Genome-wide DNA methylation reveals potential epigenetic mechanism of age-dependent viral susceptibility in grass carp

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.

Fertilization by short-term stored sperm alters DNA methylation patterns in common carp (Cyprinus carpio) embryos at single-base resolution

“…In general, the contexts of DNA methylation have been identified as CpG, CHH and CHG, but in animal genomes, DNA methylation mostly occurs on the cytosines of a CpG dinucleotide (Lee et al 2010). In fishes, high levels of CpG methylation have been reported, such as 94% in zebrafish (Potok et al 2013), 98% in grass carp ( Ctenopharyngodon idellus ) (He et al 2022), 71-73% in Chinese perch ( Siniperca chuatsi ) (Pan et al 2021), 98% in tiger pufferfish ( Takifugu rubripes ) (Zhou et al 2019), and 76-78% in ricefield eel ( Monopterus albus ) (Chen et al 2021). In this study, the average global methylation level in a CpG context across the nine different common carp embryo samples was 79.71% (Table 2), and a lower methylation level was observed in the CHH (0.86-1.01) and CHG (0.78-0.93).…”

“…Finally, there were no significant changes in epigenetic factors (Cheng et al 2023). However, due to the high variability of global methylation level even with without significant difference observed between groups of embryos derived from fresh and stored sperm (Cheng et al 2023), there may be different site-specific DNA methylation signatures (Khezri et al 2019;He et al 2022).…”

“…Finally, there were no significant changes in epigenetic factors (Cheng et al 2023). However, due to the high variability of global methylation level even with without significant difference observed between groups of embryos derived from fresh and stored sperm (Cheng et al 2023), there may be different site-specific DNA methylation signatures (Khezri et al 2019; He et al 2022). More accurate techniques need to be developed that can provide higher resolution at the single base level, such as whole-genome bisulfite sequencing (WGBS), which is a valuable and extensively used approach.…”

Transcriptomic Responses to Koi Herpesvirus in Isolated Blood Leukocytes from Infected Common Carp

“…The disruption of epigenetic regulation may have contributed towards immunosuppression associated with chronic KHV infection in carp. In grass carp, epigenetic mechanisms such as DNA methylation have been linked to immune responses and carp susceptibility to viral infection [ 78 ]. The role of epigenetic regulation on carp inflammatory responses requires further research.…”

Grass Carp Reovirus Induces Formation of Lipid Droplets as Sites for Its Replication and Assembly

“…However, grass carp aquaculture has been plagued with many diseases, especially grass carp hemorrhagic disease caused by grass carp reovirus (GCRV), the most virulent pathogen in the genus Aquareovirus ( 2 , 3 ). Consequently, GCRV has received much attention from many researchers who aim to achieve disease-resistant breeding or uncover the mechanisms underlying GCRV infection ( 4 – 8 ). The genome of GCRV consists of 11 double-stranded RNA (dsRNA) segments that encode seven structural proteins (VP1 to VP7) and five nonstructural proteins (NS80, NS38, NS31, NS26, and NS16) ( 9 , 10 ).…”