Genomic analysis of rice microRNA promoters and clusters

MicroRNAs (miRNAs) are endogenous single-stranded non-coding small RNAs with a length of about 21 nt, that negatively regulate development and stresses. Rice miRNAs are representative of the monocot miRNAs, and many of them are non-conserved in Arabidopsis and the other plant species. Previous studies have shown that a majority of plant miRNAs are expressed from independent transcription units, whereas some others are transcribed with their host genes. Despite of the fact that a growing number of rice miRNAs are discovered, little is known about the transcriptional regulation of miRNA genes. In this study, we performed genomic analysis of rice miRNA transcripts surrounding the regions of promoter/transcription start site (TSS) and TATA-box, and organization of miRNA clusters. We detected 249 promoters for 212 rice pre-miRNA sequences via bioinformatics approach and found that the conserved rice miRNA genes have a greater proportion of promoters than the non-conserved miRNA genes. We further globally analyzed the genomic organization of pri-miRNAs and found that 52 rice miRNA genes appear in 18 clusters. Alignment of the miRNA sequences in these clusters shows a number of miRNA paralogs within the cluster. The data obtained may aid our understanding of the specific sequences upstream of pre-miRNAs and the functional implications of miRNA clusters in rice plants.