Chromatin and Genomic determinants of alternative splicing

Alternative splicing significantly contributes to proteomic diversity and mis-regulation of splicing can cause diseases in human. Although both genomic and chromatin features have been shown to associate with splicing, the mechanisms by which various chromatin marks influence splicing is not clear for the most part. Moreover, it is not known whether the influence of specific genomic features on splicing is potentially modulated by the chromatin context. Here we report a deep neural network (DNN) model for predicting exon inclusion based on comprehensive genomic and chromatin features. Our analysis in three cell lines shows that, while both genomic and chromatin features can predict splicing to varying degrees, genomic features are the primary drivers of splicing, and the predictive power of chromatin features can largely be explained by their correlation with genomic features; chromatin features do not yield substantial independent contribution to splicing predictability. However, our model identified specific interactions between chromatin and genomic features suggesting that the effect of genomic elements may be modulated by chromatin context.