The 3D organization of chromatin regulates many genome functions. Our understanding of 3D genome organization requires tools to directly visualize chromatin conformation in its native context. Here we report an imaging technology for visualizing chromatin organization across multiple scales in single cells with high genomic throughput. First we demonstrate multiplexed imaging of hundreds of genomic loci by sequential hybridization, which allows high-resolution conformation tracing of whole chromosomes. Next we report a multiplexed error-robust fluorescence in situ hybridization (MERFISH)-based method for genome-scale chromatin tracing and demonstrate simultaneous imaging of more than 1,000 genomic loci and nascent transcripts of more than 1,000 genes together with landmark nuclear structures. Using this technology, we characterize chromatin domains, compartments, and trans-chromosomal interactions and their relationship to transcription in single cells. We envision broad application of this high-throughput, multi-scale, and multi-modal imaging technology, which provides an integrated view of chromatin organization in its native structural and functional context.

染色质的 3D 组织调节许多基因组功能。我们对 3D 基因组组织的理解需要工具来直接可视化其天然背景下的染色质构象。在这里，我们报告了一种成像技术，可在具有高基因组通量的单细胞中跨多个尺度可视化染色质组织。首先，我们通过顺序杂交展示了数百个基因组位点的多重成像，这使得整个染色体的高分辨率构象追踪成为可能。接下来，我们报告了一种基于多重抗错荧光原位杂交 (MERFISH) 的基因组规模染色质追踪方法，并展示了 1,000 多个基因组位点和 1,000 多个基因的新生转录本以及标志性核结构的同步成像。利用这项技术，我们表征了染色质结构域、区室和跨染色体相互作用及其与单细胞转录的关系。我们设想这种高通量、多尺度、多模式成像技术的广泛应用，它提供了染色质组织在其天然结构和功能背景下的综合视图。