Jul 2026· STAR Protocols· Vol 7, pp. 104749· 0 citations· 27 references
Medicine
TL;DR
A protocol for integrating RNA hybridization with in situ tagmentation using chromatin isolation by RNA purification-tag (ChIRP-Tag) is presented, which captures RNA-associated chromatin with high sensitivity and spatial resolution across various cell types.
Abstract
Summary 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.1
A detailed CUT&RUN protocol from sample collection through data analysis, including best practices and defined controls to ensure specific, efficient, and robust target profiling is provided.
Tessa M. Firestone, Bryan J. Venters, Katherine Novitzky et al.· Methods in molecular biology· 0 citations
A proximity-labeling protocol for identifying the chromatin-dependent protein interactome associated with specific chromatin marks, termed ChromID, which preserves native chromatin organization and captures transient chromatin-associated interactions that are often lost during conventional affinity purification workflo...
Richard Cardoso da Silva, Douwe ten Bulte, T. Baubec· Bio-protocol· 0 citations
This work presents a robust RNA FISH protocol for detecting the lncRNA Xist, a chromatin-associated master regulator of X chromosome inactivation (XCI) that serves as a paradigm for lncRNA biology and demonstrates the effectiveness of this method for investigating lncRNA localization and chromatin-associated function.
Hye-Rim Shin, Hyun-jung Oh· Methods in molecular biology· 0 citations
The protocols for ChIP-seq are outlined, including immunoprecipitation, library preparation for high-throughput sequencing, and bioinformatics analysis of sequencing data that the authors routinely perform in their lab groups, and include troubleshooting tips for each step.
Zachary Bigelow, S. Nechaev, Archana Dhasarathy· Methods in molecular biology· 0 citations
By combining reduced input requirements, high reproducibility, a shortened 3.5-day workflow and the elimination of gel-based purification, soniCLIP provides an efficient and robust approach for the identification of RNA targets of canonical and non-canonical RBPs.
Pia Sommerkamp, Sudeep Sahadevan, Thileepan Sekaran et al.· bioRxiv· 1 citation
A straightforward, enrichment-free caRNA profiling strategy: proximity crosslinking-induced RNA depletion sequencing (PCRD-seq), which exhibits potential in profiling nuclear lamina-associated RNAs, which paves the way for its application to profile RNAs associated with other chromatin subdomains.
Jinghua Han, Lan Li, Xueqing Kong et al.· Nucleic Acids Research· 0 citations
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