Determining chromatin architecture with Micro Capture-C.
Determining chromatin architecture with Micro Capture-C.
复制标题
使用 Micro Capture-C 确定染色质结构。
DOI：
10.1038/s41596-023-00817-8
复制
发表时间：
2023
期刊：
影响因子：
14.8
通讯作者：
Hamley JC
中科院分区：
文献类型：
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作者：
Hamley JC
微捕获-C（MCC）是一种染色质构象捕获（3C）方法，用于以碱基对分辨率可视化基因组特定区域的可重现三维接触。这些方法是使用邻位连接来测定染色质拓扑结构的已建立的技术家族。MCC可以通过对3C方法的多次改进以比以前的技术高得多的分辨率生成数据。使用序列不可知的核酸酶，维持细胞完整性和连接点的完全测序，MCC实现了亚核小体水平的分辨率，其可用于揭示类似于DNA酶I足迹的转录因子结合位点。基因密集区，近距离增强子-启动子接触，超级增强子内的单个增强子和多种其他类型的基因座或调控区，这些在以前用常规3C技术进行测定时具有挑战性，使用MCC很容易观察到。MCC需要接受常见分子生物学技术和生物信息学的培训，以进行实验和分析数据。对于经验丰富的分子生物学家，预计可在3周内完成方案。
Micro Capture-C (MCC) is a chromatin conformation capture (3C) method for visualizing reproducible three-dimensional contacts of specified regions of the genome at base pair resolution. These methods are an established family of techniques that use proximity ligation to assay the topology of chromatin. MCC can generate data at substantially higher resolution than previous techniques through multiple refinements of the 3C method. Using a sequence agnostic nuclease, the maintenance of cellular integrity and full sequencing of the ligation junctions, MCC achieves subnucleosomal levels of resolution, which can be used to reveal transcription factor binding sites analogous to DNAse I footprinting. Gene dense regions, close-range enhancer–promoter contacts, individual enhancers within super-enhancers and multiple other types of loci or regulatory regions that were previously challenging to assay with conventional 3C techniques, are readily observed using MCC. MCC requires training in common molecular biology techniques and bioinformatics to perform the experiment and analyze the data. The protocol can be expected to be completed in a 3 week timeframe for experienced molecular biologists.