Target sequences for microRNAs within the Tff gene cluster

Abstract

Despite the increasing interest focusing on control of gene activity by microRNAs this abundant class of thousands of regulatory transcripts still requires elucidation of open questions concerning selection of targets and mechanisms of complementarity, multiplicity and cooperativity of microRNAs, to name some immediate issues. In silico microRNA target prediction is often the first line of approaching the complex system and helping in setting search priorities for experimental validation of such mechanisms of gene control. We now used a well studied gene cluster coding for the trefoil peptide family (Tff1, Tff2, Tff3) with all its sequence data and information on factors driving gene expression and a combined computer-based set of target prediction programs to collect microRNAs involved in Tff gene regulation. The sequence preference of specific microRNAs was mapped and their multiplicity and cooperativity were denoted to establish an interactive regulatory profile. This computational venue will subsequently allow enhanced and specific in vitro confirmation of the regulatory networks in cellular systems and possibly later on in transgenic animal models.