ArticleGigaScience2025
Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot.
Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
3 citing papers in PubMed.
- Chromatin Accessibility Reveals Adaptive Regulatory Variation in a Keystone Freshwater Fish.Molecular ecology · 2026Article
- An Integrative ATAC-Seq and RNA-Seq Analysis of Spleen Tissues from Largemouth Bass (International journal of molecular sciences · 2026Article
- Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot.GigaScience · 2025Article
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Authors and funding
11 authors.
Funding
Abstract
backgroundUncovering the epigenomic regulation of immune response is essential for a comprehensive understanding of host defense mechanisms, though it remains poorly investigated in farmed fish.
resultsWe report the first annotation of the response of turbot (Scophthalmus maximus) immune cells to viral (poly I:C) and bacterial (inactive Vibrio anguillarum) mimics, integrating RNA sequencing with assay for transposase-accessible chromatin (ATAC) sequencing (ATAC-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) (H3K4me3, H3K27ac, and H3K27me3) data from head kidney (in vivo) and primary leukocyte cultures (in vitro) 24 hours after stimulation. Among the 8,797 differentially expressed genes (DEGs), we observed enrichment of transcriptional activation pathways in response to Vibrio and immune pathways-including interferon-stimulated genes-for 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.
conclusionsThis multiomics investigation provides an improved understanding of the epigenomic basis of turbot immune response to mimics of viral and bacterial stimuli, offering novel functional genomic information that provides a valuable resource for exploring immune regulation in flatfish.
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Registered trials
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