Parallel Analysis of RNA Ends Enhances Global Investigation of miRNAs and Target RNAs in Brachypodium

MicroRNAs (miRNAs) are important regulators of gene expression and they usually function by guiding the precise cleavage of complementary target RNAs in plants. To expand understanding of the miRNA population in Brachypodium distachyon, 17 small RNA libraries representing diverse tissues and stress conditions were sequenced. Using a computational pipeline, more than 115 miRNAs were identified. These included conserved and nonconserved annotated miRNAs as well as novel miRNAs. The cleavage function of the miRNAs was investigated in depth using PARE (Parallel Analysis of RNA Ends), an approach for sequencing RNA decay intermediates genome-wide. PARE libraries were constructed from key tissues and their sequencing resulted in a total of ~70 million raw sequences and ~5 million distinct genome-matched sequences.  Analysis of the PARE data provided experimental evidence for miRNA-mediated cleavage of more than 250 sites in predicted miRNA targets. Highlights from the further characterization of the miRNAs and cleaved targets of Brachypodium include tissue-preferential control of miRNA family members that can explain differential target cleavage. Using additional PARE data from other plants, examples of conserved cleavage of homologous targets in Brachypodium and bioenergy crops were evident. The knowledge gained from this global analysis should provide insight about the roles of miRNAs and the regulation of their targets in Brachypodium and related plants. This project was funded by the Plant Feedstock Genomics for Bioenergy Program of the DOE under award # DE-FG02-07ER64450.