ArticleMolecular cell2024
RNA polymerases reshape chromatin architecture and couple transcription on individual fibers.
Article in Molecular cell, 2024. 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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16 citing papers in PubMed.
- A practical guide to studying genome function using single-molecule genomics.Nature reviews. Molecular cell biology · 2026Review
- Article
- The Promoter-Proximal Pause: A Decision Point Governing RNA Polymerase II Fate.Annual review of biochemistry · 2026Review
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- 3D chromatin structures precede genome activation in Drosophila embryogenesis.Cell genomics · 2025Article
- Comprehensive Single Molecule View of Transcriptional Dynamics in Development.bioRxiv : the preprint server for biology · 2025Article
- Protamine lacunae preserve the paternal chromatin landscape in sperm.bioRxiv : the preprint server for biology · 2025Article
- FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data.Bioinformatics (Oxford, England) · 2025Article
- A haplotype-resolved view of human gene regulation.bioRxiv : the preprint server for biology · 2025Article
- The regulatory potential of transposable elements in maize.Nature plants · 2025Article
- Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming.Genome biology · 2025Article
- U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation.Molecular cell · 2025Article
- Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II.Molecular systems biology · 2025Article
- Integrating Single-Molecule Sequencing and Deep Learning to Predict Haplotype-Specific 3D Chromatin Organization in a Mendelian Condition.bioRxiv : the preprint server for biology · 2025Article
- Profiling the epigenome using long-read sequencing.Nature genetics · 2025Review
- Perspective on recent developments and challenges in regulatory and systems genomics.Bioinformatics advances · 2025Review
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6 authors.
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Abstract
RNA polymerases must initiate and pause within a complex chromatin environment, surrounded by nucleosomes and other transcriptional machinery. This environment creates a spatial arrangement along individual chromatin fibers ripe for both competition and coordination, yet these relationships remain largely unknown owing to the inherent limitations of traditional structural and sequencing methodologies. To address this, we employed long-read chromatin fiber sequencing (Fiber-seq) in Drosophila to visualize RNA polymerase (Pol) within its native chromatin context with single-molecule precision along up to 30 kb fibers. We demonstrate that Fiber-seq enables the identification of individual Pol II, nucleosome, and transcription factor footprints, revealing Pol II pausing-driven destabilization of downstream nucleosomes. Furthermore, we demonstrate pervasive direct distance-dependent transcriptional coupling between nearby Pol II genes, Pol III genes, and transcribed enhancers, modulated by local chromatin architecture. Overall, transcription initiation reshapes surrounding nucleosome architecture and couples nearby transcriptional machinery along individual chromatin fibers.
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