title: How best to identify chromosomal interactions: a comparison of approaches.
abstract: Chromosome conformation capture (3C) methods are central to understanding the link between nuclear structure and function, and the physical interactions between distal regulatory elements and promoters. However, no one method is appropriate to address all biological questions, as each variant differs markedly in resolution, reproducibility, throughput and biases. A thorough appreciation of the strengths and weaknesses of each technique is critical when choosing the correct method for a specific application or for gauging how best to interpret different sources of data. In addition, the analysis method must be carefully considered, as this choice can profoundly affect the output. In this Review, we describe and compare the different available 3C-based approaches, with a focus on the analysis of mammalian genomes.
authors.affiliation: Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom.
authors.forename: James O J
authors.identifier: 0000-0002-4108-4357
authors.initials: JO
authors.lastname: Davies
authors.affiliation: Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom.
authors.forename: A Marieke
authors.initials: AM
authors.lastname: Oudelaar
authors.affiliation: Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom.
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Higgs
authors.affiliation: Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom.
authors.forename: Jim R
authors.identifier: 0000-0002-8955-7256
authors.initials: JR
authors.lastname: Hughes
mesh_terms: D000818:Animals; D002843:Chromatin / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D002875:Chromosomes / Q000737:chemistry / Q000235:genetics; D015723:Gene Library; D005821:Genetic Techniques; D057166:High-Throughput Screening Assays / Q000379:methods; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D020014:K562 Cells; D051379:Mice; D016133:Polymerase Chain Reaction / Q000379:methods; D055748:SOXB1 Transcription Factors / Q000235:genetics; D055542:alpha-Globins / Q000235:genetics
chemical_list: D002843:Chromatin; D055748:SOXB1 Transcription Factors; C527783:Sox2 protein, mouse; D055542:alpha-Globins