Figures: Counts per nucleosome on canonical nucleosomes around AS exonsΒΆ

We counted the number of MNase ChIP-seq reads overlapping nucleosomes on three classes of exons: spliced-in, spliced-out, and constitutively expressed. For each set we look for nucleosomes overlapping 2000 bp windows center on either the 5 or 3 prime end of each exon.

For each window, nucleosomes were assigned to position ranging from -4 up to +5, based on the proximity to canonical positions (determined using genome-wide positioning of nucleosomes around AS exons). Figure 1, shows the canonical nucleosome positions using MNase reads from the 3 and 5p end of the exons.

When plotting the nucleosomes coverage around AS exons (Figure 2), it can be seen that most nucleosomes are close to the exon boundaries (either 3 or 5p). This is coherent with the genome-wide trend (Figure1).

Finally, we computed the average enrichment of all MNase ChIP-seq libraries on the canonical nucleosomes. All libraries were normalized by number of total reads. Then we plotted the ratio MNase ChIP-seq over MNase (also normalized by library size). The results are presented on Figures 3-6.

Figure 1: Canonical nucleosome positions

Figure 2: Average enrichment of 8_mnase on the canonical nucleosomes

Figure 3: Average enrichment of H3K4me3 on the canonical nucleosomes

Figure 4: Average enrichment of H3K27Ac on the canonical nucleosomes

Figure 5: Average enrichment of H3K9me3 on the canonical nucleosomes

Figure 6: Average enrichment of H3K27me3 on the canonical nucleosomes