title: Detection of short-range chromatin interactions by chromosome conformation capture (3C) in yeast.
abstract: We describe a modified 3C ("chromosome conformation capture") protocol for detection of transient, short-range chromatin interactions in the yeast Saccharomyces cerevisiae. 3C was initially described by Job Dekker and involves formaldehyde cross-linking to stabilize transient chromatin interactions, followed by restriction digestion, ligation, and locus-specific PCR. As such, 3C reveals complex three-dimensional interactions between distal genetic elements within intact cells at high resolution. Using a modified version of Dekker's protocol, we are able to detect gene loops that juxtapose promoter and terminator regions of yeast genes with ORFs as short as 1 kb. We are using this technique to define the cis- and trans-acting requirements for the formation and maintenance of gene loops, and to elucidate their physiological consequences. We anticipate that this method will be generally applicable to detect dynamic, short-range chromatin interactions, not limited to gene loops.
authors.affiliation: Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, 638 Hoes Lane West, Piscataway, NJ, 08854, USA.
authors.forename: Badri Nath
authors.initials: BN
authors.lastname: Singh
authors.forename: Michael
authors.initials: M
authors.lastname: Hampsey
mesh_terms: D011232:Chemical Precipitation; D002843:Chromatin / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D015825:Chromosomes, Fungal; D003432:Cross-Linking Reagents / Q000737:chemistry; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D005800:Genes, Fungal; D016133:Polymerase Chain Reaction / Q000379:methods; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D003432:Cross-Linking Reagents; D004271:DNA, Fungal