Genome-Wide Investigation of DNA Methylation at Single-Base Resolution in the Chicken Embryo

During the last decades, technological developments have brought about huge changes in the field of animal genetics and genomics. The functional description of the genome is now underway, and comprises epigenetic analyses, among which DNA methylation studies take an important part. Our knowledge of the DNA methylation pattern increases in animals and plants in a variety of tissues and developmental stages. However, to date, few studies have focused on the genome-wide analysis of the chicken methylome. Some studies using arrays or selective methods have provided first insights into the chicken methylome. The goal of this study was to provide the first description of a single-base resolution CpG methylome of chicken genomic DNA in 4.5 days old embryos, by using whole genome high-throughput sequencing after bisulfite treatment. Methylation profiles were obtained by mapping the reads against dedicated reference genomes, generated by sequencing genomic DNA from the same samples, allowing an improved mapping of the reads obtained. The methylation pattern observed in chicken shows common features of methylation in animals, with a high prevalence of CpG methylation over CHH or CHG regions, and a higher methylation level in exons than in upstream regions of the genes, associated to a low methylation level in CpG islands. This preliminary study constitutes a first step in deciphering the functional regulation of gene expression at single base-resolution in the developing embryo.