Bioinformatics Analysis Of Porcine Micrornas And Their Promoters

MicroRNA (miRNA) is a pivotal type of non-coding RNA genes involved in the processof post-transcriptional gene regulation. They have been found in the genomes of allmulticellular eukaryote so far and increasing evidence demonstrates that miRNAs haveevolved as a major class of gene-regulatory molecules critical for diverse biological process,such as development, apoptosis, cell fate and differentiation.The pig, Sus scrofa, is an important livestock species in animal production industry. Theanalysis on pig genome has progressed rapidly during the past years, and increasing evidencesshow that there is extensive conserved homology between pig genome and human genome.Pig is closely related to human in terms of anatomy, genetics and physiology, and representsan excellent animal model to study various human diseases.Currently, a majority of miRNAs in the pig remain unknown. This research stemmedprecisely from this perspective and the genome-wide identification of novel porcine miRNAs.Here, we proposed a novel integrative bioinformatics pipeline to identify conservative andnon-conservative novel miRNAs. We used methods such as homology searching againstknown metazoan miRNAs, conservation filtering, and ab initio approaches. As a result,222new porcine miRNAs were identified, and14more porcine miRNA gene families were found.An overall analysis of genome-scale gene locations and sequence characteristics was alsoconducted. Results showed that these newly identified pig miRNA have a similar pattern withpreviously known miRNA. Some chromosomes are relatively miRNA deserts (such aschromosomes8) while others encode large numbers of miRNAs (such as chromosomes X).Previous studies have shown that animal miRNAs are either expressed from independenttranscription or transcribed with their host genes. Currently, little is known about thetranscriptional regulation of porcine miRNAs. In this study, we conducted the genomicanalysis of the previously documented porcine miRNAs on their transcripts around thepromoter region including the transcription start site (TSSS) and the TATA-box. We identified183promoters for205porcine pre-miRNA sequences via bioinformatics approach. Amongthem, the portion of intergenic porcine miRNAs is greater than that of intronic ones. It is alsofound that the non-conserved porcine miRNAs have a greater proportion of promoters thanthe non-conserved ones. Further, the genomic organization of known porcine pre-miRNAswas globally analyzed and found that80of them were grouped into32clusters in the pig genome. Moreover, we performed the analysis of the transcriptional regulation of the miRNAclusters.Through this study, an effective alternative strategy for genome-wide miRNAidentification was developed and the number of identified porcine miRNAs increased. Also,these findings may aid our understanding of the characteristics of porcine and of the specificsequence upstream of porcine pre-miRNAs. We hope our study may make contribute tofurther researches on the function and regulatory mechanisms of miRNAs in pig.