Lower expression of genes near microRNA in C. elegans germline - PubMed (original) (raw)

Lower expression of genes near microRNA in C. elegans germline

Hidenori Inaoka et al. BMC Bioinformatics. 2006.

Abstract

Background: MicroRNAs (miRNAs) are recently discovered short non-protein-coding RNA molecules. miRNAs are increasingly implicated in tissue-specific transcriptional control and particularly in development. Because there is mounting evidence for the localized component of transcriptional control, we investigated if there is a distance-dependent effect of miRNA.

Results: 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.

Conclusion: 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.

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Figures

Figure 1

Figure 1

Localized decrease in mRNA levels near miRNAs. A and B, The expression levels around each miRNA are plotted against the window width (A: data by Kim et al. [7] and B: germline data [8]). It should be noted that only 83 and 84 miRNAs are shown in A and B, respectively. This is because no protein-coding genes are found near the other miRNAs. Also miRNAs, which were close to each other, having the same expression values of surrounding genes were grouped and treated as a cluster. The information on the numbering of the axis labeled "miRNA" in Figure 1A and 1B is found in supplemental files. C and D, Distributions of the normalized average expression in the 10 kb window (C: Kim and D: germline data) (see the navy blue bars). In these histograms, distributions of the normalized averages in other distance ranges are also plotted: the light blue and yellow bars represent a distance range between 10 kb and 100 kb and a distance range between 100 kb and 1000 kb, respectively. E and F, The average expression levels over all miRNAs are shown (E: Kim and F: germline data). The normalized expression levels of randomly selected genes are also shown in these graphs.

Figure 2

Figure 2

A subset of Kim data, which were obtained from germ cells, showed a stronger effect.

Figure 3

Figure 3

The number of seed pairings around genes in different distance ranges. Both spliced and unspliced mRNA forms of protein-coding genes were investigated.

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