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Open Access Highly Accessed Research article

Epigenetic features are significantly associated with alternative splicing

Yuanpeng Zhou, Yulan Lu and Weidong Tian*

Author Affiliations

State Key Laboratory of Genetic Engineering, Institute of Biostatistics, School of Life Science, Fudan University, 220 Handan Rd, Shanghai 2004333, China

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BMC Genomics 2012, 13:123  doi:10.1186/1471-2164-13-123

Published: 29 March 2012

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.

Conclusion

Our analysis thus suggests that epigenetic features are likely to play important roles in regulating AS.

Keywords:
Alternative splicing; Epigenetics; DNA methylation; Nucleosome occupancy; Histone modifications; Transcription factors