ZFIN ID: ZDB-PUB-130604-7
The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos
Bogdanovic, O., Fernández-Miñán, A., Tena, J.J., de la Calle-Mustienes, E., and Gómez-Skarmeta, J.L.
Date: 2013
Source: Methods (San Diego, Calif.)   62(3): 207-15 (Journal)
Registered Authors: de la Calle-Mustienes, Elisa, Gómez-Skarmeta, José Luis, Tena, Juan
Keywords: epigenomics, zebrafish, histone modifications, DNA methylation, development
MeSH Terms:
  • Animals
  • DNA Methylation
  • Embryo, Nonmammalian
  • Embryonic Development/genetics*
  • Epigenesis, Genetic
  • Genome*
  • High-Throughput Nucleotide Sequencing/instrumentation
  • High-Throughput Nucleotide Sequencing/methods*
  • High-Throughput Nucleotide Sequencing/standards
  • Histones/genetics
  • Histones/metabolism*
  • Lab-On-A-Chip Devices
  • Protein Processing, Post-Translational*
  • Zebrafish/genetics*
PubMed: 23624103 Full text @ Methods

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.