Protocol for high-resolution mapping of RNA-associated chromatin using chromatin isolation by RNA purification-tag.

Ruishuang Fu, Rongjie Zhao, Huimin Yang, Yujun Xia, Dewen Xu, Aiqin Shi, Huacheng Luo

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Article in STAR protocols, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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5 · Who and what money

Authors and funding

7 authors.

Ruishuang FuZhejiang Cancer Hospital, Zhejiang Key Laboratory of Functional Nucleic Acids for Basic and Clinical Application, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.

Rongjie ZhaoDepartment of Gynecological Radiotherapy, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.

Huimin YangZhejiang Cancer Hospital, Zhejiang Key Laboratory of Functional Nucleic Acids for Basic and Clinical Application, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.

Yujun XiaCollege of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.

Dewen XuCollege of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.

Aiqin ShiXianghu Laboratory, Hangzhou, Zhejiang 311231, China.

Huacheng LuoZhejiang Cancer Hospital, Zhejiang Key Laboratory of Functional Nucleic Acids for Basic and Clinical Application, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China. Electronic address: luohuacheng@him.cas.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Mapping the genomic binding sites of long non-coding RNAs (lncRNAs) is essential for understanding their regulatory functions. Here, we present a protocol for integrating RNA hybridization with in situ tagmentation using chromatin isolation by RNA purification-tag (ChIRP-Tag). We describe steps for performing cell permeabilization, hybridization of biotinylated probes to target RNAs, and recruiting Protein A/G-Tn5 transposase via antibodies to catalyze in situ library construction. This protocol captures RNA-associated chromatin with high sensitivity and spatial resolution across various cell types. For complete details on the use and execution of this protocol, please refer to Fu et al.

Indexed as

CancerCell cultureSequence analysisSequencing

Identifiers

PMID42531122

DOI10.1016/j.xpro.2026.104749

PMCPMC13449967

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LicenceCC BY-NC-ND

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.