Centro Andaluz de Biología del Desarrollo-CABD, CSIC-UPO-JA, 41013 Sevilla, Spain.
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.
全基因组范围内的 DNA 甲基化和组蛋白修饰谱分析回答了许多问题，例如基因在全球范围内是如何调控的，以及它们的表观遗传学组成是什么。然而，对于这些标记在早期脊椎动物胚胎发生过程中的功能知之甚少。在这里，我们提供了详细的 ChIP-seq 和 MethylCap-seq 方案，适用于四个发育阶段的斑马鱼（Danio rerio）胚胎材料。作为原理的证明，我们已经在全球范围内对包括 H3K4me1、H3K4me3 和 H3K27ac 在内的许多翻译后组蛋白修饰进行了分析。我们证明这些标记在早期发育过程中是动态的，并且这种发育转变可以通过 ChIP-seq 检测到。此外，我们还应用了 MethylCap-seq 来表明，通过这种方法可以检测到发育调节的 DNA 甲基化重塑。我们的 MethylCap-seq 数据与之前对早期斑马鱼发育的 DNA 甲基化研究一致，这使得该方法非常适合对早期脊椎动物胚胎中的 DNA 甲基化进行全面评估。
