Alternative splicing (AS), by which individual genes can produce multiple mRNA, associates with genomic complexity, disease, and development. Histone modifications show important roles in both transcription initiation and mRNA splicing. Here, we intended to find the link between AS and histone modifications in flanking regions through analyzing publicly available data in two human cell lines, GM12878 and K562 cell lines. According to exon inclusion levels, exons were classified into three types, included skipped exons, excluded skipped exons and expressed constitutive exons. We revealed that the inclusion levels of skipped exons (SEs) were negatively correlated with the enrichment of active histone marks in SEs, indicating a role of histone modifications in AS. We also found that active histone modifications were enriched in the upstream exons of SEs, especially around 5[Formula: see text] splicing sites. We inferred that the histone modifications around the 5[Formula: see text] splicing sites in upstream exon of the SEs could help RNA Polymerase II complex to recruit the effector proteins and facilitate AS. It was indicated that nucleosome occupancy had little influence on the inclusion levels of SEs. At last, we proposed an integrated model that describe how histone modifications affected the pre-mRNA splicing.
Keywords: Histone modification; alternative splicing; skipped exon.