Bioproject ID: PRJNA634937

bioproject id PRJNA634937      to NCBI
key word Challenge; GCRV; Genome-wide DNA methylation; Grass carp; Grass carp reovirus; Age-dependent viral susceptibility; Epigenetic mechanism; Immune response; Biosynthesis; Energy metabolism; provides insights; gene-expression; infection; promoter; pathways; aligner
experiment type challenge
publication He, Libo , et al. "Genome-wide DNA methylation reveals potential epigenetic mechanism of age-dependent viral susceptibility in grass carp." Immunity & Ageing 19.1(2022):1-17.
description The grass carp showed age-dependent susceptibility to GCRV. Five months old grass carp was sensitive to GCRV while three years old grass carp was resistant to the virus. However, the mechanism of this phenomenon was unclear. Therefore, we performed transcriptome sequencing of five months old and three years old grass carp aim to uncover the mechanism underlying this phenomenon.
abstract Background Grass carp are an important farmed fish in China that are infected by many pathogens, especially grass carp reovirus (GCRV). Notably, grass carp showed age-dependent susceptibility to GCRV; that is, grass carp not older than one year were sensitive to GCRV, while those over three years old were resistant to this virus. However, the underlying mechanism remains unclear. Herein, whole genome-wide DNA methylation and gene expression variations between susceptible five-month-old (FMO) and resistant three-year-old (TYO) grass carp were investigated aiming to uncover potential epigenetic mechanisms. Results Colorimetric quantification revealed that the global methylation level in TYO fish was higher than that in FMO fish. Whole-genome bisulfite sequencing (WGBS) of the two groups revealed 6214 differentially methylated regions (DMRs) and 4052 differentially methylated genes (DMGs), with most DMRs and DMGs showing hypermethylation patterns in TYO fish. Correlation analysis revealed that DNA hypomethylation in promoter regions and DNA hypermethylation in gene body regions were associated with gene expression. Enrichment analysis revealed that promoter hypo-DMGs in TYO fish were significantly enriched in typical immune response pathways, whereas gene body hyper-DMGs in TYO fish were significantly enriched in terms related to RNA transcription, biosynthesis, and energy production. RNA-seq analysis of the corresponding samples indicated that most of the genes in the above terms were upregulated in TYO fish. Moreover, gene function analysis revealed that the two genes involved in energy metabolism displayed antiviral effects. Conclusions Collectively, these results revealed genome-wide variations in DNA methylation between grass carp of different ages. DNA methylation and gene expression variations in genes involved in immune response, biosynthesis, and energy production may contribute to age-dependent susceptibility to GCRV in grass carp. Our results provide important information for disease-resistant breeding programs for grass carp and may also benefit research on age-dependent diseases in humans.

Sample Information

sample id sample name tissue strain treatment description
1. SRR11855142 TYO-1 Spleen Grass carp reovirus (GCRV) Three years old grass carp Three years old, replicate 1
2. SRR11855143 TYO-2 Spleen Grass carp reovirus (GCRV) Three years old grass carp Three years old, replicate 2
3. SRR11855144 TYO-3 Spleen Grass carp reovirus (GCRV) Three years old grass carp Three years old, replicate 3
4. SRR11855145 FMO-1 Spleen Grass carp reovirus (GCRV) Five months old grass carp Five months old, replicate 1
5. SRR11855146 FMO-2 Spleen Grass carp reovirus (GCRV) Five months old grass carp Five months old, replicate 2
6. SRR11855147 FMO-3 Spleen Grass carp reovirus (GCRV) Five months old grass carp Five months old, replicate 3