title: A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes.
abstract: Accumulating evidence demonstrates that the three-dimensional (3D) organization of chromosomes within the eukaryotic nucleus reflects and influences genomic activities, including transcription, DNA replication, recombination and DNA repair. In order to uncover structure-function relationships, it is necessary first to understand the principles underlying the folding and the 3D arrangement of chromosomes. Chromosome conformation capture (3C) provides a powerful tool for detecting interactions within and between chromosomes. A high throughput derivative of 3C, chromosome conformation capture on chip (4C), executes a genome-wide interrogation of interaction partners for a given locus. We recently developed a new method, a derivative of 3C and 4C, which, similar to Hi-C, is capable of comprehensively identifying long-range chromosome interactions throughout a genome in an unbiased fashion. Hence, our method can be applied to decipher the 3D architectures of genomes. Here, we provide a detailed protocol for this method.
authors: Institute for Stem Cell and Regenerative Medicine, University of Washington, USA. zjduan@uw.edu
authors: Zhijun
authors: Z
authors: Duan
authors: Mirela
authors: M
authors: Andronescu
authors: Kevin
authors: K
authors: Schutz
authors: Choli
authors: C
authors: Lee
authors: Jay
authors: J
authors: Shendure
authors: Stanley
authors: S
authors: Fields
authors: William S
authors: WS
authors: Noble
authors: C
authors: C
authors: Anthony Blau
mesh_terms: D000818:Animals; D019921:Biotinylation; D002874:Chromosome Mapping / Q000379:methods*; D003432:Cross-Linking Reagents / Q000737:chemistry; D053837:DNA Cleavage; D004262:DNA Restriction Enzymes / Q000737:chemistry; D004270:DNA, Circular / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D005557:Formaldehyde / Q000737:chemistry; D015723:Gene Library; D016681:Genome, Fungal; D006801:Humans; D009690:Nucleic Acid Conformation; D012372:ROC Curve; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D003432:Cross-Linking Reagents; D004270:DNA, Circular; D004271:DNA, Fungal; D005557:Formaldehyde; D004262:DNA Restriction Enzymes