Prenatal nutrition modulates hepatic long non-coding RNA regulatory elements in Nellore cattle offspring

This study investigated the effects of maternal nutrition on hepatic long non-coding RNA (lncRNA) expression in Nellore cattle offspring. To this end, a total of 126 pregnant cows were assigned to three dietary treatments: not programmed (mineral supplementation only), partial programming (late protein-energy supplementation), and full programming (protein-energy supplementation throughout pregnancy). At 676±28 days of age, liver samples were collected from the offspring to perform RNA-sequencing. Novel lncRNAs were identified with FEELnc and CPC2, and differentially expressed lncRNAs (DELs) with DESeq2. Partial correlation, information theory, and regulatory impact factor were used to identify key regulatory roles, while over-representation analysis was performed to detect enriched processes. Among the 3,257 lncRNAs identified, 17 were DELs (false discovery rate<0.1). The PPxNP comparison exhibited the highest transcriptional changes (10 DELs), including IncRNA TU7296, identified as a potential regulator of energy metabolism and immune function, as well as molecular functions associated with oxidative metabolism. The FPxNP comparison revealed distinct regulation of genes related to fatty acid transport and oxidative protein folding. The FPxPP comparison showed minimal differences, highlighting the similarity between these groups. This study provides insights into the role of maternal nutrition in modulating long-term epigenetic programming via lncRNA-mediated mechanisms in beef cattle offspring.