title: Detecting Spatial Chromatin Organization by Chromosome Conformation Capture II: Genome-Wide Profiling by Hi-C.
abstract: The chromosome conformation capture (3C) method has been invaluable in studying chromatin interactions in a population of cells at a resolution surpassing that of light microscopy, for example in the detection of functional contacts between enhancers and promoters. Recent developments in sequencing-based chromosomal contact mapping (Hi-C, 5C and 4C-Seq) have allowed researchers to interrogate pairwise chromatin interactions on a wider scale, shedding light on the three-dimensional organization of chromosomes. These methods present significant technical and bioinformatic challenges to consider at the start of the project. Here, we describe two alternative methods for Hi-C, depending on the size of the genome, and discuss the major computational approaches to convert the raw sequencing data into meaningful models of how genomes are organized.
authors.affiliation: Research Department of Cancer Biology, Cancer Institute, University College London, London, UK.
authors.forename: Matteo
authors.initials: M
authors.lastname: Vietri Rudan
authors.affiliation: Research Department of Cancer Biology, Cancer Institute, University College London, London, UK. s.hadjur@ucl.ac.uk.
authors.forename: Suzana
authors.initials: S
authors.lastname: Hadjur
authors.affiliation: Institute of Genetics and Molecular and Cellular Biology, CNRS UMR7104/INSERM U964, Illkirch, France. sexton@igbmc.fr.|University of Strasbourg, Illkirch, France. sexton@igbmc.fr.
authors.forename: Tom
authors.initials: T
authors.lastname: Sexton
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism*; D042002:Chromatin Assembly and Disassembly; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D004331:Drosophila melanogaster / Q000235:genetics; D004622:Embryo, Mammalian / Q000166:cytology / Q000378:metabolism; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods*; D022781:Hepatocytes / Q000166:cytology / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D051379:Mice
chemical_list: D002843:Chromatin
keywords: 3C (chromosome conformation capture); Chromatin interactions; Chromosome topology; Hi-C; High-throughput sequencing