ArticleMethods (San Diego, Calif.)2012
Analysis of long-range chromatin interactions using Chromosome Conformation Capture.
Article in Methods (San Diego, Calif.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 109 papers, 1 of them a synthesis that pooled it.
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
109 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genetic and regulatory mechanism of susceptibility to high-hyperdiploid acute lymphoblastic leukaemia at 10p21.2.Nature communications · 2017Pooled it
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- Jpx RNA controls Xist induction through spatial reorganization of the mouse X-inactivation center.Developmental cell · 2025Article
- The Biological Function of Genome Organization.International journal of molecular sciences · 2025Review
- TGF-β signaling controls neural crest developmental plasticity via SMAD2/3.Developmental cell · 2025Article
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- Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition.Nature genetics · 2025Article
- Identification of a distal enhancer of Ucp1 essential for thermogenesis and mitochondrial function in brown fat.Communications biology · 2025Article
- Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth.Nature structural & molecular biology · 2025Article
- Noncoding RNA,Molecular and cellular biology · 2025Article
- Chromosome-level genome assembly of the tetraploid medicinal and natural dye plant Persicaria tinctoria.Scientific data · 2024Article
- De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes.Genome research · 2024Article
- ARID1A safeguards the canalization of the cell fate decision during osteoclastogenesis.Nature communications · 2024Article
- Regulating epithelial-mesenchymal plasticity from 3D genome organization.Communications biology · 2024Review
- An intronic enhancer of Cebpa regulates adipocyte differentiation and adipose tissue development via long-range loop formation.Cell proliferation · 2024Article
49 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
4 authors.
Funding
Abstract
Chromosome Conformation Capture, or 3C, is a pioneering method for investigating the three-dimensional structure of chromatin. 3C is used to analyze long-range looping interactions between any pair of selected genomic loci. Most 3C studies focus on defined genomic regions of interest that can be up to several hundred Kb in size. The method has become widely adopted and has been modified to increase throughput to allow unbiased genome-wide analysis. These large-scale adaptations are presented in other articles in this issue of Methods. Here we describe the 3C procedure in detail, including the appropriate use of the technology, the experimental set-up, an optimized protocol and troubleshooting guide, and considerations for data analysis. The protocol described here contains previously unpublished improvements, which save time and reduce labor. We pay special attention to primer design, appropriate controls and data analysis. We include notes and discussion based on our extensive experience to help researchers understand the principles of 3C-based techniques and to avoid common pitfalls and mistakes. This paper represents a complete resource and detailed guide for anyone who desires to perform 3C.
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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.