Bioinformatics Study On Methylation Diversity Of Arabidopsis Thaliana Gene

Epigenetic is the case that does not change the sequence of DNA,but can make the gene expression change.DNA methylation is one of the most important and basic epigenetic ways in plants,which may involve in the completion of the life cycle or adaptation to environmental changes.However,some fundamental scientific issues such as variability,stability and occurrence regularity of DNA methylation have not been fully understood yet.Based on the difference of methylation profiles of Arabidopsis thaliana in different geographical locations in the Northern Hemisphere,We used bioinformatics tools to search gene function characteristics of different methylation status of genes,analyze the relationship between gene methylation level and gene expression,and the relationship between gene methylation level and quantitative traits and gene methylation variation variation characteristics in metabolic pathways and signal pathways.The main objectives in this study are to elucidate the general law of the occurrence of gene methylation and its role in gene regulation and provide data and information for DNA methylation research.Screening and functional cluster analysis of characterization of methylation genes Gene methylation can involve in perception and response to biotic and abiotic environmental stimuli,and influence natural populations of biological diversity through regulating gene expression.However,DNA methylation patterns and distribution mode remains unclear in Arabidopsisthaliana.We get the methylation status of all the genes based on the genome methylation profiles of 76 ecotypes of Arabidopsis thaliana,including columbia ecotype and 75 other ecological populations The methylation level and methylation variability of gene promoter range and gene body range were accounted in genome of Arabidopsis thaliana.Selected genes were clustered based on the functional analysis to elucidate the patterns of methylation.The results showed that the genebody and the promoter region respectively 37%and 47%of all the genes were not completely methylated in the columbia ecotypes,but completely non-methylated genes among 76 populations decreased to 4%and 2%.However,1%or more sequence-methylayed genes of the genebody methylation whichever columbia single population or 76 populations,reached 31%propotion of all the gnome.And those in the promoter for columbia single population or 76 populations reached 33%and 32%respectively.And the methylation level merging range from the gene body and promoter of columbia single population or 76 populations were 36%and 34%respectively.Taking into account of the effect of gene methylation level on gene regulation,only the genes with 1%sequence-methylated were supposed to be likely to regulate gene expression.Obviously,only about 1/3 of the Arabidopsis thaliana genes may have a biological significance of methylation.Highly-potentially methylation-regulated 5000 genes with higher methylation variation were clustered.They were supposed to contribute much to the difference of phenology and responses to environmental stress.So those genes may be further studied as a candidate gene set.Correlation analysis of methylation level and expression level In order to reveal the relationship between gene methylation and gene expression,and the proportion of methylation-regulated genes,bioinformatics studied were conducted.First,the methylation information and expression information of all genes were obtained and then regressively analyzed to reveal the correlation between gene expression and gene methylation level.The genes with significant correlation were screened out.Then we performed functional cluster analysis of these genes to understand their functions preference.The results showed that there were 1926 genes whose gene body methylation level are correlated with their gene expression,and the positively and negatively related genes were 1299 and 627.And there were 1679 genes whose gene promoter regions methylation level are correlated with their gene expression and the positively and negatively related genes were 1299 and 627.There wereexisted 438 common genes between the genebody-methylation-regulated and genepromoter-methylation-regulated genes.However,the positive and negative related genes were 1547 and 871 if the merged range of genebody and promoter methylation.The analysis result of the functional preference of genes regulated by different methylation patterns showed that genebody-methylation-regulated genes were clustered into significant gene function set.These genes were mainly enriched in cell death and protein amino acid,which are generally a number of disease resistance related proteins.But we didn't find significant functional clustering result in the promoter-methylation-regulated genes.The clustered genes mainly included signal transduction,immune response,cell death and apoptosis based on the merging genebody and promoter methylation.Correlation analysis of methylation level and quantitative traits It is believed that the gene methylation is closely related to the plasticity of plant phenologic traits.But it still lacks deeply understanding of theregulation mode.In order to understand the role of gene methylation variation in plant phenotypic trait diversity,the linear correlation was regressively analyzed between gene methylation data of different populations of Arabidopsis thaliana and 45 kinds of quantitative trait data include trichome density,sodium content,seedling growth rate,silique length etc.The genes with a significant correlation between their methylation level and the quantitative trait were screened.And the gene ontology Gene(GO)function enrichment analysis was performed.A number of related genes were selected for each trait.The numbers of clustered genes varied among different quantitative traits.The length of silique,the content of sodium ion,and trichome density as examples were further studied.In particular,for the trichome density,we also analyzed the correlation between the expression of the gene and the trichome density of the leaf.The genes we screened were closely correlated with trichome density.These genes function clustering result is consistent with the previous studies on the function of trichome.So this method may be applied to screening for functional genes based on the differences of quantitative traits and the correlation of gene expression.Methylation variation analysis of genes in biological metabolism and signal pathways We selected 120 metabolic and signal pathways in Arabidopsis thaliana KEGG(Encyclopedia of Genes and Genomes Kyoto)database by the Kyoto gene and genome Encyclopedia.Through analysis of the methylation variation and methylation status of genes in each pathway,we identified high methylation variation genes,non-methylated genes,relatively high-methylated genes,and highly methylated genes in each pathway.The of compenient genes in pathways were clustered according to the proportion of highly-methylated variant genes in pathways.Combining the function of biological pathways we assessed the possibility of methylation to regulate the gene expression from a new perspective.The analysis result of the methylation status for the gene body and promoter merge area of genes in the 120 metabolic pathways showed that all pathways have relatively high methylated genes except for 2.Only 7 pathways did not contain highly varied methylated genes,all 113 other pathways contained more or less highly varied methylated genes.There were 32 pathways with highly-methylated genes.However,the number of such genes was fewer than 1 to 4.There weree 20 pathways that contained a large proportion of highly varied methylated genes,and more than 30%of the total pathway genes were achieved.We can infer that the metabolic pathway genes were generally regulated by variable methylation among populations,which can contribute to the regulation of metabolism and signaling pathway.The proportion of highly varied methylated gene was different in each pathway.The pathway may be regulated by methylation is not randomly selected,but express preference.It may be related to the biological processes of the pathway.The gene which contains very high degree of methylation in the pathway may be in a metabolic step,which may be a key step in the pathway which can perform a switch function by the regulation of methylation.