RNA22

Rna22 is a pattern-based algorithm for the discovery of microRNA target sites and the corresponding heteroduplexes.

The algorithm is conceptually distinct from other methods for predicting microRNA:mRNA heteroduplexes in that it does not use experimentally validated heteroduplexes for training, instead relying only on the sequences of
known mature miRNAs that are found in the public databases. The key idea of rna22 is that the reverse complement of any salient sequence features that one can identify in mature microRNA sequences (using pattern discovery techniques) should allow one to identify candidate microRNA target sites in a sequence of interest: rna22 makes use of the Teiresias algorithm to discover such salient features. Once a candidate microRNA target site has been located, the targeting microRNA can be identified with the help of any of several algorithms able to compute RNA:RNA heteroduplexes. A new version (v2.0) of the algorithm is now available: v2.0-beta adds probability estimates to each prediction, gives users the ability to choose the sensitivity/specificity settings on-the-fly, is significantly faster than the original, and can be accessed through http://cm.jefferson.edu/rna22/Interactive/.

Rna22 neither relies on nor imposes any cross-organism conservation constraints to filter out unlikely candidates; this gives it the ability to discover microRNA binding sites that may not be conserved in phylogenetically proximal organisms. Also, as mentioned above, rna22 can identify putative microRNA binding sites without needing to know the identity of the targeting microRNA. A notable property of rna22 is that it does not require the presence of the exact reverse complement of a microRNA's seed in a putative target permitting bulges and G:U wobbles in the seed region of the heteroduplex. Lastly, the algorithm has been shown to achieve high signal-to-noise ratio.

Use of rna22 led to the discovery of "non-canonical" microRNA targets in the coding regions of the mouse Nanog, Oct4 and Sox2. Most of these targets are not conserved in the human orthologues of these three transcription factors even though they reside in the coding region of the corresponding mRNAs. Moreover, most of these targets contain G:U wobbles, one or more bulges, or both, in the seed region of the heteroduplex. In addition to coding regions, rna22 has helped discover non-canonical targets in 3'UTRs.

A recent study examined the problem of non-canonical miRNA targets using molecular dynamics simulations of the crystal structure of the Argonaute-miRNA:mRNA ternary complex. The study found that several kinds of modifications, including combinations of multiple G:U wobbles and mismatches in the seed region, are admissible and result in only minor structural fluctuations that do not affect the stability of the ternary complex. The study also showed that the findings of the molecular dynamics simulation are supported by HITS-CLIP (CLIP-seq) data. These results suggest that bona fide miRNA targets transcend the canonical seed-model in turn making target prediction tools like rna22 an ideal choice for exploring the newly augmented spectrum of miRNA targets.

References 

RNA
MicroRNA
Pattern matching