Fig. 4

Shortening of 3’UTR by APA correlates with high transcriptional activity and open chromatin. a cUTR and aUTR sizes of genes with different 3’UTR-APA regulations. Left, boxplot showing cUTR size of genes with shortened (Sh), lengthened (Le), or unchanged (Uc) 3’UTRs. Right, same as the plot on the left except that aUTR size is plotted. 3’UTR regulation by APA was based on the SAAP analysis (4w vs. 2w, FDR = 5 %). P values comparing different gene groups were based on the K–S test. b Genes with longer aUTRs tend to have greater 3’UTR shortening in spermatogenesis. Genes are divided into five bins based on aUTR size, as indicated. The mean RED values between adjacent time points of all genes are plotted. P values (Wilcoxon rank-sum test) comparing gene bins 1 and 5 are shown. c Log2Ratio of RNAPII ChIP-seq levels between spermatids and pachynema (pachytene stage spermatocytes) for three groups of genes, namely 3’UTR shortened, unchanged and lengthened, around the TSS (+/− 1 kb, left), in gene body (middle) and around the last pA (+/− 1 kb, right). 3’UTR regulation was based on comparison of 4w and 2w samples. P values (K–S test) comparing genes with 3’UTR shortened (blue) or lengthened (red) with 3’UTR unchanged are indicated. d Log2Ratio of H3K4me3 ChIP-seq levels between spermatids and spermatocytes for three groups of genes, namely 3’UTR shortened, unchanged and lengthened, around the TSS (+/− 1 kb, left), in gene body (middle) and around the last pA (+/− 1 kb, right). 3’UTR regulation was based on comparison of 4w and 2w samples. P values (K–S test) comparing genes with 3’UTR shortened (blue) or lengthened (red) with 3’UTR unchanged are indicated