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Differential methylation analysis for bisulfite sequencing using DSS

Quantitative Biology 2019年第4期7卷 327-334页

作者： Hao Feng Hao Wu Department of Population and Quantitative Health Sciences Case Western Reserve UniversityClevelandOH 44106USA Department of Biostatistics and Bioinformatics Emory University Rollins School of Public HealthAtlantaGA 30322USA

bisulfite sequencing(BS-seq)technology measures DNA methylation at single nucleotide resolution.A key task in BSseq data analysis is to identify differentially methylation(DM)under different *** we provide a tutorial for BS-seq DM analysis using Bioconductor package *** uses a beta-binomial model to characterize the sequence counts from BS-seq,and implements rigorous statistical method for hypothesis *** provides flexible functionalities for a variety of DM analyses.

关键词： epigenetics DNA methylation bisulfite sequencing differential methylation

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HeteroMeth： A Database of Cell-to-cell Heterogeneity in DNA Methylation

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Genomics, Proteomics & Bioinformatics 2018年第4期16卷 234-243页

作者： Qing Huan Yuliang Zhang Shaohuan Wu Wenfeng Qian State Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biology Chinese Academy of SciencesBeijing 100101China Key Laboratory of Genetic Network Biology Institute of Genetics and Developmental Biology Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

DNA methylation is an important epigenetic mark that plays a vital role in gene expression and cell differentiation. The average DNA methylation level among a group of cells has been extensively documented. However, the cell-to-cell heterogeneity in DNA methylation, which reflects the differentiation of epigenetic status among cells, remains less investigated. Here we established a gold standard of the cell-to-cell heterogeneity in DNA methylation based on single-cell bisulfite sequencing （BS-seq） data. With that, we optimized a computational pipeline for estimating the heterogeneity in DNA methylation from bulk BS-seq data. We further built HeteroMeth, a database for searching, browsing, visualizing, and downloading the data for heterogeneity in DNA methylation for a total of 141 samples in humans, mice, Arabidopsis, and rice. Three genes are used as examples to illustrate the power of HeteroMeth in the identification of unique features in DNA methylation. The optimization of the computational strategy and the construction of the database in this study complement the recent experimental attempts on single-cell DNA methylomes and will facilitate the understanding of epigenetic mechanisms underlying cell differentiation and embryonic development. HeteroMeth is publicly available at http：//***/HeteroMeth.

关键词： Cell-to-cell heterogeneity DNA methylation bisulfite sequencing Single cell Shannon entropy

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Analysis of differential DNA methylation provides insights into strain degeneration in subcultured Cordyceps militaris

Analysis of differential DNA methylation provides insights i...

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中国蚕学会2018年学术年会

作者： Xiangdong Xin Juan Yin Bei Zhang Zhiyong Li Shan Zhao Zhongzheng Gui School of Biotechnology Jiangsu University of Science and Technology Sericultural Research Institute Chinese Academy of Agricultural Science

The entomopathogenic mushroom Cordyceps militaris is a storehouse of various medicinal compounds and pharmacological effects. However, the high frequency of strain degeneration during subculture and preservation severely limits the large-scale production of C. militaris. DNA methylation is an important epigenomic modification involved in gene regulation. In this study, we used bisulfite sequencing for DNA methylation profiling of wild-type and mutant C. militaris. The differentially methylated regions（DMRs） of the two types were analyzed using Gene Ontology（GO） clustering and Kyoto Encyclopedia of Genes and Genomes（KEGG） pathway analysis. DNA methylation levels of the wild-type and mutant-type C. militaris were 0.48% and 0.56%, respectively. Methylation appeared at CHH dinucleotides in 58.62% and 58.20% of all methylated cytosine sites in the wild and mutant types, respectively. In all, 188 DMRs were identified from the wild and mutant types. Most of the DMRs ranged from 200 to 350 bp in length. KEGG pathways of DMR-related genes showed involvement mainly in pyruvate metabolism, glycerophospholipid metabolism, DNA replication, and N-glycan biosynthesis. This contributes to the knowledge and understanding of the possible mechanisms of C. militaris strain degeneration.

关键词： Cordyceps militaris bisulfite sequencing DNA methylation Degenerative Analysis

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Identification of biological feature based on high-throughput DNA Methylome

Identification of biological feature based on high-throughpu...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Jianzhong Su Haidan Yan 张岩 College of Bioinformatics Science and Technology Harbin Medical University

DNA methylation is an important epigenetic modification for genomic regulation in higher organisms that plays a crucial role in the progression of development or *** integration and mining of DNA methylome by methylation-specific PCR and genome-wide profiling technology could greatly assist the discovery of novel candidate *** permits systemslevel analysis of genomic methylation patterns associated with gene expression and chromatin structure. A comprehensive tool,CpGMPs,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 patterns for paired or multiple samples. CpGMPs accurately identifies and analyzes methylated and unmethylated CpG patterns in genomic regions from bisulfite sequencing data using hotspot *** identifies conserved and differentially methylated regions among multiple samples(cells or tissues) using linear *** 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 *** identified the methylation patterns in genomic regions from five human bisulfite sequencing data during cellular *** cell-specific methylation pattern *** potentially functional regions form candidate regions for analysis of the function of DNA methylation during cellular differentiation. CpGPs 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.

关键词： DNA methylation bisulfite sequencing Methylation patterns Differentially methylated regions

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