Investigating The Correlation Of CpG Density And Methylation

Objective:In epigenetics,DNA methylation plays a role in gene transcription.DNA methylation occurs mainly in CpG cytosine.The level of methylation in the promoter region of the gene regulates the transcriptional expression of the gene.To understand the methylation status of these genes,we can have a certain understanding and understanding of the epigenetic mechanisms of gene transcription and interaction with the cell environment.Existing research,It is mainly focused on the difference of methylation between tissues and the methylation level of cancer tissues.There was not intensive study of the relationship between CpG and methylation levels.Therefore,the study on the relationship between CpG and methylation level is very important.This experiment will study the correlation between CpG and methylation level.At the same time,according to the distribution of CpG and methylation fitted a curve.On the basis of the curve,the CpG and methylation level were divided into different parts,and we studied the biological significance of special areas.Method:The data used in this experiment is the methylation data of Illumina Hi Seq 2000.The quality of data is qualified by Fastqc.The methylation data of each tissue were compared with the reference sequence by Segemehl.The sliding window method was used to deal with the CpG locus and methylation level,and the distribution density of both of them appeared.Min-max normalization method was used to deal with the CpG density and methylation level,so that the data were in the same range.The Cor function in R language is used to calculate the correlation between CpG density and methylation level.The gene structure was divided into different parts by the method of partition,and then the relationship between CpG density and methylation level was observed.According to the distribution of CpG density and methylation level,the exponential curve fitted to their distribution was fitted.The area of CpG density and methylation level was divided by exponential curve.Using Sd function in R language to calculate the methylation difference in Gap region.The difference between the Gap and the gene structure was analyzed,and the Gap region was divided into two parts,one part was overlapped with the promoter region and the other was not overlapped with the promoter region.Combined with the data of Chipseq and RNAseq to study the regulatory role of these regions and the corresponding genes,in the promoter region of the Gap region,to study the regulation of the corresponding genes.The Gap promoter in the area far from the study,we calculated the correlation coefficient of Chipseq H3K27 ac signals of different tissue area and all of Chipseq gene promoter H3K4me3 signal two sub regions,find out the coefficient of the target gene.Results: In this study,we collected the methylation data of 18 human tissues and 16 tissues of mice in the NCBI,and got the methylation information of each tissue with the reference sequence.The distribution and correlation coefficients of methylation level and CpG density of each tissue were obtained by sliding window and min-max normalization.The negative correlation between CpG density and methylation level was also demonstrated in the gene structure by the method of segmentation.According to the distribution of CpG density and methylation level,the exponential curve fitted to their distribution was fitted.Secondly,the distribution area of the regions is divided into the following four types by the exponential curve.The difference between the Gap regions was calculated,and the Gap region with large organization difference was obtained.These Gap regions were then overlapped with the promoter region of the gene,and the Gap region of the promoter region and the Gap region far from the promoter region were obtained.In the research and analysis from the Gap promoter region near,found that the methylation level of some gene promoter region is different in certain tissues,that different genes are selectively expressed in different tissues.In the remote control of Gap region,we found that these regions have a certain degree of conservation,Motif and Dnase1,and by calculating the correlation,to find the remote control of the target gene.Conclusion: The results of this study are mainly the negatively correlated of CpG density and methylation in the normal tissue of human and mouse.The overall distribution of CpG density and methylation level was in accord with the exponential distribution.In the Gap region overlapping with Promoter,these Gap regions can be used to regulate the expression of different transcripts in the proximal region.In the Gap region that does not overlap with Promoter,these Gap regions regulate the target gene at the distal end.