Asnew studies on post-transcriptional regulation became available, increasingevidence that AS frequency is higher than expected has arisen. In spite of thegrowing number in RNA-seq studies, the analysis is not trivial and even more soin timecourse designs. Here we report the results of a genome-wide analysis of AS in Arabidopsisthaliana plants every 4 hours for 48 hours. An experiment aimed to detectcycling alternative splicing events. RNA-Seq data analysis was performed withASpli, an R/Biocoductor package combined with clustering techniques. Ourresults revealed many new alternative splicing events that cycle along the day.This reveals that circadian rhythms affect the plant transcriptome at multipleregulatory layers, and that circadian regulation of mRNA levels is likely tomediate effects on AS, thus contributing to adjust plant physiological processesto the prevailing moment of the day. Results of the analysis are presented in auser friendly manner, including plots of the most relevant AS eventsdiscovered.