转录因子结合部位的发育和进化特征基于可解释的机器学习模型集群区域
Zhangyi Ouyang1, Feng Liu2, Wanying Li1
1Academy of Military Medical Sciences, Beijing 100850, China.
Nucleic acids research
|May 30, 2024
概括
这项研究揭示了转录因子结合部位在物种和发育之间如何演变. 了解这些 cis 调节元素中的动态是解释表型变异的关键.
科学领域:
- 基因组学就是基因组学.
- 发展生物学 发展生物学
- 进化生物学 进化生物学
背景情况:
- 基因表达依赖于转录因子 (TFs) 和 cis调节元件 (CREs),但它们的分布和进化仍然具有挑战性.
- 了解TF结合位点分布如何演变对于解释时空基因表达和遗传性表型变异至关重要.
研究的目的:
- 在不同物种的胚胎发育过程中研究转录因子结合部位集群区域 (TFCRs) 的进化动态.
- 使用RegulatoryScore.评估TFCR复杂性和基因表达之间的同步.
- 识别影响基因表达的关键调控特征,如TFCR促进器距离.
主要方法:
- 收集了来自哺乳动物 (人,小鼠,牛),鱼 (斑马鱼,梅达卡) 和的染色质可访问性和基因表达数据.
- 在不同胚胎阶段对TFCR进行了表征,以分析调节进化.
- 采用可解释的机器学习模型来确定TFCR-促进者距离的重要性.
主要成果:
- 在胚胎发育过程中和跨物种的TFCR分布表现出动态变化.
- 在TFCR复杂性和跨物种基因表达之间观察到显著的同步.
- 确定TFCR和促进体之间的距离是协调基因调节的关键因素.
结论:
- 这项研究阐明了TFCR的发育和进化动态,从鱼类和到哺乳动物.
- 这些发现为转录调节和胚胎发育过程中的表型差异之间的关系提供了宝贵的见解.
- 这些数据作为未来对基因调节和进化研究的资源.
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