Mapping and analysis of a spatiotemporal H3K27ac and gene expression spectrum in pigs
Mapping and analysis of a spatiotemporal H3K27ac and gene expression spectrum in pigs
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猪时空 H3K27ac 和基因表达谱的绘图和分析
DOI：
10.1007/s11427-021-2034-5
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发表时间：
2022-01-27
影响因子：
9.1
通讯作者：
Huang, Lusheng
中科院分区：
文献类型：
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作者：
Zhu, Yaling;Zhou, Zhimin;Huang, Lusheng
基因组非编码区和调控区的知识有限，限制了我们破译猪复杂性状遗传机制的能力。在这项研究中，我们通过结合H3 K27 ac靶向的ChIP-Seq和RNA-Seq，在从亚洲土著巴马香猪和欧洲高度选择的两种性别的大白色猪中取样的胎儿（出生前74-75天）和成年（出生后132-150天）组织（脑、肝、心脏、肌肉和小肠）中表征了推定的增强子和启动子及其靶基因的时空景观。我们鉴定了101，290个H3 K27 ac峰，标记了18，521个启动子和82，769个增强子，包括在所有组织和发育阶段都有活性的峰（这可能表明外源基因插入的安全港位点）以及组织和发育阶段特异性峰（调节与组织和发育阶段特异性生理功能相匹配的基因途径）。我们发现，H3 K27 ac和DNA甲基化的启动子区域的XIST基因可能参与X染色体失活，并证明了本资源的效用，揭示了已知的因果基因的调控模式和优先考虑候选的因果变异的复杂性状的猪。此外，我们发现每个样本平均有1，124个超级增强子，并且发现它们比普通峰更有可能显示组织特异性活性。我们开发了一个Web浏览器，以提高结果的可访问性（http：segtp.jxau.edu.cn/pencode/? genome= susScr 11）。
The limited knowledge of genomic noncoding and regulatory regions has restricted our ability to decipher the genetic mechanisms underlying complex traits in pigs. In this study, we characterized the spatiotemporal landscape of putative enhancers and promoters and their target genes by combining H3K27ac-targeted ChIP-Seq and RNA-Seq in fetal (prenatal days 74–75) and adult (postnatal days 132–150) tissues (brain, liver, heart, muscle and small intestine) sampled from Asian aboriginal Bama Xiang and European highly selected Large White pigs of both sexes. We identified 101,290 H3K27ac peaks, marking 18,521 promoters and 82,769 enhancers, including peaks that were active across all tissues and developmental stages (which could indicate safe harbor locus for exogenous gene insertion) and tissue- and developmental stage-specific peaks (which regulate gene pathways matching tissue- and developmental stage-specific physiological functions). We found that H3K27ac and DNA methylation in the promoter region of theXISTgene may be involved in X chromosome inactivation and demonstrated the utility of the present resource for revealing the regulatory patterns of known causal genes and prioritizing candidate causal variants for complex traits in pigs. In addition, we identified an average of 1,124 super-enhancers per sample and found that they were more likely to show tissue-specific activity than ordinary peaks. We have developed a web browser to improve the accessibility of the results (http://segtp.jxau.edu.cn/pencode/?genome=susScr11).