Non-Coding RNAs: Striking Features in Use of Alternative Polyadenylation Sites

Alternative polyadenylation of RNA species is an evolutionarily conserved phenomenon contributing to transcriptome diversity, dynamics and flexibility that underlie the genetic underpinnings of complex phenotypes. Here, we utilized our novel WTTS-seq (whole transcriptome termini site sequencing) method to successfully derive alternative polyadenylation sites (APSs) in cattle, chicken, rat and X. tropicalis. This allowed us to characterize APSs based on five gene biotypes, including four types of non-coding RNAs: lncRNA (long non-coding RNAs), miRNA (microRNAs), pseudogenes and tRNA (transfer RNAs) and one type of coding RNA: protein-coding RNAs. We observed that APS usage differs by gene biotype. There were only 1 – 1.23 and 1.15 – 1.57 APSs per gene in tRNA and miRNAs, respectively. Moderate APS usage was observed in pseudogenes and lncRNAs, which had 1.59 – 2.06 and 1.73 – 2.67 APSs per gene, respectively. In contrast, protein coding genes contained an average of 3.44 – 5.81 APSs per gene. Intronic APSs (iAPSs) were not found in tRNAs and miRNAs , but were very common in lncRNAs and protein-coding RNAs, accounting for 22.63% - 46.37% and 22.36% - 66.13% of APSs, respectively. Usage of iAPSs in pseudogenes was dramatically different between mammals (3.83% in cattle - 5.33% in rat) and non-mammalian species (30.56% in chicken - 42.72% in frog). The abundance and magnitude of APS expression varied considerably among gene biotypes, tissues/organs assayed, developmental stage and treatment condition. Notably, average expressions of pseudogenes, miRNAs or tRNAs, rather than the protein-coding RNAs, were often higher than any of the other five gene biotypes. In addition, our data suggest that non-coding RNAs may exert hierarchical control of specific biological events. At this workshop we will demonstrate cases that explain potential contributions of both non-coding and coding RNAs and their respective involvement in determination of phenotypic diversity.