High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH

IF 45.5 1区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Cell Pub Date : 2025-04-15 DOI:10.1016/j.cell.2025.03.032

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

{"title":"High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH","authors":"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","doi":"10.1016/j.cell.2025.03.032","DOIUrl":null,"url":null,"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, <em>in vitro</em> 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 <em>FOS</em>. Oligo-LiveFISH offers a versatile platform for studying 3D genome dynamics and their links to cellular processes and disease.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"40 1","pages":""},"PeriodicalIF":45.5000,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Cell","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1016/j.cell.2025.03.032","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}

引用次数: 0

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.

Abstract Image

查看原文本刊更多论文

使用Oligo-LiveFISH进行染色质DNA通讯的高分辨率动态成像

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。在这里，我们提出了Oligo-LiveFISH，这是一个高分辨率，基于试剂的平台，用于动态跟踪各种细胞类型（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，我们表征了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。我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。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Cell 生物-生化与分子生物学

CiteScore

110.00

自引率

0.80%

发文量

396

审稿时长

2 months

期刊介绍： Cells is an international, peer-reviewed, open access journal that focuses on cell biology, molecular biology, and biophysics. It is affiliated with several societies, including the Spanish Society for Biochemistry and Molecular Biology (SEBBM), Nordic Autophagy Society (NAS), Spanish Society of Hematology and Hemotherapy (SEHH), and Society for Regenerative Medicine (Russian Federation) (RPO). The journal publishes research findings of significant importance in various areas of experimental biology, such as cell biology, molecular biology, neuroscience, immunology, virology, microbiology, cancer, human genetics, systems biology, signaling, and disease mechanisms and therapeutics. The primary criterion for considering papers is whether the results contribute to significant conceptual advances or raise thought-provoking questions and hypotheses related to interesting and important biological inquiries. In addition to primary research articles presented in four formats, Cells also features review and opinion articles in its "leading edge" section, discussing recent research advancements and topics of interest to its wide readership.