title: Dynamic changes in histone modifications precede de novo DNA methylation in oocytes.
abstract: Erasure and subsequent reinstatement of DNA methylation in the germline, especially at imprinted CpG islands (CGIs), is crucial to embryogenesis in mammals. The mechanisms underlying DNA methylation establishment remain poorly understood, but a number of post-translational modifications of histones are implicated in antagonizing or recruiting the de novo DNA methylation complex. In mouse oogenesis, DNA methylation establishment occurs on a largely unmethylated genome and in nondividing cells, making it a highly informative model for examining how histone modifications can shape the DNA methylome. Using a chromatin immunoprecipitation (ChIP) and genome-wide sequencing (ChIP-seq) protocol optimized for low cell numbers and novel techniques for isolating primary and growing oocytes, profiles were generated for histone modifications implicated in promoting or inhibiting DNA methylation. CGIs destined for DNA methylation show reduced protective H3K4 dimethylation (H3K4me2) and trimethylation (H3K4me3) in both primary and growing oocytes, while permissive H3K36me3 increases specifically at these CGIs in growing oocytes. Methylome profiling of oocytes deficient in H3K4 demethylase KDM1A or KDM1B indicated that removal of H3K4 methylation is necessary for proper methylation establishment at CGIs. This work represents the first systematic study performing ChIP-seq in oocytes and shows that histone remodeling in the mammalian oocyte helps direct de novo DNA methylation events.
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;
authors.forename: Kathleen R
authors.initials: KR
authors.lastname: Stewart
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;
authors.forename: Lenka
authors.initials: L
authors.lastname: Veselovska
authors.affiliation: Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 77030, USA;
authors.forename: Jeesun
authors.initials: J
authors.lastname: Kim
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;
authors.forename: Jiahao
authors.initials: J
authors.lastname: Huang
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom;
authors.forename: Heba
authors.initials: H
authors.lastname: Saadeh
authors.affiliation: School of Medicine, Yokohama City University, Yokohama 236-0027, Japan;
authors.forename: Shin-ichi
authors.initials: S
authors.lastname: Tomizawa
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;
authors.forename: Sébastien A
authors.initials: SA
authors.lastname: Smallwood
authors.affiliation: Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 77030, USA;
authors.forename: Taiping
authors.initials: T
authors.lastname: Chen
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Centre for Trophoblast Research, University of Cambridge CB2 3EG, Cambridge, United Kingdom.
authors.forename: Gavin
authors.initials: G
authors.lastname: Kelsey
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation; D018899:CpG Islands; D019175:DNA Methylation; D005434:Flow Cytometry; D042421:Histone Code; D056466:Histone Demethylases / Q000235:genetics; D006657:Histones / Q000378:metabolism; D051379:Mice; D009865:Oocytes / Q000201:enzymology*; D009866:Oogenesis / Q000502:physiology*; D010089:Oxidoreductases, N-Demethylating / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D006657:Histones; D056466:Histone Demethylases; C504076:KDM1a protein, mouse; D010089:Oxidoreductases, N-Demethylating; C544113:kdm1b protein, mouse
keywords: ChIP-seq; DNA methylation; genomic imprinting; histone modifications; oocytes