Alternative Splicing Of Target Transcripts Increases The Complexity Of microRNA-Based Gene Regulation

This work was motivated by two observations, namely that alternative splicing is a common phenomenon and that microRNAs (miRNAs) regulate a significant proportion of the transcriptome. We hypothesized that there may be a mechanism for gene regulation that involves both processes. To test this hypothesis, we performed a systemic search in Arabidopsis using annotated gene models as well as publically available high-throughput RNA sequencing data with a total of 570 million reads. Of the 354 high-confidence miRNA binding sites identified in Arabidopsis, we found at least 44 (12.4%) are affected by alternative splicing such that mRNA isoforms of the same miRNA target gene differ in the sequences encoding the miRNA binding sites. By simulation, we found that the frequency of alternative splicing at miRNA binding sites is significantly higher than at other regions. Comparative and functional analyses further indicated that the alternative splicing events are important for target gene expression and miRNA action. Together our results show that alternative splicing of miRNA binding sites is a plausible mechanism for attenuating miRNA-mediated gene regulation.