Genome-wide mapping of DNA methylation in chicken

Abstract

Cytosine DNA methylation is an important epigenetic modification termed as the fifth base that functions in diverse processes. Till now, the genome-wide DNA methylation maps of many organisms has been reported, such as human, Arabidopsis, rice and silkworm, but the methylation pattern of bird remains rarely studied. Here we show the genome-wide DNA methylation map of bird, using the chicken as a model organism and an immunocapturing approach followed by high-throughput sequencing. In both of the red jungle fowl and the avian broiler, DNA methylation was described separately for the liver and muscle tissue. Generally, chicken displays analogous methylation pattern with that of animals and plants. DNA methylation is enriched in the gene body regions and the repetitive sequences, and depleted in the transcription start site (TSS) and the transcription termination site (TTS). Most of the CpG islands in the chicken genome are kept in unmethylated state. Promoter methylation is negatively correlated with the gene expression level, indicating its suppressive role in regulating gene transcription. This work contributes to our understanding of epigenetics in birds.

Figure 1. Global mapping of DNA methylation in chicken.

A. Scatter plot showing the correlation between two independent meDIP-Seq experiments with RJF muscle used for DNA methylation assay. B. Snapshot of meDIP-Seq data from genome-wide DNA methylation analysis. The DNA methylation signal is shown with the sequencing tags number along the chromosome. Gene region is shown with the red boxes. Methylation patterns of selected high methylated region and low methylated region were detected by bisulfite sequencing.

Figure 2. DNA methylation distribution in gene flanking and coding regions.

DNA methylation profile in gene region was calculated by the tags that were aligned on unique locus in genome. The gene region was defined as the whole regions that contained 2 kb region upstream of the TSS, gene body from TSS to TTS and 2 kb region downstream of the TTS. In upstream and downstream 2 kb regions, the regions were split into 20 non-overlap windows and the average alignment depth was calculated for each window. In gene body, each gene was split into 20 equal windows and the average alignment depth was calculated for each window. Y-axis is the average of normalized depth for each window.

Figure 3. Relationship between promoter DNA methylation and gene expression level in chicken.

Genes were divided into 10 intervals according to expression levels. DNA methylation level was measured by the log ratio of the p value of the methylation peaks, with each point representing the mean expression level and the relative methylation level.