title: Distinct roles of DNMT1-dependent and DNMT1-independent methylation patterns in the genome of mouse embryonic stem cells.
abstract: BACKGROUND
  DNA methylation patterns are initiated by de novo DNA methyltransferases DNMT3a/3b adding methyl groups to CG dinucleotides in the hypomethylated genome of early embryos. These patterns are faithfully maintained by DNMT1 during DNA replication to ensure epigenetic inheritance across generations. However, this two-step model is based on limited data.
  
  
  RESULTS
  We generated base-resolution DNA methylomes for a series of DNMT knockout embryonic stem cells, with deep coverage at highly repetitive elements. We show that DNMT1 and DNMT3a/3b activities work complementarily and simultaneously to establish symmetric CG methylation and CHH (H = A, T or C) methylation. DNMT3a/3b can add methyl groups to daughter strands after each cycle of DNA replication. We also observe an unexpected division of labor between DNMT1 and DNMT3a/3b in suppressing retrotransposon long terminal repeats and long interspersed elements, respectively. Our data suggest that mammalian cells use a specific CG density threshold to predetermine methylation levels in wild-type cells and the magnitude of methylation reduction in DNMT knockout cells. Only genes with low CG density can be induced or, surprisingly, suppressed in the hypomethylated genome. Lastly, we do not find any association between gene body methylation and transcriptional activity.
  
  
  CONCLUSIONS
  We show the concerted actions of DNMT enzymes in the establishment and maintenance of methylation patterns. The finding of distinct roles of DNMT1-dependent and -independent methylation patterns in genome stability and regulation of transcription provides new insights for understanding germ cell development, neuronal diversity, and transgenerational epigenetic inheritance and will help to develop next-generation DNMT inhibitors.
authors.affiliation: Department of Environmental Health Sciences, Laboratory of Human Environmental Epigenomes, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Room E7816, Baltimore, MD, 21205, USA. zhiguangli2013@126.com.
authors.forename: Zhiguang
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Environmental Health Sciences, Laboratory of Human Environmental Epigenomes, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Room E7816, Baltimore, MD, 21205, USA. hongzhed@bcm.edu.
authors.forename: Hongzheng
authors.initials: H
authors.lastname: Dai
authors.affiliation: Department of Environmental Health Sciences, Laboratory of Human Environmental Epigenomes, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Room E7816, Baltimore, MD, 21205, USA. smartos1@jhu.edu.
authors.forename: Suzanne N
authors.initials: SN
authors.lastname: Martos
authors.affiliation: Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA. beixu@coh.org.
authors.forename: Beisi
authors.initials: B
authors.lastname: Xu
authors.affiliation: Department of Environmental Health Sciences, Laboratory of Human Environmental Epigenomes, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Room E7816, Baltimore, MD, 21205, USA. ygao36@jhmi.edu.
authors.forename: Yang
authors.initials: Y
authors.lastname: Gao
authors.affiliation: Department of Environmental Health Sciences, Laboratory of Human Environmental Epigenomes, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Room E7816, Baltimore, MD, 21205, USA. jacksonlt@163.com.
authors.forename: Teng
authors.initials: T
authors.lastname: Li
authors.affiliation: Department of Environmental Health Sciences, Laboratory of Human Environmental Epigenomes, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Room E7816, Baltimore, MD, 21205, USA. gzhu6@jhu.edu.
authors.forename: Guangjing
authors.initials: G
authors.lastname: Zhu
authors.affiliation: Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA. dschones@coh.org.
authors.forename: Dustin E
authors.initials: DE
authors.lastname: Schones
authors.affiliation: Department of Environmental Health Sciences, Laboratory of Human Environmental Epigenomes, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Room E7816, Baltimore, MD, 21205, USA. zwang47@jhu.edu.|Fenxian Central Hospital, 9588 Nanfeng Hwy, Fengxian District, Shanghai, 201406, China. zwang47@jhu.edu.|The Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA. zwang47@jhu.edu.
authors.forename: Zhibin
authors.initials: Z
authors.lastname: Wang
mesh_terms: D000818:Animals; D001482:Base Composition; D002478:Cells, Cultured; D004247:DNA / Q000737:chemistry; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation; D000090205:DNA Methyltransferase 3A; D053595:Embryonic Stem Cells / Q000378:metabolism*; D005786:Gene Expression Regulation; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D020084:Long Interspersed Nucleotide Elements; D051379:Mice; D018345:Mice, Knockout; D011506:Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA; D020079:Terminal Repeat Sequences; D014158:Transcription, Genetic; D000097584:DNA Methyltransferase 3B
chemical_list: D004247:DNA; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases; D000090205:DNA Methyltransferase 3A; D011506:Proteins; D000097584:DNA Methyltransferase 3B; C000717967:DNMT3A protein, human; C000715535:Dnmt3a protein, mouse; C000619381:Dnmt1 protein, mouse