A chromatin signature for alternative splicing

ENERITZ AGIRRE; NICOLAS BELLORA; REINI LUCO

Munich

Simposio; 4th Munich Chromatin Symposium on Chromatin Dynamics; 2016

Ludwig Maximilian University of Munich

Alternative splicing is an essential process for protein diversity, that affects more than 90% of human genes and whose deregulation is frequently associated with severe diseases, such as cancer. Alternative splicing regulation depends on the combinatorial recruitment of splicing factors to the pre-mRNA. However, there is an increasing evidence showing an interaction of various mechanisms of regulation between RNA, chromatin and protein factors. The discovery by several groups that nucleosomes define exons at the chromatin level, uncovered  new mechanisms of splicing regulation. In particular, others and our group have shown that histone modifications influence splicing by either modulating the elongation rate of the RNA polymerase II or by inducing binding of the splicing regulators to the pre-mRNA via recruitment of chromatin/splicing-adaptor complexes.  We are now extending these studies to a genome-wide level by studying available high-throughput sequencing data from the Roadmap epigenomics consortium (Kundaje et al. 2015) to map along differentially spliced genes, 27 histone modifications and DNA methylation in H1 embryonic stem cells. Using Machine Learning techniques with selected features, including enrichment of histone marks and methyl levels along alternatively spliced exons, together with splice site strengths, we have found relevant combinations of different histone marks and DNA methylation around alternatively spliced cassette exons depending on the level of exon inclusion. Our results suggest that different subtypes of alternative splicing events are specifically marked by different combinations of histone modifications and DNA methylation. More precisely, these histone marks are found non-randomly distributed along the alternatively spliced exons and by pairs suggesting a possible combinatorial role of chromatin in alternative splicing.  In addition, the characterization of these specifically marked subtypes of splicing events revealed differently enriched RNA binding motifs, suggesting that specific chromatin signatures might favour recruitment of specific splicing regulators to the pre-mRNA. From our results we are able to define subtypes of alternative exons that are differently mark by specific combinations of chromatin marks and that they have different RNA motifs in H1. We further plan to build a model based on these features to predict alternative splicing in other cell types, such as IMR90.