Diagenode

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


Bogdanović O, Fernández-Miñán A, Tena JJ, de la Calle-Mustienes E, Gómez-Skarmeta JL

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.

Tags
DNA shearing
Bioruptor
Chromatin Shearing
ChIP-seq
Antibody
MethylCap
H3K4me3 (C15410003)

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Published
April, 2013

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