Next generation sequencing facilitates quantitative analysis of STRAP-dependent alternative splicing events

We report the application of next generation sequencing for evaluating alternative splicing (AS) events on lineage-committed WT and Strap-KO embryoid body (EB) cells. We also analyzed AS during mouse embryo development using RNA-seq data. Of all STRAP-regulated AS, exon-skipping events were the most frequent ones with significant changes in 49% (240 out of 489) cases. Retained introns were also overrepresented (20%, 97 out of 489) as compared to other types of AS STRAP appears to function in promoting both exon inclusion and skipping at different exons. GO function revealed STRAP-regulated AS events involve in protein catabolism, molecular binding and cell motility. More specifically, they included neuronal migration and development. Together, these analyses uncovered the previous unknown role of STRAP involved in the substantial transcriptional diversity at the exon level in certain development stage. Our study also represents the first detailed analysis of AS events in the mouse early organogenesis with biologic replicates, generated by RNA-seq technology.