ArticleMolecular cell2011
Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions.
Article in Molecular cell, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 821 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
821 citing papers in PubMed, 1 synthesis or guideline pooled it, 1,273 citations in OpenAlex.
- Long-Noncoding-RNA HOTAIR Upregulation is Associated with Poor Breast Cancer Outcome: A Systematic Review and Meta Analysis.Asian Pacific journal of cancer prevention : APJCP · 2024Pooled it
- Decoding chromatin-associated RNA (caRNA) interaction networks: from genome-wide dynamic capture to epigenetic mechanisms in plants and animals.Epigenetics · 2026Review
- Protocol for high-resolution mapping of RNA-associated chromatin using chromatin isolation by RNA purification-tag.STAR protocols · 2026Article
- LncRNA HITT stabilizes SIRT6 to restrain H3/H4 acetylation and suppress colorectal cancer growth.Cell death & disease · 2026Article
- Differential human telomerase RNA knockdown by antisense oligonucleotides reveals the existence and potential function of a robust RNA domain.RNA (New York, N.Y.) · 2026Article
- Exon junction complex and nuclear pore complex components preferentially govern the nuclear export of spliced lncRNAs.Cell death discovery · 2026Article
- Article
- Improved RNA-DNA interaction calling suggests RNA-based gene regulation of phenotypic transitions.Nucleic acids research · 2026Article
- Nuclear mNature chemical biology · 2026Article
- Widespread DNA off-targeting confounds RNA chromatin occupancy studies.Nature biotechnology · 2026Article
- Neuid: A Novel Neuron-Enriched LncRNA that Connects Epigenetic Gene Silencing to Alzheimer's Disease.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Review
- Genome-wide mapping of stress-responsive lncRNA, uc.104, reveals the chromatin-mediated regulation of stress and plasticity-related genes in the hippocampus of chronic restraint rats.Molecular brain · 2026Article
- Chondrocytes reprogram chromatin in hypoxic microenvironments to activate CADM1-AS1/HDAC1 complex-mediated anti-inflammation signals.Nature communications · 2026Article
- Multiomic single-cell perturbation screens reveal critical lncRNA regulators of senescence.Nature aging · 2026Article
- Circular RNA Vv-circCOR27 modulates thermotolerance through attenuating VvHSP90.2b-VvHsfA7a interaction in grapevine.The New phytologist · 2026Article
- Tumor exosomes impact functional hallmarks of cancer.Cancer metastasis reviews · 2026Review
- Microfluidic low-input profiling reveals lncRNA roles in disease.bioRxiv : the preprint server for biology · 2026Article
- Deciphering the regulatory landscape of enhancer RNAs in health and disease.Signal transduction and targeted therapy · 2026Review
- Article
761 more citing papers are in PubMed but not listed here.
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5 authors at 2 institutions in 1 country.
Funding
Abstract
Long noncoding RNAs (lncRNAs) are key regulators of chromatin state, yet the nature and sites of RNA-chromatin interaction are mostly unknown. Here we introduce Chromatin Isolation by RNA Purification (ChIRP), where tiling oligonucleotides retrieve specific lncRNAs with bound protein and DNA sequences, which are enumerated by deep sequencing. ChIRP-seq of three lncRNAs reveal that RNA occupancy sites in the genome are focal, sequence-specific, and numerous. Drosophila roX2 RNA occupies male X-linked gene bodies with increasing tendency toward the 3' end, peaking at CES sites. Human telomerase RNA TERC occupies telomeres and Wnt pathway genes. HOTAIR lncRNA preferentially occupies a GA-rich DNA motif to nucleate broad domains of Polycomb occupancy and histone H3 lysine 27 trimethylation. HOTAIR occupancy occurs independently of EZH2, suggesting the order of RNA guidance of Polycomb occupancy. ChIRP-seq is generally applicable to illuminate the intersection of RNA and chromatin with newfound precision genome wide.
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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.