ArticleCell reports2022
Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription.
Article in Cell reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Direct roles of long non-coding RNAs in transcription activation.Nature structural & molecular biology · 2026Review
- Article
- Hierarchical Chromatin Rewiring Orchestrates Early Transcriptional Regulation in Mouse Cerebral Cortex Following Focal Ischemia.bioRxiv : the preprint server for biology · 2026Article
- Geometrically Encoded Positioning of Introns, Intergenic Segments, and Exons in the Human Genome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Single-cell dynamics of genome-nucleolus interactions captured by nucleolar laser microdissection (NoLMseq).Nature communications · 2025Article
- RNA polymerase II transcription compartments - from factories to condensates.Nature reviews. Genetics · 2025Review
- MultiVis.js: a software tool for the visualization of multiway chromatin interactions and SPRITE data.BMC bioinformatics · 2025Article
- MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures.PLoS computational biology · 2025Article
- Emerging roles for the nucleolus in development and stem cells.Development (Cambridge, England) · 2025Review
- ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements.Nature genetics · 2024Article
- Article
- The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes.Nature genetics · 2024Article
- Transcriptional condensates and phase separation: condensing information across scales and mechanisms.Nucleus (Austin, Tex.) · 2023Review
- Technological advances in probing 4D genome organization.Current opinion in cell biology · 2023Review
- Transcription and replication meet the silent X chromosome territory.Nature structural & molecular biology · 2023Article
- RNA-mediated heterochromatin formation at repetitive elements in mammals.The EMBO journal · 2023Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Mammalian genomes are organized into three-dimensional DNA structures called A/B compartments that are associated with transcriptional activity/inactivity. However, whether these structures are simply correlated with gene expression or are permissive/impermissible to transcription has remained largely unknown because we lack methods to measure DNA organization and transcription simultaneously. Recently, we developed RNA & DNA (RD)-SPRITE, which enables genome-wide measurements of the spatial organization of RNA and DNA. Here we show that RD-SPRITE measures genomic structure surrounding nascent pre-mRNAs and maps their spatial contacts. We find that transcription occurs within B compartments-with multiple active genes simultaneously colocalizing within the same B compartment-and at genes proximal to nucleoli. These results suggest that localization near or within nuclear structures thought to be inactive does not preclude transcription and that active transcription can occur throughout the nucleus. In general, we anticipate RD-SPRITE will be a powerful tool for exploring relationships between genome structure and transcription.
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