Category:ECO:0000232 ! chromosome conformation-based evidence

name: chromosome conformation-based evidence
def: "A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, DNA processing, and quantitation that serves to analyze the spatial organization of chromatin in a cell and quantify the number of interactions between genomic loci that are nearby in 3-D space." [ECO:MCC]
synonym: "3C" NARROW []
synonym: "chromosome conformation capture" NARROW []
synonym: "chromosome conformation capture-based evidence" EXACT []
is_a: ECO:0000006 ! experimental evidence
relationship: OBI:0000312: OBI:0002438 ! is_specified_output_of nuclear ligation assay
comment: Chromosome conformation capture technologies are used to study the structural properties and spatial organization of chromosomes inside cells. All types of chromosome conformation capture technology involve five primary steps: cross-linking of DNA in vivo, restriction digestion, intramolecular ligation, reversing cross-linkages, and DNA enrichment and quantitation. The last step is different for each type of chromosome conformation capture technology, and may include PCR (3C), inverse PCR (4C), or ligation-mediated amplification (5C). Methods for product quantitation can include agarose gel detection or real-time quantitative PCR in the case of 3C, or high-throughput sequencing or microarray analysis for 4C and 5C.