MicroRNA enrichment among short 'ultraconserved' sequences in insects

Abstract

MicroRNAs are short (approximately 22 nt) regulatory RNA molecules that play key roles in metazoan development and have been implicated in human disease. First discovered in Caenorhabditis elegans, over 2500 microRNAs have been isolated in metazoans and plants; it has been estimated that there may be more than a thousand microRNA genes in the human genome alone. Motivated by the experimental observation of strong conservation of the microRNA let-7 among nearly all metazoans, we developed a novel methodology to characterize the class of such strongly conserved sequences: we identified a non-redundant set of all sequences 20 to 29 bases in length that are shared among three insects: fly, bee and mosquito. Among the few hundred sequences greater than 20 bases in length are close to 40% of the 78 confirmed fly microRNAs, along with other non-coding RNAs and coding sequence.

Figure 1

Fractions of unfiltered maximal 25mer hits to repeat-masked fly genome with a given annotation from FlyBase; see caption to Table 2 for details and abbreviations. Corresponding figures for all lengths are available in Supplementary Figures 1-unfiltered and 1-filtered. Annotations were counted as described in Materials and Methods: annotations. A single hit can have multiple annotations; consequently, the sum of the hit fractions displayed in the figure may exceed unity.

Figure 2

Fraction of unfiltered maximal 25mers with annotations from FlyBase, for a 0.2% random sample of distinct 25mers from the repeat-masked fly genome, and for binary and ternary intersections with fly genome. The number of maximal 25mers in the intersection is displayed inside the parentheses, followed by P-value. Corresponding figures for all other values of N are available in Supplementary Figures 2-unfiltered and 2-filtered.