ArticleNucleic acids research2013
Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed, 89 citations in OpenAlex.
- CAD-C: An engineered nuclease enables repair-freebioRxiv : the preprint server for biology · 2026Article
- Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.Nature methods · 2023Article
- Enhancer Function in the 3D Genome.Genes · 2023Review
- Genome-Directed Cell Nucleus Assembly.Biology · 2022Article
- The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome.Epigenetics & chromatin · 2021Article
- High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale.Nature communications · 2021Article
- Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure.Frontiers in genetics · 2021Article
- Review
- Weak interactions in higher-order chromatin organization.Nucleic acids research · 2020Review
- Exonuclease combinations reduce noises in 3D genomics technologies.Nucleic acids research · 2020Article
- Methods for mapping 3D chromosome architecture.Nature reviews. Genetics · 2020Review
- Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function.Molecular cell · 2020Review
- Interchromosomal interactions: A genomic love story of kissing chromosomes.The Journal of cell biology · 2019Review
- Three-dimensional organization and dynamics of the genome.Cell biology and toxicology · 2018Review
- Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C.Molecular cell · 2018Article
- Article
- Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with the Pax5 promoter in a chicken B cell line.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Article
- FISH-ing for captured contacts: towards reconciling FISH and 3C.Nature methods · 2017Article
- Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes.Molecular psychiatry · 2017Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The current progress in the study of the spatial organization of interphase chromosomes became possible owing to the development of the chromosome conformation capture (3C) protocol. The crucial step of this protocol is the proximity ligation-preferential ligation of DNA fragments assumed to be joined within nuclei by protein bridges and solubilized as a common complex after formaldehyde cross-linking and DNA cleavage. Here, we show that a substantial, and in some cases the major, part of DNA is not solubilized from cross-linked nuclei treated with restriction endonuclease(s) and sodium dodecyl sulphate and that this treatment neither causes lysis of the nucleus nor drastically affects its internal organization. Analysis of the ligation frequencies of the mouse β-globin gene domain DNA fragments demonstrated that the previously reported 3C signals were generated predominantly, if not exclusively, in the insoluble portion of the 3C material. The proximity ligation thus occurs within the cross-linked chromatin cage in non-lysed nuclei. The finding does not compromise the 3C protocol but allows the consideration of an active chromatin hub as a folded chromatin domain or a nuclear compartment rather than a rigid complex of regulatory elements.
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