Examination of whole genome DNA methylation status of two chicken breeds. Gallus gallus

We report the genome-wide DNA methylation mapping of chicken by methylated DNA immunoprecipitation following by highthroughput sequencing, and the gene expression profile of chicken by RNA-seq. For meDIP-seq, about 17,202,074 to 27,501,760 reads were generated for the tissue and liver tissues of the red jungle fowl and the avian broiler each. We found that compared with the red jungle fowl, DNA methylation in muscle tissue of the avian broiler, showed dramatically decline on a genome-wide scale. Furthermore, the length of the highly methylated regions (HMRs) has become shorter in the avian broiler, which has suffered intense artificial selection. In addition to the global changes in DNA methylation, transcriptome-wide analysis of the two breeds of chicken revealed that the patterns of gene expression in the domestic chicken have undergone a specific bias towards a pattern that is more suited to human-made environments with variable expression in certain gene functions, such as immune response and fatty acid metabolism. Our results demonstrated a potential role of epigenetic modification in animal domestication besides the genetic variations. Overall design: Examination of whole genome DNA methylation status in liver and muscle of two chicken breeds.

本研究报道了采用甲基化DNA免疫沉淀（methylated DNA immunoprecipitation, MeDIP）结合高通量测序构建的鸡全基因组DNA甲基化图谱，以及通过RNA测序（RNA-seq）获得的鸡基因表达谱。针对MeDIP-seq实验，红原鸡与肉鸡的肌肉组织及肝脏组织分别产生了约17,202,074至27,501,760条测序读段（reads）。研究发现，与红原鸡相比，肉鸡肌肉组织的全基因组DNA甲基化水平呈现显著下降趋势。此外，在经历了高强度人工选择的肉鸡群体中，高甲基化区域（highly methylated regions, HMRs）的长度有所缩短。除DNA甲基化的全局改变外，对这两个鸡品种的全转录组分析表明，家鸡的基因表达模式已出现特定偏向，形成了更适配人工营造环境的表达模式，该模式下部分基因功能类别（如免疫应答与脂肪酸代谢）的表达呈现异质性特征。本研究结果表明，除遗传变异外，表观遗传修饰在动物驯化过程中可能发挥潜在作用。实验整体设计：检测两个鸡品种肝脏与肌肉组织的全基因组DNA甲基化状态。