Comparative analysis of microRNA promoters in Arabidopsis and rice

Endogenously-encoded microRNAs (miRNAs) are a class of small regulatory RNAs that modulate gene expression at the post-transcriptional level. In plants, miRNAs have increasingly been identified by experiments based on next-generation sequencing (NGS). However, promoter organization is currently unknown for most plant miRNAs, which are transcribed by RNA polymerase II. This deficiency prevents a comprehensive understanding of miRNA-mediated gene networks. In this study, by analyzing full-length cDNA sequences related to miRNAs, we mapped transcription start sites (TSSs) for 62 and 55 miRNAs in Arabidopsis and rice, respectively. The average free energy (AFE) profiles in the vicinity of TSSs were studied for both species. By employing position weight matrices (PWM) for 99 plant cis-elements, we discovered that three cis-elements were over-represented in the miRNA promoters of both species, while four and ten cis-elements were over-represented in Arabidopsis only and in rice only. Thus, comparison of miRNA promoters between Arabidopsis and rice provides a new perspective for studying miRNA regulation in plants.