ArticleNature methods2017
FISH-ing for captured contacts: towards reconciling FISH and 3C.
Article in Nature methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
What it found
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
83 citing papers in PubMed, 142 citations in OpenAlex.
- Genome-wide absolute quantification of chromatin looping.Nature structural & molecular biology · 2026Article
- Annotating Interchromosomal Interactions at Sub-Megabase Resolution Using Network Clustering Coefficients.bioRxiv : the preprint server for biology · 2026Article
- Live-cell imaging of enhancer-promoter dynamics reveals transient contact-driven gene activation.bioRxiv : the preprint server for biology · 2026Article
- Cohesin-mediated loop extrusion and enhancer-associated factors additively contribute toGenes & development · 2026Article
- SCUDDO: an unsupervised clustering algorithm for single-cell Hi-C maps using diagonal diffusion operators.Bioinformatics (Oxford, England) · 2026Article
- Hi-C calibration by chemically induced chromosomal interactions.EMBO reports · 2026Article
- Connecting multiway enhancer-promoter interactions to changes in gene expression in cancer.bioRxiv : the preprint server for biology · 2026Article
- Stress-induced loss of CTCF reveals an alternative, promoter-based mode of cohesin looping.bioRxiv : the preprint server for biology · 2025Article
- Motorized chromosome models of mitotic chromosome folding.Nature communications · 2025Article
- Interrogating the regulatory epigenome of cellular senescence.Cellular and molecular life sciences : CMLS · 2025Review
- Revisiting models of enhancer-promoter communication in gene regulation.Genome research · 2025Review
- Understanding and Simulating the Dynamics of a Polymer-Like Chromatin.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Inter-chromosomal contacts demarcate genome topology along a spatial gradient.Nature communications · 2024Article
- Condensin I folds the Caenorhabditis elegans genome.Nature genetics · 2024Article
- Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation.Nature reviews. Molecular cell biology · 2024Review
- Transcription decouples estrogen-dependent changes in enhancer-promoter contact frequencies and spatial proximity.PLoS genetics · 2024Article
- 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
- Insight into chromatin compaction and spatial organization in rice interphase nuclei.Frontiers in plant science · 2024Article
- Determining the Compaction State of Genes Using DNA FISH.Methods in molecular biology (Clifton, N.J.) · 2024Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Chromosome conformation capture (3C) and fluorescence in situ hybridization (FISH) are two widely used technologies that provide distinct readouts of 3D chromosome organization. While both technologies can assay locus-specific organization, how to integrate views from 3C, or genome-wide Hi-C, and FISH is far from solved. Contact frequency, measured by Hi-C, and spatial distance, measured by FISH, are often assumed to quantify the same phenomena and used interchangeably. Here, however, we demonstrate that contact frequency is distinct from average spatial distance, both in polymer simulations and in experimental data. Performing a systematic analysis of the technologies, we show that this distinction can create a seemingly paradoxical relationship between 3C and FISH, both in minimal polymer models with dynamic looping interactions and in loop-extrusion simulations. Together, our results indicate that cross-validation of Hi-C and FISH should be carefully designed, and that jointly considering contact frequency and spatial distance is crucial for fully understanding chromosome organization.
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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.