Open Access
Nucleic Acids Research, volume 41, issue 6, pages 3563-3575
Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub
Publication type: Journal Article
Publication date: 2013-02-07
Journal:
Nucleic Acids Research
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 14.9
ISSN: 03051048, 13624962
PubMed ID:
23396278
Genetics
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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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Gavrilov A. et al. Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub // Nucleic Acids Research. 2013. Vol. 41. No. 6. pp. 3563-3575.
GOST all authors (up to 50)
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Gavrilov A., Gushchanskaya E. S., Strelkova O., Zhironkina O., Kireev I., Iarovaia O. V., Разин С. В. Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub // Nucleic Acids Research. 2013. Vol. 41. No. 6. pp. 3563-3575.
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TY - JOUR
DO - 10.1093/NAR/GKT067
UR - https://doi.org/10.1093%2FNAR%2FGKT067
TI - Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub
T2 - Nucleic Acids Research
AU - Gushchanskaya, Ekaterina S
AU - Zhironkina, Oksana
AU - Iarovaia, Olga V.
AU - Разин, С. В.
AU - Gavrilov, Alexey
AU - Strelkova, Olga
AU - Kireev, I.
PY - 2013
DA - 2013/02/07 00:00:00
PB - Oxford University Press
SP - 3563-3575
IS - 6
VL - 41
PMID - 23396278
SN - 0305-1048
SN - 1362-4962
ER -
Cite this
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@article{2013_Gavrilov,
author = {Ekaterina S Gushchanskaya and Oksana Zhironkina and Olga V. Iarovaia and С. В. Разин and Alexey Gavrilov and Olga Strelkova and I. Kireev},
title = {Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub},
journal = {Nucleic Acids Research},
year = {2013},
volume = {41},
publisher = {Oxford University Press},
month = {feb},
url = {https://doi.org/10.1093%2FNAR%2FGKT067},
number = {6},
pages = {3563--3575},
doi = {10.1093/NAR/GKT067}
}
Cite this
MLA
Copy
Gavrilov, Alexey, et al. “Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub.” Nucleic Acids Research, vol. 41, no. 6, Feb. 2013, pp. 3563-3575. https://doi.org/10.1093%2FNAR%2FGKT067.