An Integrated miRNA Expression Atlas of Arabidopsis thaliana

MicroRNAs (miRNAs) are 21-24 nucleotide (nt) small non-coding RNAs that regulate a wide variety of biological processes at the posttranscriptional level. MiRNA expression often exhibits spatial and temporal specificity. However, genome-wide miRNA expression patterns in different Arabidopsis organs during plant development have not yet been fully investigated. In this study, we sequenced 59 small RNA libraries generated from different tissue types at different developmental stages of Arabidopsis. We then re-annotated Arabidopsis miRNAs based on the most recent criteria. Global analysis of miRNA expression patterns showed that most miRNAs are ubiquitously expressed in different organs or tissues. But a small set of miRNAs, either previously annotated or newly identified, show highly specific expression patterns. In addition, the expression of some miRNA members belonging to the same family is strictly regulated spatially and temporally. Unexpectedly, we found that quite a few miRNAs are produced from different arms of their hairpin precursors at different developmental stages, suggesting that arm switching could be a general and important mechanism in developmental regulation. Overall design: we constructed 59 small RNA libraries from root, shoot, leaf, flower, silique, seed and many other organs or cell types at different stages of Arabidopsis development