美国斯坦福大学Lei S. Qi研究组近日取得一项新成果。经过不懈努力，他们研究出使用Oligo-LiveFISH进行染色质DNA通讯的高分辨率动态成像。该项研究成果发表在2025年4月15日出版的《细胞》上。
研究团队提出Oligo-LiveFISH，这是一个高分辨率、基于试剂的平台，用于动态跟踪不同细胞类型（包括原代细胞）中的非重复基因组位点。Oligo-LiveFISH利用计算设计、体外转录和化学标记生成的荧光引导RNA （gRNA）寡核苷酸池，作为核糖核蛋白递送。利用机器学习，该研究组表征了gRNA设计和染色质特征对成像效率的影响。多色Oligo-LiveFISH在3D中实现了20纳米的空间分辨率和50毫秒的时间分辨率，实时捕获增强子和启动子动态。他们的测量和动态建模揭示了两种不同的染色质通讯模式，主动转录减缓了内源性基因（如FOS）的增强子-启动子动力学。Oligo-LiveFISH提供了一个多功能平台，用于研究3D基因组动力学及其与细胞过程和疾病的联系。
研究人员表示，三维（3D）基因组动力学对细胞功能和疾病至关重要。然而，实时的活细胞DNA可视化仍然具有挑战性，因为现有的方法通常局限于重复区域，分辨率低，或者需要复杂的基因组工程。
附：英文原文
Title: High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH
Author: Yanyu Zhu, Ashwin Balaji, Mengting Han, Leonid Andronov, Anish R. Roy, Zheng Wei, Crystal Chen, Leanne Miles, Sa Cai, Zhengxi Gu, Ariana Tse, Betty Chentzu Yu, Takeshi Uenaka, Xueqiu Lin, Andrew J. Spakowitz, W.E. Moerner, Lei S. Qi
Issue&Volume: 2025-04-15
Abstract: Three-dimensional (3D) genome dynamics are crucial for cellular functions and disease. However, real-time, live-cell DNA visualization remains challenging, as existing methods are often confined to repetitive regions, suffer from low resolution, or require complex genome engineering. Here, we present Oligo-LiveFISH, a high-resolution, reagent-based platform for dynamically tracking non-repetitive genomic loci in diverse cell types, including primary cells. Oligo-LiveFISH utilizes fluorescent guide RNA (gRNA) oligo pools generated by computational design, in vitro transcription, and chemical labeling, delivered as ribonucleoproteins. Utilizing machine learning, we characterized the impact of gRNA design and chromatin features on imaging efficiency. Multi-color Oligo-LiveFISH achieved 20-nm spatial resolution and 50-ms temporal resolution in 3D, capturing real-time enhancer and promoter dynamics. Our measurements and dynamic modeling revealed two distinct modes of chromatin communication, and active transcription slows enhancer-promoter dynamics at endogenous genes like FOS. Oligo-LiveFISH offers a versatile platform for studying 3D genome dynamics and their links to cellular processes and disease.
DOI: 10.1016/j.cell.2025.03.032
Source: https://www.cell.com/cell/abstract/S0092-8674(25)00350-2