ArticleNature protocols2019
Mapping RNA-chromatin interactions by sequencing with iMARGI.
Article in Nature protocols, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 66 citations in OpenAlex.
- Role of Chromatin-Associated RNAs in Eye Physiology and Pathology.Methods in molecular biology (Clifton, N.J.) · 2027Review
- Controlling for DNA dosage with whole-genome sequencing improves ATAC-seq peak calling.NAR genomics and bioinformatics · 2026Article
- Improved RNA-DNA interaction calling suggests RNA-based gene regulation of phenotypic transitions.Nucleic acids research · 2026Article
- A comparative analysis of topological domain callers over RNA-associated interactome.BMC bioinformatics · 2026Article
- Microfluidic low-input profiling reveals lncRNA roles in disease.bioRxiv : the preprint server for biology · 2026Article
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- Protein-Centric Mapping of RNA-DNA Interactions with RedChIP.Methods in molecular biology (Clifton, N.J.) · 2026Article
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- Role of RNA in genome folding: It's all about affinity.Current opinion in structural biology · 2025Review
- A U3 snoRNA is required for the regulation of chromatin dynamics and antiviral response in Drosophila melanogaster.Nucleic acids research · 2025Article
- A guide to studying 3D genome structure and dynamics in the kidney.Nature reviews. Nephrology · 2025Review
- A Joint Analysis of RNA-DNA and DNA-DNA Interactomes Reveals Their Strong Association.International journal of molecular sciences · 2025Article
- RADIP technology comprehensively identifies H3K27me3-associated RNA-chromatin interactions.Nucleic acids research · 2024Article
- HOXDeRNA activates a cancerous transcription program and super enhancers via genome-wide binding.Molecular cell · 2024Article
- The landscape of RNA-chromatin interaction reveals small non-coding RNAs as essential mediators of leukemia maintenance.Leukemia · 2024Article
- Exploring the roles of RNAs in chromatin architecture using deep learning.Nature communications · 2024Article
- Pairtools: From sequencing data to chromosome contacts.PLoS computational biology · 2024Article
- Cooltools: Enabling high-resolution Hi-C analysis in Python.PLoS computational biology · 2024Article
- Article
- Single-cell multiplex chromatin and RNA interactions in aging human brain.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
RNA-chromatin interactions represent an important aspect of the transcriptional regulation of genes and transposable elements. However, analyses of chromatin-associated RNAs (caRNAs) are often limited to one caRNA at a time. Here, we describe the iMARGI (in situ mapping of RNA-genome interactome) technique, which is used to discover caRNAs and reveal their respective genomic interaction loci. iMARGI starts with in situ crosslinking and genome fragmentation, followed by converting each proximal RNA-DNA pair into an RNA-linker-DNA chimeric sequence. These chimeric sequences are subsequently converted into a sequencing library suitable for paired-end sequencing. A standardized bioinformatic software package, iMARGI-Docker, is provided to decode the paired-end sequencing data into caRNA-DNA interactions. Compared to its predecessor MARGI (mapping RNA-genome interactions), the number of input cells for iMARGI is 3-5 million (a 100-fold reduction), experimental time is reduced, and clear checkpoints have been established. It takes a few hours a day and a total of 8 d to complete the construction of an iMARGI sequencing library and 1 d to carry out data processing with iMARGI-Docker.
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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.