RNA-binding proteins connect Exon usage to the chromatin

Exonic enrichment of histone marks hints at their role in regulating alternative splicing. This study aims to connect the transcriptome and epigenome in the context of splicing outcomes in embryonic cell lines. The tools rMATS and MANorm were used to obtain estimates of differential inclusion of exons and differential enrichment of epigenetic signals, respectively. Two classes of alternative exons were identified in embryonic cell lines: those differentially co-occurring with at least one mark among H3K27ac, H3K27me3, H3K36me3, H3K9me3, and H3K4me3, and those marked by neither of these marks. Binary classifiers were trained using RNA-binding protein (RBP) binding affinities on the flanking regions of these exons. This resulted in a set of RBPs, whose putative binding was predicted to associate local chromatin modification marking an exon with its differential inclusion, some of which have been experimentally shown to interact with histone mark reader proteins. We speculate that sequence signals harbored at exon-intron flanks regulate differential splicing of exons, marked by at least one of the five epigenetic signatures. Finally, eCLIP data from ENCODE for the HepG2 and K562 cell lines support TIA1 and U2AF2 as potential episplicing RBPs, as predicted by our model in the embryonic cell lines.