ArticleProceedings of the National Academy of Sciences of the United States of America2022
RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 30 citations in OpenAlex.
- Decoding chromatin-associated RNA (caRNA) interaction networks: from genome-wide dynamic capture to epigenetic mechanisms in plants and animals.Epigenetics · 2026Review
- Protein-Centric Mapping of RNA-DNA Interactions with RedChIP.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Chromatin-Associated RNAs Regulate Gene Expression and Chromatin Structure.Non-coding RNA · 2025Review
- Simultaneous Capture of Chromatin-Associated RNA and Global RNA-RNA Interactions With Reduced Input Requirements.Bio-protocol · 2025Article
- Identification of chromatin-associated RNAs at human centromeres.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive analysis of RNA-chromatin, RNA-, and DNA-protein interactions.NAR genomics and bioinformatics · 2025Article
- Simultaneous profiling of chromatin-associated RNA at targeted DNA loci and RNA-RNA Interactions through TaDRIM-seq.Nature communications · 2025Article
- A Joint Analysis of RNA-DNA and DNA-DNA Interactomes Reveals Their Strong Association.International journal of molecular sciences · 2025Article
- Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers.Nature communications · 2025Article
- RADIP technology comprehensively identifies H3K27me3-associated RNA-chromatin interactions.Nucleic acids research · 2024Article
- LncRNA ARGI Contributes to Virus-Induced Pancreatic β Cell Inflammation Through Transcriptional Activation of IFN-Stimulated Genes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Review
- RNA-DNA interactomes of three prokaryotes uncovered by proximity ligation.Communications biology · 2023Article
- Low-affinity CTCF binding drives transcriptional regulation whereas high-affinity binding encompasses architectural functions.iScience · 2023Article
- Approaches for Modes of Action Study of Long Non-Coding RNAs: From Single Verification to Genome-Wide Determination.International journal of molecular sciences · 2023Review
- Computational Methods to Study DNA:DNA:RNA Triplex Formation by lncRNAs.Non-coding RNA · 2023Review
- 3plex enables deep computational investigation of triplex forming lncRNAs.Computational and structural biotechnology journal · 2023Article
- Long-Distance Repression by Human Silencers: Chromatin Interactions and Phase Separation in Silencers.Cells · 2022Review
Corrections and comments
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Authors and funding
7 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nuclear noncoding RNAs (ncRNAs) are key regulators of gene expression and chromatin organization. The progress in studying nuclear ncRNAs depends on the ability to identify the genome-wide spectrum of contacts of ncRNAs with chromatin. To address this question, a panel of RNA-DNA proximity ligation techniques has been developed. However, neither of these techniques examines proteins involved in RNA-chromatin interactions. Here, we introduce RedChIP, a technique combining RNA-DNA proximity ligation and chromatin immunoprecipitation for identifying RNA-chromatin interactions mediated by a particular protein. Using antibodies against architectural protein CTCF and the EZH2 subunit of the Polycomb repressive complex 2, we identify a spectrum of
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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 OpenQuestion graph.