Fig. 5
3’UTR cis elements contribute to mRNA abundance changes and APA profiles in spermatogenesis. a Scatterplot showing genes with lengthened, shortened and unchanged 3’UTRs between 4w and 2w samples. Significant 3’UTR-APA events were based on the SAAP analysis (FDR = 5 %) using the top two most abundant 3’UTR-pA isoforms of each gene. b Significant 4-mers enriched in cUTRs and aUTRs of genes with shortened 3’UTRs. Values are − log10(P), where P was based on the Fisher’s exact test examining the enrichment of 4-mers in cUTR (left) or aUTR (right) regions of genes with shortened 3’UTRs (4w vs. 2w). c As in (b) except that genes with lengthened 3’UTRs were analyzed. d Top, schematic showing cis element analysis using genes with only one pA, i.e., having a single 3’UTR (sUTR). Middle, upregulated and downregulated sUTR genes in the 4w vs. 2w comparison, corresponding to >1.4 fold change in RPM value, were selected for 3’UTR analysis. Bottom, top enriched 4-mers for sUTRs of downregulated genes (left) or upregulated genes (right). As in (b), values are − log10(P), where P was based on the Fisher’s exact test examining 4-mer enrichment. e Comparison of 4-mer enrichment in cUTR as calculated in (b) and (c) with that in sUTR as calculated in (d). X-axis values are − log10(P)*S, where P is the 4-mer enrichment P value for upregulated vs. downregulated genes, and S is 1 if a 4-mer is more enriched for sUTRs of upregulated genes, or −1 otherwise. Y-axis values are − log10(P)*S, where P is for enrichment of 4-mer in cUTRs of shortened or lengthened 3’UTRs, whichever is greater, and S is 1 if a 4-mer is more enriched for cUTRs of shortened 3’UTRs or −1 otherwise. f As in (e) except that y-axis is for enrichment of 4-mers in aUTRs of shortened or lengthened 3’UTRs