Integrative and differential analysis of transcriptomes and chromatin accessibility regions reveals regulatory mechanisms involved in pig immune and metabolic functions

In the context of the FAANG pilot project ‘FR-AgENCODE’ to improve the functional annotation of livestock genomes, we characterised the transcriptome and the chromatin accessibility of pig hepatocytes and two types of lymphocytes. More specifically, CD3+CD4+ (‘CD4’) and CD3+CD8+ (‘CD8’) T-cells were sorted from the blood of two male and two female Large White adult pigs. These samples, along with liver samples from the same animals, were processed by strand-oriented RNA-seq and ATAC-seq experiments. Principal Component Analyses on log-transformed TMM-normalized read counts in genes (from RNA-seq) and regions of chromatin accessibility (from ATAC-seq) consistently highlighted the variability between liver and the T-cells, and to a lesser extent within T-cells (CD4 v. CD8), as well as between the male and female samples. Comparative analyses identified differentially expressed genes between cell types as well as potential regulatory sites from differentially accessible chromatin regions. As expected, ontology annotations of differentially expressed genes were enriched for either immunity- or metabolism-related terms. Interestingly, correlations between gene expression and promoter accessibility across samples were enriched for both extreme positive and negative values, which suggests that ATAC-seq can efficiently capture distinct regulatory mechanisms of gene expression. Candidate enhancers and repressors were identified by comparing ATAC-seq regions with predicted binding sites of 500+ transcription factors. By integrating these results with those from Hi-C chromosome con-formation capture on the liver samples, we further characterised the differences between ‘active’ and ‘repressed’ topological domains in terms of functional features, including gene density and general chromatin accessibility. Altogether, these results lead to a better un-derstanding of the molecular mechanisms involved in pig immune and metabolic functions, and illustrate a useful contribution to the functional annotation effort of the FAANG initiative.