In silico identification of miRNAs potentially targeting the genes that regulate protein transport and translocation in cattle in heat stress response

MicroRNAs (miRNAs) are involved in post-transcriptional gene regulation and single miRNAs regulating multiple mRNAs targets. Using bioinformatics approaches, this work aims to identify and characterize the miRNAs that could potentially bind with PDKCC, AP3S2 and SEC61A2 gene which regulate protein transport during heat stress. To resolve this problem, three freely available online miRNAs target finder databases were applied to identify the potential miRNAs which may target PDKCC, AP3S2 and SEC61A2 gene. The prediction results showed that a total of 115, 67 and 25 miRNAs for PDKCC, 267, 111 and 12 miRNAs for AP3S2 and 92, 120 and 31 miRNAs for SEC61A2 were identified as a possible potential candidate by TargetScan, MirTarget2 and miRanda respectively. Following the clustering process, we found eight miRNAs for PDKCC, three for AP3S2 and nine for SEC61A2s identified as possible candidates by all three databases. Five miRNAs in PDKCC, four in AP3S2 and five in the SEC61A2 gene have 100% identical sequence resemblance between human and bovine miRNAs. miRNAs binding site analysis showed that miR-34a in AP3S2 and miR-377 in SEC61A2 has the highest number of binding sites while miR-30b and miR-30c have two binding sites in 3 ' UTR of SEC61A2 gene whereas the rest of the miRNAs have the lowest number of the binding site in PDKCC and SEC61A2 gene respectively. Our study identified total four potential miRNAs that have different binding sites at the AP3S2 and SEC61A2 3 ' UTR site along with seven miRNAs which have single binding site and can modulate protein transport, translocation and other cellular pathways.