title: The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos.
abstract: Genome-wide profiling of DNA methylation and histone modifications answered many questions as to how the genes are regulated on a global scale and what their epigenetic makeup is. Yet, little is known about the function of these marks during early vertebrate embryogenesis. Here we provide detailed protocols for ChIP-seq and MethylCap-seq procedures applied to zebrafish (Danio rerio) embryonic material at four developmental stages. As a proof of principle, we have profiled on a global scale a number of post-translational histone modifications including H3K4me1, H3K4me3 and H3K27ac. We demonstrate that these marks are dynamic during early development and that such developmental transitions can be detected by ChIP-seq. In addition, we applied MethylCap-seq to show that developmentally-regulated DNA methylation remodeling can be detected by such a procedure. Our MethylCap-seq data concur with previous DNA methylation studies of early zebrafish development rendering this method highly suitable for the global assessment of DNA methylation in early vertebrate embryos.
authors.affiliation: Centro Andaluz de Biología del Desarrollo-CABD, CSIC-UPO-JA, 41013 Sevilla, Spain.
authors.forename: Ozren
authors.initials: O
authors.lastname: Bogdanović
authors.forename: Ana
authors.initials: A
authors.lastname: Fernández-Miñán
authors.forename: Juan J
authors.initials: JJ
authors.lastname: Tena
authors.forename: Elisa
authors.initials: E
authors.lastname: de la Calle-Mustienes
authors.forename: José Luis
authors.initials: JL
authors.lastname: Gómez-Skarmeta
mesh_terms: D000818:Animals; D019175:DNA Methylation; D004625:Embryo, Nonmammalian; D047108:Embryonic Development / Q000235:genetics*; D044127:Epigenesis, Genetic; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation / Q000379:methods* / Q000592:standards; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D056656:Lab-On-A-Chip Devices; D011499:Protein Processing, Post-Translational; D015027:Zebrafish / Q000235:genetics*
chemical_list: D006657:Histones
keywords: DNA methylation; Development; Epigenomics; Histone modifications; Zebrafish