Xu Hang, Zhang Shijie, Yi Xianfu, Plewczynski Dariusz, Li Mulin Jun
2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China.
Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
Comput Struct Biotechnol J. 2020 Feb 28;18:558-570. doi: 10.1016/j.csbj.2020.02.013. eCollection 2020.
Mechanisms underlying gene regulation are key to understand how multicellular organisms with various cell types develop from the same genetic blueprint. Dynamic interactions between enhancers and genes are revealed to play central roles in controlling gene transcription, but the determinants to link functional enhancer-promoter pairs remain elusive. A major challenge is the lack of reliable approach to detect and verify functional enhancer-promoter interactions (EPIs). In this review, we summarized the current methods for detecting EPIs and described how developing techniques facilitate the identification of EPI through assessing the merits and drawbacks of these methods. We also reviewed recent state-of-art EPI prediction methods in terms of their rationale, data usage and characterization. Furthermore, we briefly discussed the evolved strategies for validating functional EPIs.
基因调控的潜在机制是理解具有各种细胞类型的多细胞生物如何从相同的遗传蓝图发育而来的关键。增强子与基因之间的动态相互作用在控制基因转录中起着核心作用，但连接功能性增强子 - 启动子对的决定因素仍然难以捉摸。一个主要挑战是缺乏可靠的方法来检测和验证功能性增强子 - 启动子相互作用（EPI）。在这篇综述中，我们总结了当前检测EPI的方法，并通过评估这些方法的优缺点描述了发展中的技术如何促进EPI的鉴定。我们还从原理、数据使用和特征描述方面回顾了最近的先进EPI预测方法。此外，我们简要讨论了验证功能性EPI的改进策略。
