MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; School of Medicine, Tsinghua University, Beijing, 100084, China.
MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China.
Nat Commun. 2017 Nov 20;8(1):1622. doi: 10.1038/s41467-017-01754-3.
In human cells, DNA is hierarchically organized and assembled with histones and DNA-binding proteins in three dimensions. Chromatin interactions play important roles in genome architecture and gene regulation, including robustness in the developmental stages and flexibility during the cell cycle. Here we propose in situ Hi-C method named Bridge Linker-Hi-C (BL-Hi-C) for capturing structural and regulatory chromatin interactions by restriction enzyme targeting and two-step proximity ligation. This method improves the sensitivity and specificity of active chromatin loop detection and can reveal the regulatory enhancer-promoter architecture better than conventional methods at a lower sequencing depth and with a simpler protocol. We demonstrate its utility with two well-studied developmental loci: the beta-globin and HOXC cluster regions.
在人类细胞中，DNA 与组蛋白和 DNA 结合蛋白一起在三维空间中进行层次化组织和组装。染色质相互作用在基因组结构和基因调控中发挥着重要作用，包括在发育阶段的稳健性和细胞周期中的灵活性。在这里，我们提出了一种名为 Bridge Linker-Hi-C（BL-Hi-C）的原位 Hi-C 方法，用于通过限制酶靶向和两步邻近连接来捕获结构和调节染色质相互作用。与传统方法相比，该方法提高了活性染色质环检测的灵敏度和特异性，并且可以在更低的测序深度和更简单的方案下更好地揭示调节增强子-启动子结构。我们用两个研究得很好的发育基因座：β-珠蛋白和 HOXC 簇区域来证明其用途。
