ArticleNucleic acids research2014
Quantitative analysis of genomic element interactions by molecular colony technique.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 26 citations in OpenAlex.
- Techniques to detect physical interactions between genomic regions.Epigenomics · 2025Review
- Enhancer Function in the 3D Genome.Genes · 2023Review
- The Toolbox for Untangling Chromosome Architecture in Immune Cells.Frontiers in immunology · 2021Review
- Purification of specific DNA species using the CRISPR system.Biology methods & protocols · 2019Review
- Enhancer hubs and loop collisions identified from single-allele topologies.Nature genetics · 2018Article
- 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
- Regulation of disease-associated gene expression in the 3D genome.Nature reviews. Molecular cell biology · 2016Review
- A novel single cell method to identify the genetic composition at a single nuclear body.Scientific reports · 2016Article
- The second decade of 3C technologies: detailed insights into nuclear organization.Genes & development · 2016Review
- In vivo formaldehyde cross-linking: it is time for black box analysis.Briefings in functional genomics · 2015Article
- Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C.BMC genomics · 2015Article
- The Role of Crowding Forces in Juxtaposing β-Globin Gene Domain Remote Regulatory Elements in Mouse Erythroid Cells.PloS one · 2015Article
- Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization.Genes & development · 2014Article
- Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application.BMC genomics · 2014Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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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Registered trials
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