ArticleNucleic acids research2020
Studying RNA-DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 68 citations in OpenAlex.
- Controlling for DNA dosage with whole-genome sequencing improves ATAC-seq peak calling.NAR genomics and bioinformatics · 2026Article
- Decoding chromatin-associated RNA (caRNA) interaction networks: from genome-wide dynamic capture to epigenetic mechanisms in plants and animals.Epigenetics · 2026Review
- Improved RNA-DNA interaction calling suggests RNA-based gene regulation of phenotypic transitions.Nucleic acids research · 2026Article
- Widespread DNA off-targeting confounds RNA chromatin occupancy studies.Nature biotechnology · 2026Article
- Direct roles of long non-coding RNAs in transcription activation.Nature structural & molecular biology · 2026Review
- Sequence-Based Models for RNA-Protein Interactions Imputation Might Be Insufficient for Novel Signal Prediction in eCLIP Data.International journal of molecular sciences · 2026Article
- ChRD-PET: A Method for Mapping RNA-DNA Interactions.Methods in molecular biology (Clifton, N.J.) · 2026Article
- 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
- Causal machine learning for single-cell genomics.Nature genetics · 2025Review
- 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
- BaRDIC: robust peak calling for RNA-DNA interaction data.NAR genomics and bioinformatics · 2024Article
- Cooltools: Enabling high-resolution Hi-C analysis in Python.PLoS computational biology · 2024Article
- Article
- RNA-DNA interactomes of three prokaryotes uncovered by proximity ligation.Communications biology · 2023Article
- RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome.Database : the journal of biological databases and curation · 2023Article
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Non-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA-DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. Analysis of the RNA-DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.
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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.