数字农科院2.0

Simultaneous Capture of Chromatin-Associated RNA and Global RNA–RNA Interactions With Reduced Input Requirements

文献类型： 外文期刊

作者： Cheng Ding;Guoting Chen;Shiping Luan;Yuanyuan Gong;Cuilin Gui;Chen Yang;Zihe Xiang;Junjie Du;Mohamed F. Foda;Jiapei Yan;Xingwang Li

作者机构：

关键词： （0-1-4）Chromatin-associated RNAs (caRNAs);DNA element;Low-input requirement;Multi-omics;RNA–DNA interactomes;RNA–RNA interactomes;TaDRIM-seq

期刊名称： Bio-protocol

ISSN： 2331-8325

年卷期： 2025 年 15 卷 17 期

页码：

收录情况： ESCI（2025版）

摘要： Chromatin-associated RNAs (caRNAs) have been increasingly recognized as key regulators of gene expression and genome architecture. A few technologies, such as ChRD-PET and RedChIP, have emerged to assess protein-mediated RNA–chromatin interactions, but each has limitations. Here, we describe the TaDRIM-seq (targeted DNA-associated RNA and RNA–RNA interaction mapping by sequencing) technique, which combines Protein G (PG)-Tn5-targeted DNA tagmentation with in situ proximity ligation to simultaneously profile caRNAs across genomic regions and capture global RNA–RNA interactions within intact nuclei. This approach reduces the required cell input, shortens the experimental duration compared to existing protocols, and is applicable to both mammalian and plant systems.

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