Are all the miRBase-registered microRNAs true?

In this survey, we did a large-scale re-examination of the currently registered plant microRNAs (miRNAs) in miRBase (release 17), which were annotated based on the already established criteria. Huge public small RNA (sRNA) high-throughput sequencing (HTS) data sets were employed to interrogate the accuracy of the miRBase registries based on the secondary structures of the miRNA precursors and the expression levels of the miRNAs and the miRNA*s. Our results raised the caveat that the current miRNA lists in miRBase should be carefully refined, and more strict criteria should be implemented for new miRNA registration. Through this work, we proposed a structure- and expression-based strategy to validate a set of defined miRNA genes, or even to annotate novel ones based on currently available sRNA HTS data sets. We also hope to inspire further research efforts on the manual refinement of the current miRNA gene lists.