Global survey on sequence characteristics of plant microRNA genes: <i>Cis</i>-regulatory SNPs in promoters and microRNA precursors

MicroRNAs (miRNAs) are tiny molecules with multiple essential roles in plant growth and development. So far, numerous miRNA families, both highly conserved and species-specific, have been identified and functionally characterized. However, we are still far from a thorough understanding of these molecules, including their sequence characteristics. In this bioinformatics study, <i>cis</i>-acting regulatory elements located within plant miRNA promoters were predicted, and a comprehensive list of single nucleotide polymorphisms (SNPs) residing within these <i>cis</i>-elements, designated as <i>cis</i>-regulatory SNPs, was identified. These SNPs potentially contribute to the distinct expression patterns of miRNA genes in various Arabidopsis (<i>Arabidopsis thaliana</i>) or rice (<i>Oryza sativa</i>) subspecies. Additionally, sequence conservation analysis was carried out for all the currently miRBase-registered pre-miRNAs (precursor miRNAs) belonging to numerous plant species. Together, these analyses provide a basis to gain deeper insights into the biological role of miRNA sequence characteristics.