ArticleNature structural & molecular biology2017
Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells.
Article in Nature structural & molecular biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
45 citing papers in PubMed, 103 citations in OpenAlex.
- Phase separation of ecDNA condensates establishes in-trans contact domains that boost selective MYC regulatory interactions.Nature communications · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci.Biophysical journal · 2025Article
- A Multiscale Perspective on Chromatin Architecture through Polymer Physics.Physiology (Bethesda, Md.) · 2025Review
- Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot.GigaScience · 2025Article
- Transcription processes compete with loop extrusion to homogenize promoter and enhancer dynamics.Science advances · 2024Article
- Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion.Genome biology · 2024Article
- Article
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 2024Review
- Epigenetic regulatory layers in the 3D nucleus.Molecular cell · 2024Review
- Competition between transcription and loop extrusion modulates promoter and enhancer dynamics.Research square · 2023Article
- Enhancer-promoter contact formation requires RNAPII and antagonizes loop extrusion.Nature genetics · 2023Article
- Competition between transcription and loop extrusion modulates promoter and enhancer dynamics.bioRxiv : the preprint server for biology · 2023Article
- Unveiling the Machinery behind Chromosome Folding by Polymer Physics Modeling.International journal of molecular sciences · 2023Review
- Genome modeling: From chromatin fibers to genes.Current opinion in structural biology · 2023Review
- Mini-review: Gene regulatory network benefits from three-dimensional chromatin conformation and structural biology.Computational and structural biotechnology journal · 2023Review
- Pluripotency factors regulate the onset ofScience advances · 2022Article
- Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding.Nature communications · 2022Article
- Uncovering the Principles of Genome Folding by 3D Chromatin Modeling.Cold Spring Harbor perspectives in biology · 2022Review
- 3D or Not 3D: Shaping the Genome during Development.Cold Spring Harbor perspectives in biology · 2022Review
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 3 countries.
Funding
Abstract
Gene expression states influence the 3D conformation of the genome through poorly understood mechanisms. Here, we investigate the conformation of the murine HoxB locus, a gene-dense genomic region containing closely spaced genes with distinct activation states in mouse embryonic stem (ES) cells. To predict possible folding scenarios, we performed computer simulations of polymer models informed with different chromatin occupancy features that define promoter activation states or binding sites for the transcription factor CTCF. Single-cell imaging of the locus folding was performed to test model predictions. While CTCF occupancy alone fails to predict the in vivo folding at genomic length scale of 10 kb, we found that homotypic interactions between active and Polycomb-repressed promoters co-occurring in the same DNA fiber fully explain the HoxB folding patterns imaged in single cells. We identify state-dependent promoter interactions as major drivers of chromatin folding in gene-dense regions.
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Registered trials
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.