Gestational Feed Restriction Induces Differential Expression of Novel Long Non-Coding RNAs in Offspring Skeletal Muscle

Abstract

This study aimed to investigate how maternal feed restriction at different gestational stages alters the expression of novel long non-coding RNAs (lncRNAs) in the skeletal muscle of goat offspring. LncRNAs are emerging as important regulators of biological processes, including myogenesis, yet their role in fetal programming remains largely unexplored. Using RNA sequencing (RNA-Seq), we analyzed lncRNA expression in the Longissimus thoracis muscle of kids born to goats submitted to two feeding diets: early gestation restriction (50% of maintenance from Day 8–84 of gestation, then 100% until parturition; RM, n = 6) and late gestation restriction (100% from Day 8–84, then 50% until parturition; MR, n = 8). RNA-Seq data underwent quality control, alignment, transcript assembly, and differential expression analysis using Cufflinks and FEELnc pipelines. Three differentially expressed (DE; FDR ≤ 0.05) lncRNAs were identified and classified based on genomic position and predicted regulatory potential. The upregulated lncRNA_10996.1 in the RM group was linked to acyl-CoA dehydrogenase family member 10 and GTP-binding nuclear protein Ran-like genes. The downregulated lncRNAs, lncRNA_1180.1 and lncRNA_7992.1, were associated with ZNF546, PSMC4, SNORA65, ZNF79, LRSAM1, and RPL12 genes. Overall, these results suggest that maternal nutrition restriction is associated with alterations in lncRNA expression profile and may influence muscle development through potential regulatory interactions with protein-coding genes. These findings identified candidate lncRNAs and provide exploratory insights into the molecular mechanisms potentially involved in fetal programming in livestock.