ArticleNature methods2022
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation.
Article in Nature methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 26 citations in OpenAlex.
- Review
- Methodological advances in studying protein-centered RNA-protein interactions.Science China. Life sciences · 2026Article
- Review
- Step-by-Step Protocol for In Situ Profiling of RNA Subcellular Localization Using TATA-seq.Bio-protocol · 2026Article
- Role of RNA in genome folding: It's all about affinity.Current opinion in structural biology · 2025Review
- Profiling RNA subcellular localization in situ by TATA-seq.RNA (New York, N.Y.) · 2025Article
- Chromatin-Associated RNAs Regulate Gene Expression and Chromatin Structure.Non-coding RNA · 2025Review
- Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues.Nature methods · 2025Article
- SLAM-RT&Tag: spatiotemporal profiling of RNA within nuclear compartments in situ.Nature reviews. Genetics · 2025Article
- Decoding RNA-Protein Interactions: Methodological Advances and Emerging Challenges.Advanced genetics (Hoboken, N.J.) · 2025Review
- Deaminase-based RNA recording enables high throughput mutational profiling of protein-RNA interactions.bioRxiv : the preprint server for biology · 2025Article
- Profiling transcriptome composition and dynamics within nuclear compartments using SLAM-RT&Tag.Molecular cell · 2025Article
- Functions and Therapeutic Potentials of Long Noncoding RNA in Skeletal Muscle Atrophy and Dystrophy.Journal of cachexia, sarcopenia and muscle · 2025Review
- Simultaneous profiling of chromatin-associated RNA at targeted DNA loci and RNA-RNA Interactions through TaDRIM-seq.Nature communications · 2025Article
- A noncanonical role of roX RNAs in autosomal epigenetic repression.Nature communications · 2025Article
- RADIP technology comprehensively identifies H3K27me3-associated RNA-chromatin interactions.Nucleic acids research · 2024Article
- Cut&tag: a powerful epigenetic tool for chromatin profiling.Epigenetics · 2024Review
- Chrom-seq identifies RNAs at chromatin marks.Science advances · 2024Article
- OpenTn5: Open-Source Resource for Robust and Scalable Tn5 Transposase Purification and Characterization.bioRxiv : the preprint server for biology · 2024Article
- Processivity and specificity of histone acetylation by the male-specific lethal complex.Nucleic acids research · 2024Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Whereas techniques to map chromatin-bound proteins are well developed, mapping chromatin-associated RNAs remains a challenge. Here, we describe Reverse Transcribe and Tagment (RT&Tag), in which RNAs associated with a chromatin epitope are targeted by an antibody followed by a protein A-Tn5 transposome. Localized reverse transcription generates RNA/cDNA hybrids that are subsequently tagmented by Tn5 transposases for downstream sequencing. We demonstrate the utility of RT&Tag in Drosophila cells for capturing the noncoding RNA roX2 with the dosage compensation complex and maturing transcripts associated with silencing histone modifications. We also show that RT&Tag can detect N6-methyladenosine-modified mRNAs, and show that genes producing methylated transcripts are characterized by extensive promoter pausing of RNA polymerase II. The high efficiency of in situ antibody tethering and tagmentation makes RT&Tag especially suitable for rapid low-cost profiling of chromatin-associated RNAs.
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Registered trials
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.