ArticleGenome biology2020
Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed, 148 citations in OpenAlex.
- Chromatin remodelling: a driving force in reverse mechanotransduction.RNA biology · 2026Review
- Regulation of immune signal integration and memory by inflammation-induced chromosome conformation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Transcription and Three-Dimensional Genome Organization: Cause, Consequence, or Coordination?BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Kilobase-scale compartments enabled by CRUSH reveal regulatory programs across cell types, single-cells, and ancient mammoths.bioRxiv : the preprint server for biology · 2026Article
- Profiling the transcriptional regulatory network reveals putative shared regulatory elements within homoeologs in polyploid Brassica napus.Genome biology · 2026Article
- A functional overlap between actively transcribed genes and chromatin insulator elements.The EMBO journal · 2026Article
- Postmitotic transcription and 3D regulation show locus-specific and differentiation-specific sensitivity to cohesin depletion.Nature genetics · 2026Article
- Impaired cohesin loading disrupts pancreatic differentiation by Polycomb-driven chromatin rewiring and loop collapse.Communications biology · 2026Article
- HiChIA-Rep quantifies the similarity between enrichment-based chromatin interactions datasets.bioRxiv : the preprint server for biology · 2026Article
- Dissecting the contribution of transposable elements to interphase chromosome structure.Genome biology · 2026Article
- Natural degradation of RNA polymerase II is essential for oocyte chromatin reorganization and maternal-to-zygotic transition.Nature communications · 2025Article
- Transcriptional pause release at enhancers mediates cell identity.NAR cancer · 2025Review
- RNA polymerase II transcription compartments - from factories to condensates.Nature reviews. Genetics · 2025Review
- Nelfb promotes dermal white adipose tissue formation through RNA polymerase II-mediated adipogenic gene regulation.Development (Cambridge, England) · 2025Article
- A molecular census to elucidate the demixing mechanism of membraneless organelles.Genome biology · 2025Article
- Article
- INO80/SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape.Nucleic acids research · 2025Article
- Article
- Emerging roles for the nucleolus in development and stem cells.Development (Cambridge, England) · 2025Review
- Insulation between adjacent TADs is controlled by the width of their boundaries through distinct mechanisms.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
29 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe relationship between transcription and the 3D chromatin structure is debated. Multiple studies have shown that transcription affects global Cohesin binding and 3D genome structures. However, several other studies have indicated that inhibited transcription does not alter chromatin conformations.
resultsWe provide the most comprehensive evidence to date to demonstrate that transcription plays a relatively modest role in organizing the local, small-scale chromatin structures in mammalian cells. We show degraded Pol I, Pol II, and Pol III proteins in mESCs cause few or no changes in large-scale 3D chromatin structures, selected RNA polymerases with a high abundance of binding sites or active promoter-associated interactions appear to be relatively more affected after the degradation, transcription inhibition alters local, small loop domains, as indicated by high-resolution chromatin interaction maps, and loops with bound Pol II but without Cohesin or CTCF are identified and found to be largely unchanged after transcription inhibition. Interestingly, Pol II depletion for a longer time significantly affects the chromatin accessibility and Cohesin occupancy, suggesting that RNA polymerases are capable of affecting the 3D genome indirectly. These direct and indirect effects explain the previous inconsistent findings on the influence of transcription inhibition on the 3D genome.
conclusionsWe conclude that Pol I, Pol II, and Pol III loss alters local, small-scale chromatin interactions in mammalian cells, suggesting that the 3D chromatin structures are pre-established and relatively stable.
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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.