Identification of the highly accumulated microRNA*s in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa).

Plant microRNAs (miRNAs) are crucial for the regulation of gene expression, which is involved in almost all the important biological processes. In the cytoplasm, the miRNA strand is selectively incorporated into a specific Argonaute (AGO)-associated gene silencing complex, while the miRNA* is degraded rapidly. Thus, most miRNAs were thought to be biologically meaningless. Interestingly, several recent reports in both plants and animals have shaken this notion. Many miRNAs were demonstrated to possess regulatory roles in gene expression. However, the low accumulation levels of most miRNAs raise the question whether the activities of this small RNA (sRNA) species are widespread in plants. Here, by using publicly available sRNA high-throughput sequencing data, we found that the accumulation levels of several miRNAs could be much higher than those of their miRNA partners in certain organs, mutants and/or AGO-associated silencing complexes of both Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Based on target prediction and degradome sequencing data-based validation, some of these highly accumulated miRNAs were indicated to possess cleavage-based potential regulatory role on certain targets. Besides, some interesting biological interpretations were obtained based on the accumulation patterns of the miRNAs, the annotations of the target genes, and literature mining. Taken together, the expanded list of the highly accumulated miRNAs along with their potential target genes discovered in this study further strengthened the current notion that certain members of the miRNA species are biologically relevant, which needs further inspection.