ArticlePloS one2013
Actual ligation frequencies in the chromosome conformation capture procedure.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A hybrid stochastic interpolation and compression method for kernel matrices.Journal of computational physics · 2023Article
- Enhancer Function in the 3D Genome.Genes · 2023Review
- Application of the 3C Method to Study the Developmental Genes inFrontiers in genetics · 2022Article
- Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure.Frontiers in genetics · 2021Article
- Exonuclease combinations reduce noises in 3D genomics technologies.Nucleic acids research · 2020Article
- Analysis of Chromatin Interactions Mediated by Specific Architectural Proteins in Drosophila Cells.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Chromosome conformation capture technologies and their impact in understanding genome function.Chromosoma · 2017Review
- A cautionary note on the use of chromosome conformation capture in plants.Plant methods · 2017Article
- 3C-digital PCR for quantification of chromatin interactions.BMC molecular biology · 2016Article
- Capture of associated targets on chromatin links long-distance chromatin looping to transcriptional coordination.Nature communications · 2016Article
- Minor Loops in Major Folds: Enhancer-Promoter Looping, Chromatin Restructuring, and Their Association with Transcriptional Regulation and Disease.PLoS genetics · 2015Review
- An Overview of Genome Organization and How We Got There: from FISH to Hi-C.Microbiology and molecular biology reviews : MMBR · 2015Review
- Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization.Genes & development · 2014Article
- Dissecting the function of the adult β-globin downstream promoter region using an artificial zinc finger DNA-binding domain.Nucleic acids research · 2014Article
- Quantitative analysis of genomic element interactions by molecular colony technique.Nucleic acids research · 2014Article
- The statistical-mechanics of chromosome conformation capture.Nucleus (Austin, Tex.)Review
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Authors and funding
3 authors.
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Abstract
Chromosome conformation capture (3C) and derivative experimental procedures are used to estimate the spatial proximity between different genomic elements, thus providing information about the 3D organization of genomic domains and whole genomes within the nucleus. All C-methods are based on the proximity ligation-the preferential ligation of joined DNA fragments obtained upon restriction enzyme digestion of in vivo cross-linked chromatin. Here, using the mouse beta-globin genes in erythroid cells as a model, we estimated the actual frequencies of ligation between the fragments bearing the promoter of the major beta-globin gene and its distant enhancers and showed that the number of ligation products produced does not exceed 1% of all fragments subjected to the ligation. Although this low yield of 3C ligation products may be explained entirely by technical issues, it may as well reflect a low frequency of interaction between DNA regulatory elements in vivo.
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