title: Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells.
abstract: Global demethylation is part of a conserved program of epigenetic reprogramming to naive pluripotency. The transition from primed hypermethylated embryonic stem cells (ESCs) to naive hypomethylated ones (serum-to-2i) is a valuable model system for epigenetic reprogramming. We present a mathematical model, which accurately predicts global DNA demethylation kinetics. Experimentally, we show that the main drivers of global demethylation are neither active mechanisms (Aicda, Tdg, and Tet1-3) nor the reduction of de novo methylation. UHRF1 protein, the essential targeting factor for DNMT1, is reduced upon transition to 2i, and so is recruitment of the maintenance methylation machinery to replication foci. Concurrently, there is global loss of H3K9me2, which is needed for chromatin binding of UHRF1. These mechanisms synergistically enforce global DNA hypomethylation in a replication-coupled fashion. Our observations establish the molecular mechanism for global demethylation in naive ESCs, which has key parallels with those operating in primordial germ cells and early embryos.
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK.
authors.forename: Ferdinand
authors.initials: F
authors.lastname: von Meyenn
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK.
authors.forename: Mario
authors.initials: M
authors.lastname: Iurlaro
authors.affiliation: Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA Nijmegen, the Netherlands.
authors.forename: Ehsan
authors.initials: E
authors.lastname: Habibi
authors.affiliation: Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA Nijmegen, the Netherlands.
authors.forename: Ning Qing
authors.initials: NQ
authors.lastname: Liu
authors.affiliation: Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
authors.forename: Ali
authors.initials: A
authors.lastname: Salehzadeh-Yazdi
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK.
authors.forename: Fátima
authors.initials: F
authors.lastname: Santos
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK.
authors.forename: Edoardo
authors.initials: E
authors.lastname: Petrini
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK.
authors.forename: Inês
authors.initials: I
authors.lastname: Milagre
authors.affiliation: Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
authors.forename: Miao
authors.initials: M
authors.lastname: Yu
authors.affiliation: Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA.
authors.forename: Zhenqing
authors.initials: Z
authors.lastname: Xie
authors.affiliation: Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Nijmegen Medical Centre and Radboudumc Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands.
authors.forename: Leonie I
authors.initials: LI
authors.lastname: Kroeze
authors.affiliation: Developmental Epigenetics Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
authors.forename: Tatyana B
authors.initials: TB
authors.lastname: Nesterova
authors.affiliation: Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Nijmegen Medical Centre and Radboudumc Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands.
authors.forename: Joop H
authors.initials: JH
authors.lastname: Jansen
authors.affiliation: Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA.
authors.forename: Hehuang
authors.initials: H
authors.lastname: Xie
authors.affiliation: Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
authors.forename: Chuan
authors.initials: C
authors.lastname: He
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK. Electronic address: wolf.reik@babraham.ac.uk.
authors.forename: Wolf
authors.initials: W
authors.lastname: Reik
authors.affiliation: Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA Nijmegen, the Netherlands. Electronic address: h.stunnenberg@ncmls.ru.nl.
authors.forename: Hendrik G
authors.initials: HG
authors.lastname: Stunnenberg
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives / Q000378:metabolism; D000818:Animals; D022762:CCAAT-Enhancer-Binding Proteins; D002478:Cells, Cultured; D065150:Cellular Reprogramming; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D049308:Dioxygenases; D053595:Embryonic Stem Cells / Q000378:metabolism*; D044127:Epigenesis, Genetic; D018507:Gene Expression Regulation, Developmental; D006657:Histones / Q000378:metabolism; D051379:Mice; D008957:Models, Genetic; D009154:Mutation; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D011518:Proto-Oncogene Proteins / Q000235:genetics / Q000378:metabolism; D013997:Time Factors; D014162:Transfection; D044767:Ubiquitin-Protein Ligases
chemical_list: D022762:CCAAT-Enhancer-Binding Proteins; D004268:DNA-Binding Proteins; D006657:Histones; D009687:Nuclear Proteins; D011518:Proto-Oncogene Proteins; C540839:TET1 protein, mouse; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D049308:Dioxygenases; C551914:Tet2 protein, mouse; D044767:Ubiquitin-Protein Ligases; C117054:Uhrf1 protein, mouse