A Multi-Tissue Yak (Bos grunniens) ceRNA Atlas with Ribo-Seq-Informed lncRNA Curation and Candidate Prioritization

The yak (Bos grunniens) thrives under chronic hypoxia and cold on the Qinghai-Tibet Plateau, yet a cross-tissue view of post-transcriptional regulation in this species remains limited. Here, we integrated multi-tissue RNA-seq and miRNA-seq data (tissues pooled from three Maiwa yaks) to construct and compare tissue-specific competing endogenous RNA (ceRNA) networks, while explicitly addressing a major source of false positives in ceRNA inference-misclassified lncRNA candidates with translational signatures. We cataloged 10,037 high-confidence lncRNAs (9360 non-redundant), 234 circRNAs, and 1030 miRNAs across six tissues. We then used Ribo-seq as an orthogonal quality-control layer to remove lncRNA candidates showing clear ribosome-association signals prior to network construction. Using a shared-target strategy (7mer-m8 seed matches; a ceRNA edge required ≥5 shared miRNAs), we assembled ceRNA networks for liver, lung, spleen, testis, and small intestine; skeletal muscle was excluded owing to insufficient Ribo-seq support for consistent filtering. Network topology varied substantially across tissues, with the testis network exhibiting the highest connectivity. ceRNA edges showed minimal overlap between tissues, indicating strong tissue dependence, whereas miRNA load/use profiles were moderately concordant, supporting a hierarchical conserved core-variable periphery organization. Importantly, the Ribo-seq-filtered lncRNA set provides a separate pool of ribosome-associated candidates for targeted follow-up, although ribosome association alone does not establish stable micropeptide production. Together, our results deliver a multi-tissue ceRNA resource and a reproducible, evidence-aware workflow for prioritizing candidate regulators while reducing annotation-driven false positives in yak.