ArticleNature communications2023
Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells.
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 25 papers.
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Who cites it
25 citing papers in PubMed.
- 3D Genome Engineering Using CRISPR/dCas Systems.International journal of molecular sciences · 2026Review
- Long non-coding RNA triplex-dependent regulation of melanoma gene networks.NAR genomics and bioinformatics · 2026Article
- Transcription and Three-Dimensional Genome Organization: Cause, Consequence, or Coordination?BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Genome-wide mapping of RNA-protein associations through sequencing.Nature biotechnology · 2026Article
- UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity.Genome biology · 2026Article
- Repeat expansions inbioRxiv : the preprint server for biology · 2026Article
- UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity.bioRxiv : the preprint server for biology · 2026Article
- Dissecting the contribution of transposable elements to interphase chromosome structure.Genome biology · 2026Article
- Identity rather than 3D position informs splicing of rare introns in the human genome.iScience · 2026Article
- Article
- Spatial Chromatin Organization Across the Cell Cycle: Insights from Auxin-Inducible Protein Depletion.Cells · 2025Review
- The METTL3-YTHDC1 axis mediates architectural RNA mMolecular cancer · 2025Article
- Decoding the interactions and functions of non-coding RNA with artificial intelligence.Nature reviews. Molecular cell biology · 2025Review
- Direction and modality of transcription changes caused by TAD boundary disruption in Slc29a3/Unc5b locus depends on tissue-specific epigenetic context.Epigenetics & chromatin · 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
- Transcriptional machinery as an architect of genome structure.Current opinion in structural biology · 2024Review
- Improved simultaneous mapping of epigenetic features and 3D chromatin structure via ViCAR.Genome biology · 2024Article
- Exploring the roles of RNAs in chromatin architecture using deep learning.Nature communications · 2024Article
- CCAT1 lncRNA is chromatin-retained and post-transcriptionally spliced.Histochemistry and cell biology · 2024Article
Corrections and comments
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Authors and funding
19 authors.
Funding
Abstract
The interphase genome is dynamically organized in the nucleus and decorated with chromatin-associated RNA (caRNA). It remains unclear whether the genome architecture modulates the spatial distribution of caRNA and vice versa. Here, we generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human cells. These maps reveal the chromosomal domains demarcated by locally transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the spreading of caRNA is constrained by the boundaries of topologically associating domains (TADs), demonstrating the role of the 3D genome structure in modulating the spatial distribution of RNA. Conversely, stopping transcription or acute depletion of RNA induces thousands of chromatin loops genome-wide. Activation or suppression of the transcription of specific genes suppresses or creates chromatin loops straddling these genes. Deletion of a specific caRNA-producing genomic sequence promotes chromatin loops that straddle the interchromosomal target sequences of this caRNA. These data suggest a feedback loop where the 3D genome modulates the spatial distribution of RNA, which in turn affects the dynamic 3D genome organization.
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