In silico Discovery of Conserved and Novel miRNAs from Expressed Sequence Tags in the Chicken (Gallus gallus

MicroRNAs (miRNAs) and other types of small non-coding RNAs play a crucial role in the regulation of gene expression in eukaryotes either by post-transcriptional degradation or attenuating translation of messenger RNAs. In the case of the chicken (Gallus gallus), knowledge regarding miRNAs is still limited. In the present study, a computational approach was employed to screen miRNAs from the Expressed Sequence Tags (ESTs) of the chicken. A total of 21,298 known miRNAs belonging to 114 metazoan species were searched for homology against more than 192,020 EST sequences of the chicken. Consequently, 60 potential miRNA candidates were identified according to a range of filtering criteria. As a result, four novel miRNAs were found among the identified miRNAs including gga-miR-92a, gga-miR-2438, gga-miR-2970-5p, and gga-miR-2970-3p belonging to miR-92, miR-2438 and miR-2970 families. To predict their targeted genes, a BLAST search was done against the chicken 3' UTR mRNA database. As a result, 678, 422, 171 and 110 targets were determined for gga-miR-92a, gga-miR-2438, gga-miR-2970- 5p, and gga-miR-2970-3p, respectively. Most of the predicted target genes participate in multiple biological processes, including immune system, regulation of cAMP biosynthesis, regulation of cyclase activity and regulation of lyase activity. Finally, a phylogenetic analysis of gga-miR-2970 and gga-miR-92a sequences revealed a close relationship between the chicken and Taeniopygia guttata, while gga-miR-2438 shares maximum percentage sequence similarity with bta-miR-2438 in Bos taurus. The present study is the first attempt to screen microRNAs from ESTs originating from the chicken leading to the identification of novel miRNAs.