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Cited by 87Genomics and Chromatin DynamicsNuclear Structure and FunctionChromatin Remodeling and Cancer

Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub

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Gavrilov, Alexey A., Gushchanskaya, Ekaterina S., Strelkova, Olga, Zhironkina, Oksana, Kireev, Igor I., Iarovaia, Olga V., Razin, Sergey V.·2013·Nucleic Acids Research
DOI 10.1093/nar/gkt067PMC PMC3616722
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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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  • Spatial proximity between distant genomic elements can only be observed within the folded chromatin fibril.

    “However, subsequent studies have shown that spatial proximity between distant genomic elements can only be observed within the folded chromatin fibril [100].”

    From Enhancer Function in the 3D Genome (2023) · cites this paper as [100]

    The Discussion (page not provided) says that characteristic 3C ligation products may be generated only within non-lysed nuclei and proposes a folded chromatin domain or nuclear compartment as a model for an active chromatin hub. That supports proximity being detected in that structural setting, but not the broader claim that spatial proximity between distant genomic elements can only be observed within a folded chromatin fibril. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Gavrilov, A. A., Gushchanskaya, E. S., Strelkova, O., Zhironkina, O., Kireev, I. I., Iarovaia, O. V., & Razin, S. V.
Affiliations
Russian Academy of Sciences (RU)
Corresponding author
Razin, Sergey V.
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2013-02-07
Volume
41
Issue
6
Pages
3563-3575
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkt067
PMC
PMC3616722
OpenAlex
W2023595114
Cited by
87
References
3
Citations by year
2026: 1 · 2025: 3 · 2024: 2 · 2023: 2 · 2022: 2 · 2021: 6 · 2020: 7 · 2019: 6 · 2018: 6 · 2017: 10 · 2016: 11 · 2015: 15 · 2014: 10 · 2013: 5
FWCI
6.13
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Keywords
proximity ligation, chromosome conformation capture, chromatin structure, interphase chromosome organization, formaldehyde crosslinking, nuclear compartments, chromatin folding
MeSH terms
Animals, Cell Nucleus, Chromatin, DNA, DNA Restriction Enzymes, Histones, Liver, Sodium Dodecyl Sulfate, Solubility, Mice, beta-Globins

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