ArticleNature communications2024
Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization.
Article in Nature communications, 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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Who cites it
16 citing papers in PubMed.
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- Transcription and Three-Dimensional Genome Organization: Cause, Consequence, or Coordination?BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Modeling the spatial organization of replicated chromosomes in yeast reveals a loose asymmetric cohesion between sister chromatids.Nucleic acids research · 2026Article
- Condensin loop extrusion properties, roadblocks, and role in homology search during recombination in S. cerevisiae.The EMBO journal · 2026Article
- Spatial Chromatin Organization Across the Cell Cycle: Insights from Auxin-Inducible Protein Depletion.Cells · 2025Review
- Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes.Genome biology · 2025Article
- Dynamics of microcompartment formation at the mitosis-to-G1 transition.Nature structural & molecular biology · 2025Article
- Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP.Nature communications · 2025Article
- RNA Pol II-based regulations of chromosome folding.Cell genomics · 2025Article
- The Biological Function of Genome Organization.International journal of molecular sciences · 2025Review
- Toward decoding the mechanisms that shape sub-megabase-scale genome organization.Current opinion in structural biology · 2025Review
- The genome in space and time comes of age.Nucleus (Austin, Tex.) · 2024Article
- Transcriptional machinery as an architect of genome structure.Current opinion in structural biology · 2024Review
- DNA Gene's Basic Structure as a Nonperturbative Circuit Quantum Electrodynamics: Is RNA Polymerase II the Quantum Bus of Transcription?Current issues in molecular biology · 2024Article
- Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization.Nature communications · 2024Article
- Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL.Nature communications · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Although our understanding of the involvement of heterochromatin architectural factors in shaping nuclear organization is improving, there is still ongoing debate regarding the role of active genes in this process. In this study, we utilize publicly-available Micro-C data from mouse embryonic stem cells to investigate the relationship between gene transcription and 3D gene folding. Our analysis uncovers a nonmonotonic - globally positive - correlation between intragenic contact density and Pol II occupancy, independent of cohesin-based loop extrusion. Through the development of a biophysical model integrating the role of transcription dynamics within a polymer model of chromosome organization, we demonstrate that Pol II-mediated attractive interactions with limited valency between transcribed regions yield quantitative predictions consistent with chromosome-conformation-capture and live-imaging experiments. Our work provides compelling evidence that transcriptional activity shapes the 4D genome through Pol II-mediated micro-compartmentalization.
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Registered trials
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