Differential Analysis Of Epigenomics And Transcriptome In Liver Between One- And Three-year-old Grass Carps

Farming practices show that the diseases of grass carp usually occur in the juvenile stage.Grass carp disease usually occurs at the juvenile stage,before the age of one,but less in adult after the age of three.Previous researches have reported that certain immunocompetence is gradually acquired during growth.Until now,the correlation between immune response to grass carp diseases and growing age,especially in this process,the research on the regulation of gene expression remain elusive,and the molecular mechanism of DNA methylation as the entry point to study the importance of animal gene regulation mechanism is not deep enough.At present,most of the studies focus on exogenous infection and its response in grass carp,in which studied tissues tend to select the immune organs,such as the spleen and gill,while ignoring the liver,which has important functions in immunity,digestion and hematopoiesis.In view of the current research status,this study selected normal-developed one- and three-year-old grass carp(GC1Y and GC3Y)livers as the research objects,and performed transcriptome sequencing,whole genome methylation sequencing.The DNA methylation profiling was compared to find changes in DNA methylation levels at different growth ages under natural growth conditions and explore its correlations with gene expression,focusing on immune-related genes and their functional effects on grass carp growth.The results are as follows:1)The level of DNA methylation showed a global decline during the development of grass carp in genome-wide,but increased in the promoter region,the initial exons and introns,which are potentially related to gene transcription.2)Distribution of DNA methylation sites has remarkable characteristics.A total of 3440 differential methylation sites(DMS)were identified,of which down-regulated DMS had a higher proportion(the total of 60%).Approximately,53.2% of DMS were located in introns that is 2.7 times more than exons.The identified methylation sites are clustered in the initial introns or exons,especially in the first intron.3)A total of 2048 DNA differentially methylated genes(DMGs)were identified,including 797 with increased methylation level and 1,223 with decreased levels.The transcriptome data identified 4992 differentially expressive genes(DEGs).There were377 genes belonging to both DMGs and DEGs(DMGs&DEGs).4)Functional annotation shows that differentially expressed genes(DEGs),differentially methylated genes(DMGs),and both differentially methylated genes and differentially expressed genes(DMGs&DEGs)are mainly concentrated in the PI3K-Akt signaling pathway that is related Pathways of the immune pathway.5)The molecular network was constructed for analyzing immune genes,then 13DMGs&DEGs that serve as hubs genes in network diagram were selected to verify robustness in the expression level.As a result,all the methylation levels were up-regulated while the transcription levels were suppressed,suggesting that methylation changes in the upstream regions of these genes had an important impact on gene expression.6)Through subcellular localization prediction analysis,it was concluded that DMGs localized on the cell membrane are very concentrated,especially in calcium signaling pathways and neuroactive ligand-receptor interaction pathways.The differential methylation status of many G protein coupled receptor genes suggests that G protein coupled receptor methylation has important regulatory effects on growth and development.In summary,this study will provide a certain degree of guidance for future research of grass carp autoimmunity and development.