Fig. 7

Regulation of CDS-APA in spermatogenesis. a Schematic of CDS-APA. CDS-APA isoforms are those using pAs in introns or non-3’-most exons. b Heatmap showing relative expression (RE) values of CDS-APA isoforms vs. 3’-most exon isoforms. RE values are mean-centered and clustered using hierarchical clustering with Pearson correlation coefficient as metric. c Normalized number of genes with significant regulation of CDS-APA as identified by GAAP and SAAP analyses (FDR = 5 %) (see Methods for details). The ratio of number of genes with upregulated (UP) CDS-APA isoforms to that with downregulated (DN) isoforms is indicated. d Regulation of isoforms using pAs in different introns. Introns were divided into five groups, i.e., the first and second introns (+1 and +2, respectively), the last and second to last introns (−1 and −2, respectively) and middle introns (M). The expression change of isoform is based on RPM values. e Gene expression changes vs. CDS-pA regulation. Genes were divided into three indicated groups based on CDS-APA regulation between comparing samples (SAAP analysis, FDR = 5 %). The median value for each group is indicated by a dotted vertical line. The P value (K–S test) for difference between genes with upregulated or downregulated CDS-APA and those with unchanged CDS-APA is shown in each graph (in red or blue, respectively). RNA-seq data with CDS reads were used for gene expression analysis. f ChIP-seq analysis of H3K4me3 levels on genes with CDS-APA regulation. Log2Ratio of ChIP-seq levels between spermatids and spermatocytes for the three gene groups is shown. CDS-APA regulation was based on comparison of 4w and 2w samples, corresponding to spermatid and spermatocyte stages, respectively. P value (K–S test) comparing genes having downregulated (blue) or upregulated (red) CDS-pA isoforms with genes having CDS-APA unchanged is indicated