Fig. 2

ReadZS detects developmentally regulated RNAP in human and mouse spermatogenesis. A The ReadZS detects a global trend of 3′ UTR shortening in both human (left) and mouse (right) spermatogenesis datasets, indicated by significant negative correlation between ReadZS and pseudotime. Significance is defined as |Spearman’s correlation| > 0.3 and Bonferroni-corrected p-value < 0.05. Histogram bin width = 0.02. B The ReadZS reveals evolutionarily conserved 3′ UTR regulation in human and mouse. Left: windows containing the 3′ end of ZFAND6 were significantly correlated with pseudotime in both human (Spearman’s correlation = −0.341, Bonferroni-corrected p-value < 1E−39) and mouse (Spearman’s correlation = −0.757, Bonferroni-corrected p-value < 1E−84). Vertical red lines indicate peak positions. Right: the 3′ UTR region of ZFAND6 in human shows high conservation with other vertebrates (UCSC Genome Browser). Red lines correspond to peak positions from the left plot. C The ReadZS discovers fine-scale developmental regulation of RNAP in human spermatogenesis, including in regions where neighboring APA sites create highly overlapping peaks. Note that the scatterplots show ReadZS before sign correction based on gene direction. Left, top to bottom: windows with significant correlation between ReadZS and pseudotime within the first 0 to 25% of pseudotime: OAZ1, which is both significantly correlated over all pseudotime (Spearman’s correlation = 0.131, Bonferroni-corrected p-value = 1.5E−06) and within the first 0 to 25% of pseudotime (Spearman’s correlation = 0.59, Bonferroni-corrected p-value < 1E−55), and MED21, which is only significantly correlated when restricting the first 0 to 25% of pseudotime (Spearman’s correlation = −0.535, Bonferroni-corrected p-value < 1E−23), not across all of pseudotime. Right, top to bottom: the windows with the two highest correlation values when calculated over all of pseudotime: ARPP19 (Spearman’s correlation = 0.74, Bonferroni-corrected p-value < 1E−223) and S100A10 (Spearman’s correlation = 0.666, Bonferroni-corrected p-value < 1E−88). Red lines highlight peak positions