ArticleNature communications2025
High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Selective control of HLA-DRB1 and HLA-DQA1 transcription through DR/DQ super enhancer microelements.Cell reports · 2026Article
- Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer.Genome biology · 2026Article
- Direct analysis of transcription factor protected cfDNA in plasma by ChIP-seq: measurement of altered CTCF binding in cancer is a novel biomarker for liquid biopsy.Clinical epigenetics · 2026Article
- Mapping 3D genome organization at nucleosome-scale with Micro-C and Region Capture Micro-C (RCMC).Nature protocols · 2026Review
- 3D chromatin architecture-related genes orchestrate LUAD evolution and therapy resistance: insights from integrative machine learning and spatial single-cell mapping.Functional & integrative genomics · 2026Article
- The Electromechanical Connectome: Integrating Voltage, Mechanical Nano-Forces, and Subcellular Fluid Phase Dynamics in Human Neural Computation.International journal of molecular sciences · 2026Review
- A low-input Micro-C protocol for high-resolution 3D genome mapping.Biology methods & protocols · 2026Article
- Mandibular Prognathism in Dolang Sheep: Hi-C Evidence for Localized TAD Remodeling at Craniofacial Loci.Animals : an open access journal from MDPI · 2025Article
- Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP.Nature communications · 2025Article
- CTCF Mediates the Cis-Regulatory Hubs in Mouse Hearts.International journal of molecular sciences · 2025Article
- Structural obstruction to full DNA replication in terminally differentiated skeletal muscle cells.EMBO reports · 2025Article
- RETRACTED: Kinetic organization of the genome revealed by ultraresolution multiscale live imaging.Science (New York, N.Y.) · 2025Article
- Ectopic Recruitment of the CTCF N-Terminal Domain with Two Proximal Zinc-Finger Domains as a Tool for 3D Genome Engineering.International journal of molecular sciences · 2025Article
- Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis.Nature communications · 2025Article
- Fdo1, Fkh1, Fkh2, and the Swi6-Mbp1 MBF complex regulate Mcd1 levels to impact eco1 rad61 cell growth in Saccharomyces cerevisiae.Genetics · 2024Article
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12 authors.
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Abstract
Cohesin-mediated DNA loop extrusion enables gene regulation by distal enhancers through the establishment of chromosome structure and long-range enhancer-promoter interactions. The best characterized cohesin-related structures, such as topologically associating domains (TADs) anchored at convergent CTCF binding sites, represent static conformations. Consequently, loop extrusion dynamics remain poorly understood. To better characterize static and dynamically extruding chromatin loop structures, we use MNase-based 3D genome assays to simultaneously determine CTCF and cohesin localization as well as the 3D contacts they mediate. Here we present CTCF Analyzer (with) Multinomial Estimation (CAMEL), a tool that identifies CTCF footprints at near base-pair resolution in CTCF MNase HiChiP. We also use Region Capture Micro-C to identify a CTCF-adjacent footprint that is attributed to cohesin occupancy. We leverage this substantial advance in resolution to determine that the fully extruded (CTCF-CTCF loop) state is rare genome-wide with locus-specific variation from ~1-10%. We further investigate the impact of chromatin state on loop extrusion dynamics and find that active regulatory elements impede cohesin extrusion. These findings support a model of topological regulation whereby the transient, partially extruded state facilitates enhancer-promoter contacts that can regulate transcription.
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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.