title: DNA methylation profiling in zebrafish.
abstract: DNA methylation on cytosine in vertebrates such as zebrafish serves to silence gene expression by interfering with the binding of certain transcription factors and through the recruitment of repressive chromatin machinery. Cytosine DNA methylation is chemically stable and heritable through the germline - but also reversible through many modes, making it a useful and dynamic epigenetic modification. Virtually all of the enzymes and factors involved in the deposition, binding, and removal of cytosine methylation are conserved in zebrafish, and therefore the organism an excellent model for understanding the use of DNA methylation in the control of gene regulation and other processes. Here, we discuss the main approaches to quantifying DNA methylation levels genome-wide in zebrafish: one is an established method for revealing regional methylation (methylated DNA immunoprecipitation (MeDIP)), and the other is an emerging method that reveals DNA methylation at base-pair resolution (shotgun bisulphite sequencing). We also introduce some of the analytical methods that are useful for identifying regions of hypo- or hyper-methylation, and ways to identify differentially methylated regions.
authors.affiliation: Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
authors.forename: Shan-Fu
authors.initials: SF
authors.lastname: Wu
authors.forename: Haiying
authors.initials: H
authors.lastname: Zhang
authors.forename: Saher Sue
authors.initials: SS
authors.lastname: Hammoud
authors.forename: Magdalena
authors.initials: M
authors.lastname: Potok
authors.forename: David A
authors.initials: DA
authors.lastname: Nix
authors.forename: David A
authors.initials: DA
authors.lastname: Jones
authors.forename: Bradley R
authors.initials: BR
authors.lastname: Cairns
mesh_terms: D000818:Animals; D004247:DNA / Q000302:isolation & purification; D019175:DNA Methylation; D015254:DNA Modification Methylases / Q000235:genetics; D044127:Epigenesis, Genetic; D029941:Fish Proteins / Q000235:genetics; D018507:Gene Expression Regulation, Developmental; D015972:Gene Expression Regulation, Neoplastic; D016678:Genome; D042822:Genomic Instability; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D015027:Zebrafish / Q000235:genetics*
chemical_list: D029941:Fish Proteins; D004247:DNA; D015254:DNA Modification Methylases