title: Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes.
abstract: DNA methylation is a key epigenetic mark that is critical for gene regulation in multicellular eukaryotes. Although various human cell types may have the same genome, these cells have different methylomes. The systematic identification and characterization of methylation marks across cell types are crucial to understand the complex regulatory network for cell fate determination. In this study, we proposed an entropy-based framework termed SMART to integrate the whole genome bisulfite sequencing methylomes across 42 human tissues/cells and identified 757 887 genome segments. Nearly 75% of the segments showed uniform methylation across all cell types. From the remaining 25% of the segments, we identified cell type-specific hypo/hypermethylation marks that were specifically hypo/hypermethylated in a minority of cell types using a statistical approach and presented an atlas of the human methylation marks. Further analysis revealed that the cell type-specific hypomethylation marks were enriched through H3K27ac and transcription factor binding sites in cell type-specific manner. In particular, we observed that the cell type-specific hypomethylation marks are associated with the cell type-specific super-enhancers that drive the expression of cell identity genes. This framework provides a complementary, functional annotation of the human genome and helps to elucidate the critical features and functions of cell type-specific hypomethylation.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China hongbo919@gmail.com.
authors.forename: Hongbo
authors.initials: H
authors.lastname: Liu
authors.affiliation: Department of Rehabilitation, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, China.
authors.forename: Xiaojuan
authors.initials: X
authors.lastname: Liu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Shumei
authors.initials: S
authors.lastname: Zhang
authors.affiliation: School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Lv
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Song
authors.initials: S
authors.lastname: Li
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Shipeng
authors.initials: S
authors.lastname: Shang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Shanshan
authors.initials: S
authors.lastname: Jia
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Yanjun
authors.initials: Y
authors.lastname: Wei
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Fang
authors.initials: F
authors.lastname: Wang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Jianzhong
authors.initials: J
authors.lastname: Su
authors.affiliation: School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Wu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China tyozhang@ems.hrbmu.edu.cn.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D015415:Biomarkers; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D018899:CpG Islands; D019175:DNA Methylation; D053595:Embryonic Stem Cells / Q000378:metabolism; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism; D006801:Humans; D059372:Nucleotide Motifs; D009928:Organ Specificity / Q000235:genetics; D059467:Transcriptome
chemical_list: D015415:Biomarkers; D002843:Chromatin; D006657:Histones