Expression patterns of intronic microRNAs in Caenorhabditis elegans

We performed a systematic analysis of genomic regions surrounding intronic miRNAs in the nematode Caenorhabditis elegans and found that, in many cases, there are extended intronic sequences immediately upstream of the miRNAs that are well-conserved between the nematodes. We have generated transcriptional green fluorescent protein reporter fusions in transgenic C. elegans lines and demonstrated that, in all seven investigated cases, the conserved sequences show promoter properties and produce specific expression patterns that are different from the host gene expression patterns. The observed expression patterns are corroborated by the published small RNA sequencing data.Our analysis reveals that the number of intronic miRNAs that do not rely on their host genes for expression is substantially higher than previously appreciated. At least one-third of the same-strand intronic miRNAs in C. elegans posses their own promoters and, thus, could be transcribed independently from their host genes. These findings provide a new insight into the regulation of miRNA genes and will be useful for the analysis of interactions between miRNAs and their host genes.MicroRNAs (miRNA) are ~22 nucleotide (nt) single-stranded RNA molecules that originate from hairpin precursors and regulate gene expression at the post transcriptional level by basepairing with target messenger RNA (mRNA) and blocking its translation or inducing its degradation (reviewed in [1]). In specific cases, miRNAs can also stabilize target mRNAs [2] or even activate their translation [3]. Substantial progress has been made in recent years in the understanding of miRNA biogenesis process (reviewed in [4]). Most miRNA genes are transcribed by RNA polymerase II as long primary transcripts, or primary (pri)-miRNAs [5,6], but some miRNAs can be also transcribed by RNA polymerase III [7]. The pri-miRNA transcripts fold into stem-loop structures that are recognized and cleaved in the nucleus by RNase III-type nuclease Drosha