Talukder Amlan, Hu Haiyan, Li Xiaoman
Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA.
Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32816, USA.
BMC Genomics. 2021 Mar 8;22(1):163. doi: 10.1186/s12864-021-07440-5.
It is still challenging to predict interacting enhancer-promoter pairs (IEPs), partially because of our limited understanding of their characteristics. To understand IEPs better, here we studied the IEPs in nine cell lines and nine primary cell types.
By measuring the bipartite clustering coefficient of the graphs constructed from these experimentally supported IEPs, we observed that one enhancer is likely to interact with either none or all of the target genes of another enhancer. This observation implies that enhancers form clusters, and every enhancer in the same cluster synchronously interact with almost every member of a set of genes and only this set of genes. We perceived that an enhancer can be up to two megabase pairs away from other enhancers in the same cluster. We also noticed that although a fraction of these clusters of enhancers do overlap with super-enhancers, the majority of the enhancer clusters are different from the known super-enhancers.
Our study showed a new characteristic of IEPs, which may shed new light on distal gene regulation and the identification of IEPs.
预测相互作用的增强子-启动子对（IEP）仍然具有挑战性，部分原因是我们对其特征的了解有限。为了更好地理解IEP，我们在此研究了9种细胞系和9种原代细胞类型中的IEP。
通过测量由这些实验支持的IEP构建的图的二分聚类系数，我们观察到一个增强子可能与另一个增强子的所有或无目标基因相互作用。这一观察结果表明增强子形成簇，并且同一簇中的每个增强子与一组基因中的几乎每个成员同步相互作用，并且仅与这组基因相互作用。我们发现一个增强子与同一簇中的其他增强子之间的距离可能长达两个兆碱基对。我们还注意到，尽管这些增强子簇中的一部分确实与超级增强子重叠，但大多数增强子簇与已知的超级增强子不同。
我们的研究显示了IEP的一个新特征，这可能为远端基因调控和IEP的鉴定提供新的线索。
