A compendium and comparative analysis of hepatic transcriptome and chromatin accessibility in primiparous lactating cows with different nitrogen utilization efficiency

Background The liver is central to regulating nitrogen utilization efficiency (NUE), defined as the ratio of milk nitrogen yield (g/d) to nitrogen intake (g/d) in dairy cows. Identifying the regulatory elements in the liver that affect nitrogen utilization is essential for understanding the factors influencing NUE. Results This study employed RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin sequencing (ATAC-seq) to profile the liver transcriptome and chromatin accessibility in primiparous lactating cows with divergent NUE. We monitored 16 primiparous lactating cows with days in milk ranging from 95 to 115. Over a period of 7 consecutive days, we measured their nitrogen intake and milk nitrogen yield to calculate individual NUE. Based on the NUE values obtained, the cows were categorized into two groups: low NUE (LNUE) with an average NUE of 22.6 ±6.2% (n = 8) and high NUE (HNUE) with an average NUE of 33.1 ±2.2% (n = 8). Liver samples were used for RNA-Seq and ATAC-Seq analysis, identifying 213 differentially expressed genes (DEGs, |fold change| ≥ 1.5, P < 0.05) and 3716 differential accessible regions (DARs, |fold change| ≥ 1.5, P < 0.01), respectively. Among these, 109 DEGs and 1342 DARs were upregulated, while 104 DEGs and 2374 DARs were downregulated in HNUE samples compared to LNUE samples. The DEGs were significantly enriched in 126 biological processes (gene ontology), with 97 normalized enrichment scores (NES) being positive, primarily related to immune processes, while 29 NES were negative, mainly related to metabolic processes and the maintenance of liver structure and function. Promoter-annotated DAR-associated genes were significantly enriched in 173 biological processes, primarily related to the maintenance of liver structure and function. Protein-protein interaction network analysis showed that 47 DEGs generated 37 protein-protein interactions, with genes PRKG1 and HBB being central in the network. Integrated analysis of RNA-seq and ATAC-seq identified one overlapping upregulated gene, TGM5 , and one overlapping downregulated gene, ROR1 . Conclusion These findings demonstrate that hepatic transcriptome and chromatin accessibility epigenetically regulate NUE in primiparous lactating cows.