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Cited by 25Genomics and Chromatin DynamicsChromosomal and Genetic VariationsChromatin Remodeling and Cancer

Quantitative analysis of genomic element interactions by molecular colony technique

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Gavrilov, Alexey A., Chetverina, Helena V., Chermnykh, Elina S., Razin, Sergey V., Chetverin, Alexander B.·2014·Nucleic Acids Research
DOI 10.1093/nar/gkt1322PMC PMC3950710
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Abstract

Distant genomic elements were found to interact within the folded eukaryotic genome. However, the used experimental approach (chromosome conformation capture, 3C) enables neither determination of the percentage of cells in which the interactions occur nor demonstration of simultaneous interaction of >2 genomic elements. Each of the above can be done using in-gel replication of interacting DNA segments, the technique reported here. Chromatin fragments released from formaldehyde–cross-linked cells by sodium dodecyl sulfate extraction and sonication are distributed in a polyacrylamide gel layer followed by amplification of selected test regions directly in the gel by multiplex polymerase chain reaction. The fragments that have been cross-linked and separate fragments give rise to multi- and monocomponent molecular colonies, respectively, which can be distinguished and counted. Using in-gel replication of interacting DNA segments, we demonstrate that in the material from mouse erythroid cells, the majority of fragments containing the promoters of active β-globin genes and their remote enhancers do not form complexes stable enough to survive sodium dodecyl sulfate extraction and sonication. This indicates that either these elements do not interact directly in the majority of cells at a given time moment, or the formed DNA–protein complex cannot be stabilized by formaldehyde cross-linking.

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  • Even the strongest C-captured contacts are detected in less than 10% of cells.

    “This can explain why even the strongest C-captured contacts are detected in less than 10% of cells [107,108,109].”

    From Enhancer Function in the 3D Genome (2023) · cites this paper as [109]

    The Results and Discussion (page unavailable) report that complexes between selected β-globin promoters and enhancers, if present, occurred in fewer than 3% of the chromosomes analyzed. That supports a low frequency for these specific contacts, but not the claim that even the strongest chromosome-conformation-capture contacts occur in fewer than 10% of cells. The Discussion also says that 3C results cannot establish the proportion of cells containing a contact. (LLM, conf=0.84)

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Cited by

Sorted by citations

Authors
Gavrilov, A. A., Chetverina, H. V., Chermnykh, E. S., Razin, S. V., & Chetverin, A. B.
Affiliations
Lomonosov Moscow State University (RU)
Corresponding author
Razin, Sergey V.
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2013-12-24
Volume
42
Issue
5
Pages
e36-e36
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkt1322
PMC
PMC3950710
OpenAlex
W1994967929
Cited by
25
References
4
Citations by year
2025: 2 · 2023: 1 · 2022: 1 · 2021: 1 · 2019: 2 · 2018: 3 · 2017: 2 · 2016: 3 · 2015: 6 · 2014: 4
FWCI
1.94
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Keywords
3D genome organization, multiplex PCR, formaldehyde crosslinking, sodium dodecyl sulfate extraction, sonication, erythroid cells, protein-DNA complex, chromosome conformation capture
MeSH terms
Acrylic Resins, Animals, Chromatin, DNA, Regulatory Sequences, Nucleic Acid, Polymerase Chain Reaction, Genomics, Erythroid Cells, Mice, beta-Globins, Genetic Loci

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