Whole Transcriptome Termini Site Sequencing Reveals Gender Differences in Genome-Wide Usage of Alternative Polyadenylation Sites

Males and females can be considered genomically equal based on X chromosome inactivation and gene escape models. However, causes of the many physiological, psychological and pathological differences between genders in structurally equal genomes remain largely unknown. Using X. tropicalis as a model organism, we report dramatic differences in genome-wide usage of alternative polyadenylation sites (APSs) between adult males and females. A total of 66,426 APSs were detected using our newly developed whole transcriptome termini site sequencing (WTTS-seq) method. Although males used 13,200 and 7,120 less APSs with evidence and RPM (reads per million)≥1 than females, gene use differences were minimal (≤667). Males tended to use APSs located in introns while females favored exons, particularly for distal sites. Female frogs had more than twice the number of DE-APSs (differentially expressed APSs) than males (2,962 vs 1,337, FDR (false discovery rate)≤0.05), but each set was enriched for distinct functional pathways. The male top pathways included 1) muscle-related structures & processes; 2) cell/tissue/organ development; 3) cell movement; 4) cell junctions; and 5) transport, while the females had top pathways related to 1) cell cycle; 2) RNA processes; and 3) DNA processes. Furthermore, APS expressions in non-coding RNA genes were different between males and females. Gender differences in APS usage may provide novel insights into phenotypic differences between sexes.