Fig. 3

Dynamic 3′ UTR shortening during late meiotic and early haploid phases of spermatogenesis. a Density plots showing changes in 3′ UTR length of RNP-enriched mRNAs from pachytene spermatocytes to round (upper panel) and from round to elongating spermatids (lower panel). Note that the 3′ UTR length was deduced based on the total length and the position of the stop codon of all SpliceR CDS transcripts. The RNP-enriched transcripts were defined as those with upregulated levels in the RNP of one cell type when compared to another (Student’s t-test and Wilcoxon rank sum test). The 3′ UTR length of RNP-enriched transcripts becomes increasingly shorter from pachytene spermatocytes to round, and then to elongating spermatids. b Density plots showing changes in the 3′ UTR length of polysome-enriched mRNAs from pachytene spermatocytes to round (upper panel) and from round to elongating spermatids (lower panel). The polysome-enriched transcripts are defined as those with upregulated levels in the polysome fractions of one cell type when compared to another (Student’s t-test and Wilcoxon rank sum test). While the 3′ UTR length of polysome-enriched transcripts becomes significantly shorter from round to elongating spermatids, this change does not appear to be significant between pachytene spermatocytes and round spermatids. c Correlation between 3′ UTR length and expression level in the RNP fractions of pachytene spermatocytes and round and elongating spermatids. The RNP-enriched transcripts are defined as those significantly upregulated in RNPs compared to polysomes (Student’s t-test and Wilcoxon rank sum test) in each of the three cell types. The regression lines were plotted to show the average expression levels of RNP-enriched mRNAs. Note that the transcripts enriched in elongating spermatid RNP fractions display significantly shorter 3′ UTRs but higher expression levels. Boxplots if the inset demonstrate that the 3′ UTR length of RNP-enriched transcripts was increasingly shorter from pachytene spermatocytes to round and elongating spermatids (Student’s t-test and Wilcoxon rank sum test, p values ranged from 2.2e-16 to 2.3e-3; see Additional file 1: Table S4 for details). d Correlation between 3′ UTR length and expression levels in polysome fractions of pachytene spermatocytes and round and elongating spermatids. The polysome-enriched transcripts are defined as those significantly upregulated in polysome compared to RNP fractions (Student’s t-test and Wilcoxon rank sum test; see Additional file 1: Table S4 for p values) in each of the three cell types. The regression lines were plotted to show the average expression levels of polysome-enriched mRNAs. Note that the transcripts enriched in elongating spermatid polysome fractions display significantly shorter 3′ UTRs but higher expression. Boxplots in the inset demonstrate that the 3′ UTR length of polysome-enriched transcripts was significantly shorter from round to elongating spermatids (Student’s t-test and Wilcoxon rank sum test; see Additional file 1: Table S4 for p values), but it appears to increase from pachytene spermatocytes to round spermatids, although this is statistically insignificant. e Expression profiles of four genes (Cebpg, Eif4h, Ubp1, and Hip1), each with multiple transcript isoforms, in late meiotic (pachytene spermatocytes) and haploid (round and elongating) male germ cells. One longer 3′ UTR transcript isoform (in blue) and one shorter 3′ UTR isoform (in red) with the largest fold changes (FC) are shown for each of the four genes. Note that the longer 3′ UTR isoforms, in general, were downregulated, whereas the shorter 3′ UTR isoforms were upregulated. P values are based on Student’s t-test. Asterisks indicate statistically significant p values