Fig. 4: A proportion of last exons exhibit strong m6A deposition inhibition by exon-intron boundary.
a, d, g, j The heatmap visualized ΔProbability (a), m6A Probability (d), m6A Probability by last intron deletion (g), and counts of RAC sites (j) in the first 200 nt of last exon. The 200 nt was binned into 40 intervals (5 nt per interval). Genes were clustered (see details in Methods) into two clusters (Cluster1, Cluster2) based on ΔProbability. b, c Positional plot of ΔProbability (b for Cluster1, c for Cluster2) for the RAC sites located in the first 500 nt region of last exons (n = 1500). Red, blue, and gray dots were those sites that had increased (> 0.1), decreased (< −0.1), or not change probability (|ΔProbability| <= 0.1) respectively by last intron deletion. e, f The m6A density around original last exon start (e for Cluster1, f for Cluster2) were compared for transcripts with full length (black line), last intron deletion (pink line). h, i Positional plot for the frequency of top 50 m6A enhancers (h for Cluster1, Fig. 4i for Cluster2) in mRNA sequences around the RAC sites. Increase sites (red line, ΔProbability > 0.1), and no change sites (gray line, |ΔProbability| <= 0.1). k, l The density of RAC sites around last exon start (k for Cluster1, l for Cluster2). m, n Pentamer enrichment in different last exon start regions comparing Cluster1 vs. Cluster2. The y-axis showed the −log10(two-sided Fisher-exact test P-value), and the x-axis indicated the log2(odds ratio values). In m, NRACN motifs were highlighted in red. In n, top 50 m6A enhancers or silencers were highlighted in red or blue respectively. o, p Dendrogram showed clustering of 20 most enriched (o) or avoided (p) motifs comparing Cluster1 vs. Cluster2.
