Alternatively spliced exons¶

We tested whether histone marks and nucleosome enrichment correlates with splicing output, we separated nucleosomes into two sets:

nucleosomes overlapping spliced-in exons, and

nucleosomes overlapping spliced-out exons

For both types of exons, we requiered that each nucleosome location should be supported by at least 3 MNase reads.

Then, we counted for each nucleosome the number of MNase ChIP-seq and MNAsed reads on them. We also included sonicated ChIP-seq libraries as references. For each histone marks/nucleosome library we tested whether the distribution on spliced-in vs spliced-out exons differ significantly using the Kolmogorov-Smirnov test.

The results, Figures 1 to 5, show that:

H3K4me3 are not significantly different on sonicated ChIP-seq but they are on MNase ChIP-seq libraries

H3K27Ac are significantly different on both MNase ChIP-seq and sonicated ChIP-seq libraries

H3K9me3 are not significantly different on sonicated ChIP-seq, and results are mixed for MNase ChIP-seq libraries

H3K27me3 are significatnly different on MNase ChIP-seq but not sonicated ChIP-seq libraries

MNase library is not significantly different.

Figure 1: H3K4me3

Figure 1: H3K27Ac

Figure 1: H3K9me3

Figure 1: H3K27me3

Figure 5: MNase