Comparison of the genome-wide DNA methylation profiles between fast-growing and slow-growing broilers

Chicken growth traits are important in poultry production, however, little is known for its regulatory mechanism at epigenetic level. Therefore, this study aims to compare DNA methylation profiles between fast- and slow-growing broilers in order to identify candidate genes underlying chicken growth. Methylated DNA immunoprecipitation-sequencing (MeDIP-seq) was used to investigate the genome-wide DNA methylation pattern in high and low tails of Recessive White Rock (WRRh, WRRl) and that of Xinhua Chickens (XHh, XHl). The results showed that the average of methylation density was the lowest in CGIs followed by promoters. Within the gene body, the methylation density of introns was higher than UTRs and exons. Moreover, different methylation levels were observed in different repeat types with the highest in LINE/CR1. Methylated CGIs were prominently distributed in the intergenic regions and were enriched in the size range of 200-300 bp. In total 13,294 methylated genes were found in four samples, including 4,085 differentially methylated genes between WRRh and WRRl, 5,599 between XHh and XHl, 4,204 between WRRh and XHh, as well as 7,301 between WRRl and XHl. Moreover, 132 differentially methylated genes related to growth and metabolism were observed in both inner contrasts (WRRh Vs. WRRl and XHh Vs. XHl), whereas 129 differentially methylated genes related to growth and metabolism were found in both across-breed contrasts (WRRh Vs. XHh and WRRl Vs. XHl). Further analysis showed that overall 75 genes exhibited altered DNA methylation in all four contrasts, which included some well-known growth factors of IGF1R, FGF12, FGF14, FGF18, FGFR2, and FGFR3. In addition, we further validate the MeDIP-seq results by bisulfite sequencing in some regions. Overall design: 12 Breast muscle samples were collected from two breeds of different growth rate, Recessive White Rock (WRR) and Xinhua Chickens (XH). Each breed included low and high-weight groups and 3 samples from each group were pooled equally for methylated DNA immunoprecipitation-sequencing (MeDIP-seq).

鸡生长性状在家禽生产中具有重要价值，但目前对其表观遗传层面的调控机制仍缺乏系统认知。为此，本研究旨在通过比较快、慢生长肉鸡的DNA甲基化谱，筛选调控鸡生长的候选基因。本研究采用甲基化DNA免疫共沉淀测序（methylated DNA immunoprecipitation-sequencing, MeDIP-seq）技术，分析了隐性白洛克鸡（Recessive White Rock, WRR）高、低体重组（WRRh、WRRl）以及新华鸡（Xinhua Chickens, XH）高、低体重组（XHh、XHl）的全基因组DNA甲基化模式。结果显示，CpG岛（CGI）的平均甲基化密度最低，启动子区域次之。在基因本体区域内，内含子的甲基化密度高于非翻译区（UTR）与外显子。此外，不同重复序列类型的甲基化水平存在显著差异，其中LINE/CR1家族的甲基化水平最高。甲基化CGI主要分布于基因间区，且在200~300 bp的长度区间内显著富集。四个样本中共鉴定到13294个甲基化基因，其中WRRh与WRRl间差异甲基化基因4085个，XHh与XHl间5599个，WRRh与XHh间4204个，WRRl与XHl间7301个。在品种内对比（WRRh vs. WRRl与XHh vs. XHl）中，共鉴定到132个与生长和代谢相关的差异甲基化基因；而在跨品种对比（WRRh vs. XHh与WRRl vs. XHl）中，共鉴定到129个与生长和代谢相关的差异甲基化基因。进一步分析显示，共有75个基因在所有四组对比中均出现DNA甲基化水平改变，其中包括IGF1R、FGF12、FGF14、FGF18、FGFR2、FGFR3等经典生长因子。此外，本研究通过亚硫酸氢盐测序对部分区域的MeDIP-seq结果进行了验证。整体实验设计：采集两种生长速率存在差异的肉鸡品种——隐性白洛克鸡（WRR）与新华鸡（XH）的12份胸肌样本。每个品种设置低、高体重组，每组各取3份样本等量混合后进行MeDIP-seq测序。