• Calendar

August 7, Tuesday
12:00 – 13:00

MicroRNAs (miRNAs) are an abundant class of small non-coding RNAs that can affect gene expression by post-transcriptional regulation of mRNAs. miRNAs have been shown to play important roles in various cellular and pathogenic processes. Some viral organisms also encode miRNAs, a fact that contributes to the complex interactions between viruses and their hosts. miRNAs down-regulate translation of genes via imperfect binding of the miRNA to a specific site or sites on their coding transcripts. A critical step in miRNA functional studies is to identify the target genes that are directly regulated by miRNAs. The current target prediction tools have two major limitations. First, they are time consuming for large datasets. Second, they are noisy and predict an excess of targets for each miRNA. To overcome the first limitation, we developed our own method for target prediction, which extends the "threshold all-against-all" sequence alignment algorithm. To get over the second limitation, we developed methods, related to bi-clustering, that combine target prediction results with new host-viral post transcriptional regulation modes and additional information sources, and narrow the list of target genes to more reliable candidates. Our algorithm, called bi-targeting, searches for modules of miRNAs (host and viral) and their common host target genes that have a similar biological function. We applied it to the discovery of modules consisting of human and Epstein-Barr virus (EBV) miRNAs and human genes, in a cooperating mode of regulation. Later we relaxed the bi-targeting algorithm to compute quasi-modules, where many more interactions were captured and reported. We used our new relaxed bi-targeting algorithm to study the compensating regulation of miRNAs in Human cytomegalovirus (HCMV) infection, using new expression data of miRNAs in HCMV infected vs. un-infected cells. Since not much is known about the function of viral miRNAs, finding modules that link the viral miRNAs and the human miRNAs, might help in understanding the role of miRNAs in host-viral interactions. Furthermore, since the identification and validation of miRNA targets remains a hard problem, focusing on small sets of miRNAs and their effects on particular biological pathways may give a significant advantage in target identification.