3D ATAC-PALM: super-resolution imaging of the accessible genome
3D ATAC-PALM: super-resolution imaging of the accessible genome
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3D ATAC-PALM：可访问基因组的超分辨率成像
DOI：
10.1038/s41592-020-0775-2
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发表时间：
2020-03-16
期刊：
影响因子：
48
通讯作者：
Liu, Zhe
中科院分区：
文献类型：
--
作者：
Xie, Liangqi;Dong, Peng;Liu, Zhe
3D ATAC-PALM 将 ATAC 与超分辨率成像相结合，以实现可访问基因组的纳米级视图。当与 FISH、蛋白质荧光和遗传扰动相结合时，该方法能够对可及染色质进行原位研究。为了对可及基因组进行纳米级原位成像，我们开发了转座酶可及染色质光激活定位显微镜三维测定法 (3D ATAC-PALM)，它将转座酶可及染色质测定法与可视化、PALM 超分辨率成像和点阵光片显微镜相结合。 3D ATAC-PALM 与 Oligopaint DNA 荧光原位杂交 (FISH)、RNA-FISH 和蛋白质荧光多重结合，连接显微镜和基因组数据，揭示空间隔离的可及染色质结构域 (ACD)，其中包含活性染色质和转录基因。使用这些方法分析遗传干扰的细胞，我们证明基因组结构蛋白 CTCF 可以防止可及染色质过度聚集并解压 ACD。这些结果凸显了 3D ATAC-PALM 作为探测基因组结构和组织机制的有用工具。
3D ATAC-PALM integrates ATAC with super-resolution imaging for nanoscale views of the accessible genome. When combined with FISH, protein fluorescence and genetic perturbation, the method enables investigation of accessible chromatin in situ.To image the accessible genome at nanometer scale in situ, we developed three-dimensional assay for transposase-accessible chromatin-photoactivated localization microscopy (3D ATAC-PALM) that integrates an assay for transposase-accessible chromatin with visualization, PALM super-resolution imaging and lattice light-sheet microscopy. Multiplexed with oligopaint DNA-fluorescence in situ hybridization (FISH), RNA-FISH and protein fluorescence, 3D ATAC-PALM connected microscopy and genomic data, revealing spatially segregated accessible chromatin domains (ACDs) that enclose active chromatin and transcribed genes. Using these methods to analyze genetically perturbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs. These results highlight 3D ATAC-PALM as a useful tool to probe the structure and organizing mechanism of the genome.