ArticleNature biotechnology2014
Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification.
Article in Nature biotechnology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
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Who cites it
100 citing papers in PubMed, 182 citations in OpenAlex.
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- Nucleolar FRG2 lncRNAs inhibit rRNA transcription and cytoplasmic translation, linking FSHD to dysregulation of muscle-specific protein synthesis.Nucleic acids research · 2025Article
- Decoding RNA-Protein Interactions: Methodological Advances and Emerging Challenges.Advanced genetics (Hoboken, N.J.) · 2025Review
- Biomolecules Interacting with Long Noncoding RNAs.Biology · 2025Review
- LncRNAs, RNA Therapeutics, and Emerging Technologies in Liver Pathobiology.Seminars in liver disease · 2025Review
- From the genome's perspective: Bearing somatic retrotransposition to leverage the regulatory potential of L1 RNAs.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- A noncanonical role of roX RNAs in autosomal epigenetic repression.Nature communications · 2025Article
- N-terminus ofeLife · 2024Article
- 3D chromatin structures associated with ncRNAScience advances · 2024Article
- Interaction of MLE with CLAMP zinc finger is involved in proper MSL proteins binding to chromosomes inOpen biology · 2024Article
- Novel insights into the role of long non-coding RNA in the human malaria parasite, Plasmodium falciparum.Nature communications · 2023Article
- RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome.Database : the journal of biological databases and curation · 2023Article
- Reversing the Central Dogma: RNA-guided control of DNA in epigenetics and genome editing.Molecular cell · 2023Review
- Functional Relationships between Long Non-Coding RNAs and Estrogen Receptor Alpha: A New Frontier in Hormone-Responsive Breast Cancer Management.International journal of molecular sciences · 2023Review
- Exploring the regulatory role of lncRNA in cancer immunity.Frontiers in oncology · 2023Review
- Methods to Study RNA-Chromatin Interactions.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Small molecule quercetin bindsMolecular therapy. Nucleic acids · 2022Article
- Detecting TAD-like domains from RNA-associated interactions.Nucleic acids research · 2022Article
40 more citing papers are in PubMed but not listed here.
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7 authors at 3 institutions in 2 countries.
Funding
Abstract
Little is known about the functional domain architecture of long noncoding RNAs (lncRNAs) because of a relative paucity of suitable methods to analyze RNA function at a domain level. Here we describe domain-specific chromatin isolation by RNA purification (dChIRP), a scalable technique to dissect pairwise RNA-RNA, RNA-protein and RNA-chromatin interactions at the level of individual RNA domains in living cells. dChIRP of roX1, a lncRNA essential for Drosophila melanogaster X-chromosome dosage compensation, reveals a 'three-fingered hand' ribonucleoprotein topology. Each RNA finger binds chromatin and the male-specific lethal (MSL) protein complex and can individually rescue male lethality in roX-null flies, thus defining a minimal RNA domain for chromosome-wide dosage compensation. dChIRP improves the RNA genomic localization signal by >20-fold relative to previous techniques, and these binding sites are correlated with chromosome conformation data, indicating that most roX-bound loci cluster in a nuclear territory. These results suggest dChIRP can reveal lncRNA architecture and function with high precision and sensitivity.
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