Splicing genes as main targets of differential splicing

Abstract

Splicing of transcripts via the spliceosome machinery is a complex process involving a multitude of proteins and short noncoding RNAs. In addition to full-length transcripts with all exons in the genomically encoded order, alternatively spliced transcripts can also be produced through alternative splicing of pre-mRNA. We have attempted to identify which genes are most frequently targeted by differential splicing using both downloaded and original RNA-Seq data from several species and tissue types. In order to identify splicing variation on an individual-to-individual basis, random contrasting of samples within compatible sets of samples was done. Both when analyzing sequence data from similar source material (same tissue from individuals kept under similar conditions) and when contrasting samples that are more different, such as different tissue types, genes associated with the splicing process itself seem to be the most recurring targets.