Loss of multiple micro-RNAs uncovers multi-level restructuring of gene regulation in rodents.

BACKGROUND: The regulatory network that coordinates gene expression ultimately determines the phenotype of an organism. Micro-RNAs (miRNAs) are post-transcriptional regulators involved in key biological processes. Lineage-specific losses of multiple miRNA families are rare, and reported cases of multiple miRNA losses coincide with significant changes in gene regulation resulting in body plan modifications. Recently, 15 mammalian miRNA families were found to be missing in the Eumuroidea, the rodent lineage that includes the model organisms mouse and rat. However, the impact of their absence on the gene regulatory networks in this lineage remains unknown. RESULTS: The in silico characterization of all 15 miRNAs revealed that their absence is best explained by multiple independent losses. Analyzing their target genes in humans reveals a significant enrichment of GO-terms linked to cellular and developmental processes. Overexpressing two of the co-absent miRNAs, Mir-197 and Mir-769, in human and mouse inducible pluripotent stem cells (iPSCs) resulted in significantly perturbed expression patterns in both species. In silico target site prediction revealed a significant enrichment of direct targets exclusively in the down-regulated genes. Four genes were down-regulated in both mouse and human and maximum parsimony suggests that the corresponding miRNA target sites were already present in the last common ancestor of mammals. The response of these genes to miRNA overexpression in mice, therefore, unveils remnants of the ancient gene regulatory network that have persisted until today. The evolutionary age of these regulatory connections provides initial evidence that the miRNA losses in Eumuroidea must have had consequences for the regulation of gene expression. We further show that the miRNA loss is embedded into a broader context of regulatory adaptation in the Eumuroidea, since it coincides with the largest lineage-specific loss of transcription factors observed within mammals. CONCLUSIONS: The impact of miRNA losses has thus far been investigated on a gene-by-gene basis. Our findings indicate that cooperative effects between miRNAs should be considered when assessing the impact of miRNA loss. We provide evidence that the Eumuroidea have modified their gene regulatory networks on two levels, transcriptionally and post-transcriptionally. It will now be interesting to precisely chart the differences in gene regulation and assess their combined impact on the suitability of mice and rats as model systems for human disease. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-11815-3.