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.

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

Figure 1

The association of DNA methylation and nucleosome occupancy with AS. (a) The distribution of genomic CpG dinucleotides level (CG) around the splice sites of different types of AS events. (b) The distribution of DNA methylation level (mCG) around the splice sites of different types of AS events. In both a and b, a sliding window of 147 bp is used for generating the profile for the figure; the x-axis is the position relative to acceptor site (left) and donor site (right); the y-axis is the CG percentage for a and the methylation percentage for b. (c) The distribution of nucleosome occupancy around the splice sites of different types of AS events. In c, no sliding window is used (see Methods for details); the x-axis is as in a, and the y-axis represents the ChIP signal level. (ES (exon skipping), ME (mutually exclusive exon, A5SS (alternative 5' splice site selection) A3SS (alternative 3' splice site selection), IR (intron retention)).

Figure 2

The association of histone modification with AS. The color scheme and plotting method are the same as that of nucleosome occupancy (Figure 1c). (ES (exon skipping), ME (mutually exclusive exon), A5SS (alternative 5' spice site selection), A3SS (alternative 3' splice site selection), IR (intron retention)).

Figure 3

The association of protein features with AS. The color scheme and plotting method is the same as that of nucleosome occupancy (Figure 1c). (ES (exon skipping), ME (mutally exclusive exon), A5SS (alternative 5' splice site selection), A3SS (alternative 3' splice site selection), IR (intron retention)).

Figure 4

Clustering of epigenetic features on the basis of their association with AS. K-means clustering is used to identify four clusters of epigenetic features. The profile for clustering is generated by converting the p-value of the association of each epigenetic feature with different types of AS events in each bin around the splice sites, see Methods section for details. (ES (exon skipping), ME (mutually exclusive exon), A5SS (alternative 5' splice site selection), A3SS (alternative 3' splice site selection), IR (intron retention)).

Figure 5

Epigenetic features strongly associated with different types of AS. Epigenetic features strongly associated with different types of AS events are shown inside the circle of ESRP and ASSP. The features showing higher level and lower level in AS events than in CNE are colored in red and green, respectively. The features inside the dashed black box are those common in both ESRP and ASSP; note their association patterns are very different in between ESRP and ASSP. (ES (exon skipping), ME (mutually exclusive exon), A5SS (alternative 5' splice site selection), A3SS (alternative 3' splice site selection), IR (intron retention)).

Figure 6

The association of epigenetic features after correcting for ChIP-seq input and nucleosome occupancy. (a) The distribution of ChIP-seq input around the splice sites of different types of AS events, the plotting method is the same as that in Figure 1c. (b-c) The distribution of Cluster 1 features (identified in Figure 4) corrected by nucleosome occupancy around the splice sites of different types of AS events in CD4+ cell line.*(d-i) The distribution of Cluster 1 features corrected by ChIP-seq input around the splice sites of different types of AS events in K562 cell line. (ES (exon skipping), ME (mutually exclusive exon), A5SS (alternative 5' splice site selection), A3SS (alternative 3' splice site selection), IR (intron retention)). * The nucleosome corrected signal level is low because the nucleosome occupancy has high signal level while the data of CD4+ are generate in 2007 and have less reads than other data source.