RT Journal Article
T1 Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot
A1 Aramburu González, Óscar
A1 Gómez Pardo, María Belén
A1 Rodríguez Villamayor, Paula
A1 Blanco Hortas, Andrés
A1 Lamas Fernández, Jesús
A1 Bouza Fernández, María Carmen
A1 Martínez Portela, Paulino
K1 Turbot
K1 Immune response
K1 Epigenomics
K1 Chromatin state
K1 Transcription factor
AB 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.
PB Oxford University Press
SN 2047-217X
YR 2025
FD 2025-07-15
LK https://hdl.handle.net/10347/43070
UL https://hdl.handle.net/10347/43070
LA eng
NO Oscar Aramburu, Belén Gómez-Pardo, Paula Rodríguez-Villamayor, Andrés Blanco-Hortas, Jesús Lamas, Pooran Dewari, Diego Perojil-Morata, Pierre Boudinot, Daniel J Macqueen, Carmen Bouza, Paulino Martínez, Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot, GigaScience, Volume 14, 2025, giaf077, https://doi.org/10.1093/gigascience/giaf077
NO This study was funded by the AQUA-FAANG project, which received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 817923. Additional funding was provided by the Xunta de Galicia local government (Spain) (ED431C 2022/33), which also supported the research fellowships of O.A. and P.R.V. (refs. ED481A-2020/119 and ED481A-2020/491430, respectively). Contributions from the Roslin Institute were further supported by the BBSRC Institutional Strategic Programme grants BBS/E/D/10002070, BBS/E/D/20002174, BBS/E/RL/230001B, and BBS/E/RL/ 230002B.
DS Minerva
RD 24 abr 2026