Fig. 1

Significant 3’UTR shortening during spermatogenesis. a Schematic of the first wave spermatogenesis in mouse. ES, elongated spermatids; MI and MII, meiosis phases I and II; PGC, primordial germ cells; RS, round spermatids; Sg, spermatogonia; Spc, spermatocytes. b Schematic of APA analysis. Relative expression (RE) of two selected pA isoforms using proximal (Prx) and distal (Dis) pAs was based on the formula indicated. The region between the two pAs is alternative UTR (aUTR). c Heatmap showing gene RE values during spermatogenesis. Each row is a pA pair of a gene, whose RE values in different samples (columns) were normalized to the mean of each row. Two-way clustering was conducted using the Pearson correlation coefficient as metric. Only genes with read number ≥20 for Prx-pA and Dis-pA isoforms combined were selected for analysis (a total of 2,766 genes). d Normalized number of genes with significant regulation of 3’UTR-APA between adjacent stages. The global analysis of alternative polyadenylation (GAAP) and significance analysis of alternative polyadenylation (SAAP) methods were used (see Methods for details). The numbers of genes with 3’UTR lengthened (Le) and shortened (Sh) are plotted separately, as indicated. Error bars are standard deviation based on 20 times of data sampling. The log2Ratio of number of Sh genes to that of Le genes, or log2(Sh#/Le#), for each comparison is shown on the right. e Boxplots of weighted mean of 3’UTR size (see Methods for its calculation). Median values are indicated. f APA of an example gene Eif4h in spermatogenesis. Only the 3’-most exon is shown. The maximum RPM value for each track (y-axis) and the weighted 3’UTR size at each time point are shown. The relative expression difference (RED) value between two adjacent time points is indicated. The conservation track was based on the PhyloP score