CONICET | Buscador de Institutos y Recursos Humanos

BACKGROUND: Alternative splicing (AS) has been proposed as a post-transcriptional regulatory mechanism to increase transcript diversity in eukaryotic organisms, allowing a cell to generate different transcripts from the same genomic locus. AS involves the interaction of splicing factors with their targets in a coordinated and combinatorial way in an fashion that is currently unclear. RESULTS: In this work we studied global organizational patterns that emerge on the co-splicing level and its relationship with transcriptional regulation in order to understand subgenic regulation at the systems level. We consider an Arabidopsis thaliana cold stress RNA-Seq dataset consisting of a timecourse for 4 different temperatures: 12º, 17º, 22º and 28º. First we compiled a list of 750 known transcription factors (TF) and built a transcriptional biweight midcorrelation network between TF and their targets for each temperature.Then, we used ASpli, an RNA-Seq analysis pipeline developed in our lab, to characterize changes associated with exon and intron (collectively referred to as bins in our pipeline) differential usage (DU) for each temperature. In order to remove gene effects on bin counts, ASpli normalizes bin expression level by gene expression level. Then, to detect DU, it compares bin counts for different times vs. a reference time (usually the first time on the timecourse). Once the DU bins were detected, we built normalized bins correlation networks and then ?pruned? the networks to remove spurious links using up to second order partial correlation conditional on the transitive bins. Finally, we integrated both regulatory layers using bin usage and gene expression correlation, to uncover regulatory patterns. CONCLUSIONS: Using ASpli, an RNA-Seq analysis pipeline developed in our lab, we were able to build and integrate co-splicing and transcription factors networks, uncovering interesting regulatory patterns with possible biological relevance.