The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos

Methods. 2013 Aug 15;62(3):207-15. doi: 10.1016/j.ymeth.2013.04.011. Epub 2013 Apr 23.


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.

Keywords: DNA methylation; Development; Epigenomics; Histone modifications; Zebrafish.

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*


  • Histones