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

## TL;DR

This study explores how long non-coding RNAs may influence fertility in a specific horse breed by regulating gene expression through DNA:RNA triplex structures.

## Contribution

The study identifies potential lncRNA-gene interactions in fertility-related regions of the horse genome using triplex formation predictions.

## Key findings

- Potential lncRNA-gene interactions were predicted in CpG islands near fertility-related genes in Pura Raza Española mares.
- The predicted lncRNAs are localized within 50 kb of target genes, suggesting cis-regulatory roles.
- Results highlight lncRNAs as possible regulators of reproductive fitness through epigenetic mechanisms.

## Abstract

Reproductive fitness is a key factor in the success of equine breeding programs. However, the molecular mechanisms underlying fertility in mares remain largely unknown. In this study, we focus on long non-coding RNAs, non-coding transcripts that have been recognized as crucial regulators of gene expression. One mechanism through which long non-coding RNAs can regulate gene activity is the formation of DNA:RNA triplex structures. Using computational methods, we analyzed previously published genomic data to predict which long non-coding RNAs could bind to genes known to influence reproductive efficiency in Pura Raza Española mares via triplex formation. The analysis revealed several potential regulatory interactions, mostly found in regions of the genome known as CpG islands, which are often associated with gene promoters and play a key role in the epigenetic regulation of gene expression. These results suggest that long non-coding RNAs may modulate the expression of fertility-related genes through the recruitment of epigenetic regulators. Characterizing these molecular interactions could advance our understanding of the regulatory mechanisms underlying reproductive fitness in horses and identify non-coding regions that may contribute to functionally informed genomic prediction, subject to empirical validation.

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.