title: Epigenetic features are significantly associated with alternative splicing.
abstract: 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.
  
  
  CONCLUSIONS
  Our analysis thus suggests that epigenetic features are likely to play important roles in regulating AS.
authors.affiliation: State Key Laboratory of Genetic Engineering, Institute of Biostatistics, School of Life Science, Fudan University, Shanghai, China.
authors.forename: Yuanpeng
authors.initials: Y
authors.lastname: Zhou
authors.forename: Yulan
authors.initials: Y
authors.lastname: Lu
authors.forename: Weidong
authors.initials: W
authors.lastname: Tian
mesh_terms: D000107:Acetylation; D017398:Alternative Splicing / Q000235:genetics*; D000076246:CCCTC-Binding Factor; D002460:Cell Line; D016000:Cluster Analysis; D019295:Computational Biology; D019175:DNA Methylation; D044127:Epigenesis, Genetic / Q000235:genetics*; D006657:Histones / Q000235:genetics / Q000378:metabolism; D006801:Humans; D009707:Nucleosomes / Q000235:genetics; D012319:RNA Polymerase II / Q000378:metabolism; D012097:Repressor Proteins / Q000378:metabolism
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D006657:Histones; D009707:Nucleosomes; D012097:Repressor Proteins; D012319:RNA Polymerase II