ArticleGenes & development2014
Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization.
Article in Genes & development, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
142 citing papers in PubMed, 249 citations in OpenAlex.
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- Cell type- and transcription-independent spatial proximity between enhancers and promoters.Molecular biology of the cell · 2024Article
- Heterochromatic 3D genome organization is directed by HP1a- and H3K9-dependent and independent mechanisms.Molecular cell · 2024Article
- Transcription decouples estrogen-dependent changes in enhancer-promoter contact frequencies and spatial proximity.PLoS genetics · 2024Article
- Super-enhancers: drivers of cells' identities and cells' debacles.Epigenomics · 2024Review
- Increased enhancer-promoter interactions during developmental enhancer activation in mammals.Nature genetics · 2024Article
- Differential roles of positive and negative supercoiling in organizing the E. coli genome.Nucleic acids research · 2024Article
- Dispersal of PRC1 condensates disrupts polycomb chromatin domains and loops.Life science alliance · 2023Article
- Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.Nature methods · 2023Article
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- Long range inter-chromosomal interaction of Oct4 distal enhancer loci regulates ESCs pluripotency.Cell death discovery · 2023Article
- Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription.Cell reports · 2022Article
- The relevance of chromatin architecture to genome rearrangements inPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Promoter and enhancer RNAs regulate chromatin reorganization and activation of miR-10b/HOXD locus, and neoplastic transformation in glioma.Molecular cell · 2022Article
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- Nuclear Architecture in the Nervous System.Results and problems in cell differentiation · 2022Review
- High-Throughput DNA FISH (hiFISH).Methods in molecular biology (Clifton, N.J.) · 2022Article
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82 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 3 countries.
Funding
Abstract
Although important for gene regulation, most studies of genome organization use either fluorescence in situ hybridization (FISH) or chromosome conformation capture (3C) methods. FISH directly visualizes the spatial relationship of sequences but is usually applied to a few loci at a time. The frequency at which sequences are ligated together by formaldehyde cross-linking can be measured genome-wide by 3C methods, with higher frequencies thought to reflect shorter distances. FISH and 3C should therefore give the same views of genome organization, but this has not been tested extensively. We investigated the murine HoxD locus with 3C carbon copy (5C) and FISH in different developmental and activity states and in the presence or absence of epigenetic regulators. We identified situations in which the two data sets are concordant but found other conditions under which chromatin topographies extrapolated from 5C or FISH data are not compatible. We suggest that products captured by 3C do not always reflect spatial proximity, with ligation occurring between sequences located hundreds of nanometers apart, influenced by nuclear environment and chromatin composition. We conclude that results obtained at high resolution with either 3C methods or FISH alone must be interpreted with caution and that views about genome organization should be validated by independent methods.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.