Supporting data for "Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot"

Uncovering the epigenomic regulation of immune response is essential for a comprehensive understanding of host defence mechanisms, though it remains poorly investigated in farmed fish.<br>We report the first annotation of the response of turbot (<i>Scophthalmus maximus</i>) immune cells to viral (poly I:C) and bacterial (inactive <i>Vibrio anguillarum</i>) mimics, integrating RNA-Seq with ATAC-Seq and ChIP-Seq (H3K4me3, H3K27ac, and H3K27me3) data from head kidney (in vivo) and primary leukocyte cultures (in vitro) 24 hours post-stimulation. Among the 8,797 differentially expressed genes (DEGs), we observed enrichment of transcriptional activation pathways in response to <i>Vibrio</i> and immune pathwaysincluding interferon-stimulated genesfor poly I:C. We identified notable differences in chromatin accessibility (20,617 in vitro, 59,892 in vivo) and H3K4me3-bound regions (11,454 in vitro, 10,275 in vivo) between stimulations and controls. Overlap of DEGs with promoters showing differential accessibility or histone mark binding revealed significant coupling of the transcriptome and chromatin state. DEGs with activation marks in their promoters were enriched for similar functions to the global DEG set, but not always, suggesting key regulatory genes being in a poised state. Active promoters and putative enhancers were enriched in specific transcription factor binding motifs, many common to viral and bacterial responses. An in-depth analysis of chromatin state surrounding key DEGs encoding transcription factors was also performed to understand turbot immune response.<br>This multi-omics investigation provides an improved understanding of the epigenomic basis of turbot immune response to mimics of viral and bacterial stimuli and offers novel functional genomic information that provides a valuable resource for exploring immune regulation in flatfish.