Lower expression of genes near microRNA in C. elegans germline

We analyzed gene expression levels around the 84 of 113 know miRNAs for which there are nearby gene that were measured in the data in two independent C. elegans expression data sets. The expression levels are lower for genes in the vicinity of 59 of 84 (71%) miRNAs as compared to genes far from such miRNAs. Analysis of the genes with lower expression in proximity to the miRNAs reveals increased frequency matching of the 7 nucleotide "seed"s of these miRNAs.We found decreased messenger RNA (mRNA) abundance, localized within a 10 kb of chromosomal distance of some miRNAs, in C. elegans germline. The increased frequency of seed matching near miRNA can explain, in part, the localized effects.MicroRNAs (miRNAs) are short (~22 nt-long) non-protein-coding RNAs. In metazoans, miRNA initially thought to be primarily involved in post-transcriptional control [1] have now been shown to have profound and tissue-specific effects on mRNA transcript abundance across significant fractions of the transcriptome [2]. Concurrently it has been demonstrated that miRNAs have a central role in development and organogenesis [3,4]. In the context of the apparent interactions between miRNA and transcriptional control and mounting evidence for the localized component of transcriptional control [5,6], we performed a genome-wide study of C. elegans to determine a) if there were localized effects of miRNA on transcription and b) if previously identified "seed matching" between miRNA and their gene targets could explain, in part, the observed decrease in expression around some miRNAs.First, the 113 known miRNAs in C. elegans were mapped to the worm genome and genes near each miRNAs were sought. Ninety-six miRNAs were found with at least one gene within 10 kb and 31 miRNA were found within the introns of protein-coding genes. Detailed information about the miRNAs is found in supplemental data. Two experiments of genome-wide expression profiling in C. elegans were analyzed. The first dataset by Kim e