ArticleNature biotechnology2021
Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Systematic evaluation of the heterogeneity of topologically associating domain boundaries in a large genomic context in humans.NAR genomics and bioinformatics · 2026Article
- 3D chromatin structure remodelling in cancer.Cell communication and signaling : CCS · 2026Review
- 3D Chromatin Architecture During Early Development: New Methods and New Findings.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Revisiting models of enhancer-promoter communication in gene regulation.Genome research · 2025Review
- snoRNA-facilitated protein secretion revealed by transcriptome-wide snoRNA target identification.Cell · 2025Article
- Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions.Nature communications · 2024Article
- KARR-seq maps higher-order RNA structures and RNA-RNA interactions across the transcriptome.Nature biotechnology · 2024Article
- Transcriptional machinery as an architect of genome structure.Current opinion in structural biology · 2024Review
- KARR-seq reveals cellular higher-order RNA structures and RNA-RNA interactions.Nature biotechnology · 2024Article
- Epigenetic Explorations of Neurological Disorders, the Identification Methods, and Therapeutic Avenues.International journal of molecular sciences · 2024Review
- Regulating epithelial-mesenchymal plasticity from 3D genome organization.Communications biology · 2024Review
- Mechanistic drivers of chromatin organization into compartments.Current opinion in genetics & development · 2024Review
- A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics.Nature communications · 2024Article
- Advances in the multimodal analysis of the 3D chromatin structure and gene regulation.Experimental & molecular medicine · 2024Review
- Cell-type differential targeting of SETDB1 prevents aberrant CTCF binding, chromatin looping, and cis-regulatory interactions.Nature communications · 2024Article
- Assessing chromatin relocalization in 3D using the patient rule induction method.Biostatistics (Oxford, England) · 2023Article
- Chromatin alternates between A and B compartments at kilobase scale for subgenic organization.Nature communications · 2023Article
- Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments.Nature genetics · 2023Article
- Transcription shapes 3D chromatin organization by interacting with loop extrusion.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- 3D genomics and its applications in precision medicine.Cellular & molecular biology letters · 2023Article
Corrections and comments
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9 authors.
Funding
Abstract
Determining the spatial organization of chromatin in cells mainly relies on crosslinking-based chromosome conformation capture techniques, but resolution and signal-to-noise ratio of these approaches is limited by interference from DNA-bound proteins. Here we introduce chemical-crosslinking assisted proximity capture (CAP-C), a method that uses multifunctional chemical crosslinkers with defined sizes to capture chromatin contacts. CAP-C generates chromatin contact maps at subkilobase (sub-kb) resolution with low background noise. We applied CAP-C to formaldehyde prefixed mouse embryonic stem cells (mESCs) and investigated loop domains (median size of 200 kb) and nonloop domains (median size of 9 kb). Transcription inhibition caused a greater loss of contacts in nonloop domains than loop domains. We uncovered conserved, transcription-state-dependent chromatin compartmentalization at high resolution that is shared from Drosophila to human, and a transcription-initiation-dependent nuclear subcompartment that brings multiple nonloop domains in close proximity. We also showed that CAP-C could be used to detect native chromatin conformation without formaldehyde prefixing.
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