Tagmeth:A Method To Detect Allele-Specific DNA Methylation

Among the most well-known functions of DNA methylation is in mediating imprinted gene expression by differentially marking specific regulatory regions on maternal and paternal alleles.Imprinted genes are expressed from one of the two parental alleles in mammals,thereby rendering the organism functionally haploid.Imprinting has been tied to the evolution of placental mammals and defects in imprinting have been associated with human diseases.The Next Generation Sequencing technology makes the study of DNA methylation has undergone great changes,the whole genome bisulfite sequencing methylation(WGBS),methylated DNA immunoprecipitation sequencing(MeDIP-Seq),and using enzyme digestion methylation sequencing simplified way(RRBS)and other methylation analysis tools allow us to analyze cell methyl with the single base-pair resolution.In the genomic imprinting research,in order to distinguish the resources we use some genetic markers.In normal,we use single nucleotide polymorphism(SNP)to find the resource by two different strains of mice hybridized.In this study,we used a new method to find the region of allele specific methylation(ASM).First we focus on the fragment of WGBS,each fragment will has a methylation level,then multiple fragments will be associated with convolution method to describe the methylation status.Although this model can't distinguish the resource,it can identify the allele methylation specific region accurately.We analyze a set WGBS data about mice embryos development with our model and get the ASM region of different development stage,our model can get the ASM region accurate verified by the DMR of two different strains.with the analysis of mouse allele specific methylation regions,we found that in mice the developmental stage,these regions have a higher conservatism,and these regional characteristics appear to cluster in the genome,rich in the promoter regions of high CpG density region.This method can accurately find ASM without the genome type information of parents.It can do better research with the data which don't include parental genome type information.