Transcriptomic profiling of long non-coding RNAs as regulatory elements associated with bovine feed efficiency

Description

This study investigated the hypothesis that hepatic long non-coding RNAs (lncRNAs) contribute to variation in feed efficiency in dairy cattle and respond to differences in dietary composition. Publicly available liver RNA-Seq data (NCBI GEO: GSE92398) from Jersey cattle classified as low- or high-residual feed intake (RFI) and sampled following exposure to both a control and a high-concentrate diet were used to characterize the hepatic lncRNA repertoire. Transcriptome reconstruction and lncRNA discovery yielded 4,929 high-confidence lncRNA transcripts, which were subsequently analyzed for differential expression. The data show that lncRNA expression was influenced by both diet and FE phenotype. More differentially expressed lncRNAs were identified under the HC diet than under the control diet, and low-RFI animals exhibited a greater transcriptional response to dietary change than high-RFI animals. Co-localization and expression analyses identified potential regulatory relationships between lncRNAs and protein-coding genes, including SLC1A2 and GIMAP8. Functional enrichment analyses implicated biological processes related to autophagy, vesicle trafficking, and metabolism.These findings suggest that lncRNAs may contribute to diet-responsive regulatory networks associated with FE. This repository contains supplementary outputs derived from the analytical pipeline applied to this dataset, including differential expression results for low-RFI animals, FEELnc lncRNA annotation outputs, and supporting visualizations.

Institutions

• University of Guelph

  Ontario, Guelph

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