ArticleNature communications2023
Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed, 25 citations in OpenAlex.
- Integrative Mapping of SNHG1 RNA-Chromatin Contacts onto the Cancer-Specific Super-Enhancer Landscape in HCT116 Colorectal Cancer Cells.International journal of molecular sciences · 2026Article
- The crosstalk of m6A modification and non-coding RNAs in gastric cancer: biomarkers and therapeutic potentials.Cancer cell international · 2025Review
- Role of the SAF-A/HNRNPU ATPase and RGG domains in X chromosome inactivation, nuclear dynamics, transcription, splicing, and cell proliferation.bioRxiv : the preprint server for biology · 2025Article
- Role of RNA in genome folding: It's all about affinity.Current opinion in structural biology · 2025Review
- Histone H3 lysine methyltransferase activities control compartmentalization of human centromeres.bioRxiv : the preprint server for biology · 2025Article
- Identification of chromatin-associated RNAs at human centromeres.bioRxiv : the preprint server for biology · 2025Article
- Role of the SAF-A/HNRNPU SAP domain in X chromosome inactivation, nuclear dynamics, transcription, splicing, and cell proliferation.PLoS genetics · 2025Article
- Transcriptional coordination between intergenic RNA polymerase II-bound regions and nearby genes reveals functional specialization and disease associations in peripheral blood.Computational and structural biotechnology journal · 2025Article
- Transcription of a centromere-enriched retroelement and local retention of its RNA are significant features of the CENP-A chromatin landscape.Genome biology · 2024Article
- Nuclear RNA: a transcription-dependent regulator of chromatin structure.Biochemical Society transactions · 2024Review
- Review
- Transcriptomic Approaches to Cardiomyocyte-Biomaterial Interactions: A Review.ACS biomaterials science & engineering · 2024Review
- Molecular insights into regulatory RNAs in the cellular machinery.Experimental & molecular medicine · 2024Review
- BaRDIC: robust peak calling for RNA-DNA interaction data.NAR genomics and bioinformatics · 2024Article
- Functional identification of cis-regulatory long noncoding RNAs at controlled false discovery rates.Nucleic acids research · 2024Article
- Editorial: RNA-chromatin interactions: biology, mechanism, disease, and therapeutics-volume 2.Frontiers in genetics · 2024Article
- Review
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Non-coding RNAs (ncRNAs) are transcribed throughout the genome and provide regulatory inputs to gene expression through their interaction with chromatin. Yet, the genomic targets and functions of most ncRNAs are unknown. Here we use chromatin-associated RNA sequencing (ChAR-seq) to map the global network of ncRNA interactions with chromatin in human embryonic stem cells and the dynamic changes in interactions during differentiation into definitive endoderm. We uncover general principles governing the organization of the RNA-chromatin interactome, demonstrating that nearly all ncRNAs exclusively interact with genes in close three-dimensional proximity to their locus and provide a model predicting the interactome. We uncover RNAs that interact with many loci across the genome and unveil thousands of unannotated RNAs that dynamically interact with chromatin. By relating the dynamics of the interactome to changes in gene expression, we demonstrate that activation or repression of individual genes is unlikely to be controlled by a single ncRNA.
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What OpenQuestion holds
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.