Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.
PLoS One. 2013;8(2):e56411. doi: 10.1371/journal.pone.0056411. Epub 2013 Feb 18.
Growth traits are important in poultry production, however, little is known for its regulatory mechanism at epigenetic level. Therefore, in this study, we aim to compare DNA methylation profiles between fast- and slow-growing broilers in order to identify candidate genes for 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 (WRR(h); WRR(l)) and that of Xinhua Chickens (XH(h); XH(l)) at 7 weeks of age. The results showed that the average methylation density was the lowest in CGIs followed by promoters. Within the gene body, the methylation density of introns was higher than that of 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 ranging 200-300 bp. In total 13,294 methylated genes were found in four samples, including 4,085 differentially methylated genes of WRR(h) Vs. WRR(l), 5,599 of XH(h) Vs. XH(l), 4,204 of WRR(h) Vs. XH(h), as well as 7,301 of WRR(l) Vs. XH(l). Moreover, 132 differentially methylated genes related to growth and metabolism were observed in both inner contrasts (WRR(h) Vs. WRR(l) and XH(h) Vs. XH(l)), whereas 129 differentially methylated genes related to growth and metabolism were found in both across-breed contrasts (WRR(h) Vs. XH(h) and WRR(l) Vs. XH(l)). 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 validate the MeDIP-seq results by bisulfite sequencing in some regions.
This study revealed the global DNA methylation pattern of chicken muscle, and identified candidate genes that potentially regulate muscle development at 7 weeks of age at methylation level.
生长性状在禽类生产中很重要，但在表观遗传水平上对其调控机制知之甚少。因此，本研究旨在比较快长型和慢长型肉鸡之间的 DNA 甲基化谱，以鉴定鸡生长的候选基因。使用甲基化 DNA 免疫沉淀测序（MeDIP-seq）来研究 7 周龄隐性白洛克（WRR(h)；WRR(l)）和新华鸡（XH(h)；XH(l)）高尾和低尾的全基因组 DNA 甲基化模式。结果表明，CGI 之后是启动子，平均甲基化密度最低。在基因体内，内含子的甲基化密度高于 UTR 和外显子。此外，不同重复类型的甲基化水平不同，LINE/CR1 最高。甲基化的 CGI 主要分布在基因间区，并且在 200-300bp 的大小范围内富集。在四个样本中共发现 13294 个甲基化基因，包括 WRR(h)与 WRR(l)的 4085 个差异甲基化基因、XH(h)与 XH(l)的 5599 个、WRR(h)与 XH(h)的 4204 个以及 WRR(l)与 XH(l)的 7301 个。此外，在两个内对照（WRR(h)与 WRR(l)和 XH(h)与 XH(l)）中观察到 132 个与生长和代谢相关的差异甲基化基因，在两个跨品种对照（WRR(h)与 XH(h)和 WRR(l)与 XH(l)）中观察到 129 个与生长和代谢相关的差异甲基化基因。进一步分析表明，在所有四个对照中，共有 75 个基因的 DNA 甲基化发生改变，其中包括 IGF1R、FGF12、FGF14、FGF18、FGFR2 和 FGFR3 等一些著名的生长因子。此外，我们在一些区域通过亚硫酸氢盐测序验证了 MeDIP-seq 的结果。
本研究揭示了鸡肌肉的全基因组 DNA 甲基化模式，并鉴定了在 7 周龄时可能在甲基化水平上调节肌肉发育的候选基因。
