Stationary Analysis the Alternative Splicing Profile Reveals the Splicing Code

Abstract

Recent works indicated that the regulatory function of RBPs showed context dependent manners, but the details of the regulatory function of most RBPs and importance are unknown. Here we integrated hundreds of eCLIP-seq and RNA-seq from ENCODE project and used RBP-position combinations on events to predict if the events are spliced out or not and the results showed that only a small of them can regulate the alternative splicing process in a degree. We observed SRSF1, LIN28B, FMR1, SRSF7, RBM22, PRPF8, SF3B4, TIA1 and hnRNP M are important features by binding the exon or intron region respectively. SF3B4 and RBM22 show opposite regulatory function when binding exons downstream and upstream intron. This supports the asymmetric exon decision model that state the exon exclusion pathway compete with the exon inclusion pathway to regulate splicing. We also observed that some peaks locate in exon-exon junction regions and indicate some splicing related RBPs also bind on mRNAs.