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DNA methylation is an important epigenetic modification for genomic regulation in higher organisms that plays a crucial role in the progression of development or diseases.The integration and mining of DNA methylome by methylation-specific PCR and genome-wide profiling technology could greatly assist the discovery of novel candidate biomarkers.It permits systemslevel analysis of genomic methylation patterns associated with gene expression and chromatin structure.A comprehensive tool, CpG_MPs, is developed for identification and analysis of unmethylated and methylated regions from bisulfite sequencing data, and to identify conserved and differentially methylated regions of various methylation pattems for paired or multiple samples.CpG_MPs accurately identifies and analyzes methylated and unmethylated CpG patterns in genomic regions from bisulfite sequencing data using hotspot extension.CpG_MPs identifies conserved and differentially methylated regions among multiple samples (cells or tissues) using linear iteration.The methylation patterns of genomic regions are qualitatively and dynamically identified using the methylation status of neighboring CpGs, without knowledge of predefined regions or the average methylation of CpGs in the genomic regions.CpG_MPs identified the methylation patterns ingenomic regions from five human bisulfite sequencing data during cellular differentiation.Significant cell-specific methylation pattern observed.These potentially functional regions form candidate regions for analysis of the function of DNA methylation during cellular differentiation.CpG_MPs is the first user-friendly tool for identifying methylation patterns of genomic regions from bisulfite sequencing data, permitting further investigation of the biological functions of genome-scale methylation patterns .