BACKGROUND: While alternative splicing (AS) contributes greatly to protein 
diversities, the relationship between various types of AS and epigenetic factors 
remains largely unknown.
RESULTS: In this study, we discover that a number of epigenetic features, 
including DNA methylation, nucleosome occupancy, specific histone modifications 
and protein features, are strongly associated with AS. To further enhance our 
understanding of the association between these features and AS, we cluster our 
investigated features based on their association patterns with each AS type into 
four groups, with H3K36me3, EGR1, GABP, SRF, SIN3A and RNA Pol II grouped 
together and showing strongest association with AS. In addition, we find that 
the AS types can be classified into two general classes, namely the exon 
skipping related process (ESRP), and the alternative splice site selection 
process (ASSP), based on their association levels with the epigenetic features.
CONCLUSION: Our analysis thus suggests that epigenetic features are likely to 
play important roles in regulating AS.