Functional Characterization of Long Non-Coding RNAs Associated with Reproductive Fitness in Pura Raza Española Mares

Long non-coding RNAs (lncRNAs) are transcripts constituted of more than 200 nucleotides that have been associated with the regulation of different biological processes by modulating the expression of key genes. In horses, evidence suggests that lncRNAs play a role in female reproductive fitness, yet their functional implications remain poorly characterized. The objective of this study was to investigate potential DNA:RNA triplex interactions between the promoter regions of fertility-related genes and lncRNAs transcribed from non-coding loci located within ±50 kb of these genes. By doing so, we aimed to elucidate the regulatory mechanisms underlying fertility in Pura Raza Española (PRE) horses. The observed distances (1.2-49.8 kb) were consistent with cis-acting lncRNAs. Furthermore, genomic context and structural accessibility analyses revealed that some predicted DNA-binding sites reside within CpG islands. This strategic localization in active promoter regions points toward a regulatory mechanism where lncRNAs may modulate transcriptional activity via triplex formation. Our results provide a concrete set of biologically plausible lncRNAs within fertility-associated genomic regions, representing targets for further functional validation and potential applications in genomic improvement strategies.