Clustering and conservation patterns of human microRNAs

Yael Altuvia, Pablo Landgraf, Gila Lithwick, Naama Elefant, Sébastien Pfeffer, Alexei Aravin, Michael J Brownstein, Thomas Tuschl, Hanah Margalit, Yael Altuvia, Pablo Landgraf, Gila Lithwick, Naama Elefant, Sébastien Pfeffer, Alexei Aravin, Michael J Brownstein, Thomas Tuschl, Hanah Margalit

Abstract

MicroRNAs (miRNAs) are approximately 22 nt-long non-coding RNA molecules, believed to play important roles in gene regulation. We present a comprehensive analysis of the conservation and clustering patterns of known miRNAs in human. We show that human miRNA gene clustering is significantly higher than expected at random. A total of 37% of the known human miRNA genes analyzed in this study appear in clusters of two or more with pairwise chromosomal distances of at most 3000 nt. Comparison of the miRNA sequences with their homologs in four other organisms reveals a typical conservation pattern, persistent throughout the clusters. Furthermore, we show enrichment in the typical conservation patterns and other miRNA-like properties in the vicinity of known miRNA genes, compared with random genomic regions. This may imply that additional, yet unknown, miRNAs reside in these regions, consistent with the current recognition that there are overlooked miRNAs. Indeed, by comparing our predictions with cloning results and with identified miRNA genes in other mammals, we corroborate the predictions of 18 additional human miRNA genes in the vicinity of the previously known ones. Our study raises the proportion of clustered human miRNAs that are <3000 nt apart to 42%. This suggests that the clustering of miRNA genes is higher than currently acknowledged, alluding to its evolutionary and functional implications.

Figures

Figure 1
Figure 1
Cumulative distance distribution of miRNA genes and other types of human genomic functional elements. For each of the described elements, the distances (in nucleotides) between every two same-chromosome same-strand successive elements were calculated. Distance is drawn on a logarithmic scale. The different elements are marked: orange (exon of protein-coding genes), green (protein-coding gene), black (snoRNA), blue (tRNA), red (miRNA) and cyan (snRNA). The genomic coordinates were derived from the UCSC July 2003 human genome assembly build 34, hg16 (20,21) (). Protein-coding genes and exons were based on the refGene and knownGene tables. SnoRNA, tRNA and snRNA pseudogenes were excluded.
Figure 2
Figure 2
Conservation patterns of known and predicted human miRNAs. The conservation patterns are based on the UCSC phastCons scores (22,23) (). The chromosomal regions of the miRNAs with an additional 3000 nt flanking on both sides are presented. The chromosomal coordinates follow the build 34 assembly (hg16) of the human genome from UCSC (20,21) (). For simplicity the x-axis displays the relative positions. Known miRNAs are designated by their Rfam name omitting the ‘hsa’ prefix (19). The predicted miRNAs that were verified experimentally fall into two categories: (E)-verified experimentally in this study, and (S)-verified by similarity to a homologous miRNA in another organism. The miRNA orientation is marked by an arrow. (A) known large miRNA cluster; (B) known miRNA clustered pair; (C) example of a miRNA prediction that extends a known pair cluster; (D) reveals a new multi-member cluster; and (E) reveals a new clustered pair. The plots are not plotted to scale and, therefore, the conserved region width is a function of the length of the presented region; the longer the region, the narrower is the presented profile).

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