Title:In-Silico Algorithms for the Screening of Possible microRNA Binding Sites and Their Interactions
VOLUME: 14 ISSUE: 2
Author(s):Harsh Dweep, Carsten Sticht and Norbert Gretz
Affiliation:Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg, D-68167 Mannheim, Germany.
Keywords:microRNAs, miRWalk, Target prediction, Promoter, CDS, UTR, Prediction algorithm, Database
Abstract:MicroRNAs (miRNAs) comprise a recently discovered class of small, non-coding RNA molecules of 21-25
nucleotides in length that regulate the gene expression by base-pairing with the transcripts of their targets i.e. proteincoding
genes, leading to down-regulation or repression of the target genes. However, target gene activation has also been
described. miRNAs are involved in diverse regulatory pathways, including control of developmental timing, apoptosis,
cell proliferation, cell differentiation, modulation of immune response to macrophages, and organ development and are
associated with many diseases, such as cancer. Computational prediction of miRNA targets is much more challenging in
animals than in plants, because animal miRNAs often perform imperfect base-pairing with their target sites, unlike plant
miRNAs which almost always bind their targets with near perfect complementarity. In the past years, a large number of
target prediction programs and databases on experimentally validated information have been developed for animal miRNAs
to fulfil the need of experimental scientists conducting miRNA research. In this review we first succinctly describe
the prediction criteria (rules or principles) adapted by prediction algorithms to generate possible miRNA binding site interactions
and introduce most relevant algorithms, and databases. We then summarize their applications with the help of
some previously published studies. We further provide experimentally validated functional binding sites outside 3’-UTR
region of target mRNAs and the resources which offer such predictions. Finally, the issue of experimental validation of
miRNA binding sites will be briefly discussed.
