Ohno-miRNAs: miRNA pairs derived from whole-genome duplication

Two rounds of whole-genome duplication (WGD) occurred about 500 million years ago and played a major role in the evolution of the vertebrate genomes. Human genes derived from WGD are called “ohnologs”. Ohnologs are involved in fundamental biological processes and significantly contributed to the complexity of the human gene regulatory network. Given the central role of miRNAs in gene regulation, we investigated the contribution of ohnolog miRNAs (ohno-miRNAs) to the human gene regulatory network. We identified intragenic ohno-miRNAs as having higher retention rates compared to intragenic Small Scale Duplicated (SSD) miRNAs. Ohno-miRNAs also show high sequence similarity, a stronger tendency to regulate common target genes and are typically more expressed compared to miRNAs unrelated to WGD events. Analyzing the role of ohno-miRNAs in the human gene regulatory network, we showed that ohno-miRNAs are statistically overrepresented in specific network motifs commonly associated with redundancy and complexity, highlighting their central role in gene regulation.