title: Chromosome Conformation Capture on Chip (4C): Data Processing.
abstract: 4C methods are useful to investigate dependencies between regulatory mechanisms and chromatin structures by revealing the frequency of chromatin contacts between a locus of interest and remote sequences on the chromosome. In this chapter we describe a protocol for the data analysis of microarray-based 4C experiments, presenting updated versions of the methods we used in a previous study of the large-scale chromatin interaction profile of a Polycomb response element in Drosophila. The protocol covers data preparation, normalization, microarray probe selection, and the multi-resolution detection of regions with enriched chromatin contacts. A reanalysis of two independent mouse datasets illustrates the versatility of this protocol and the importance of data processing in 4C. Methods were implemented in the R package MRA.TA (Multi-Resolution Analyses on Tiling Array data), and they can be used to analyze ChIP-on-chip data on broadly distributed chromatin components such as histone marks.
authors.affiliation: Institut de Génétique Humaine, CNRS UPR 1142, 141, rue de la Cardonille, 34396, Montpellier, France. benjamin.leblanc@bric.ku.dk.|BRIC - University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark. benjamin.leblanc@bric.ku.dk.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Leblanc
authors.affiliation: Institut de Génétique Humaine, CNRS UPR 1142, 141, rue de la Cardonille, 34396, Montpellier, France.|BRIC - University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark.
authors.forename: Itys
authors.initials: I
authors.lastname: Comet
authors.affiliation: Institut de Génétique Humaine, CNRS UPR 1142, 141, rue de la Cardonille, 34396, Montpellier, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Bantignies
authors.affiliation: Institut de Génétique Humaine, CNRS UPR 1142, 141, rue de la Cardonille, 34396, Montpellier, France.
authors.forename: Giacomo
authors.initials: G
authors.lastname: Cavalli
mesh_terms: D000818:Animals; D002843:Chromatin / Q000737:chemistry / Q000235:genetics*; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002874:Chromosome Mapping / Q000379:methods*; D002875:Chromosomes / Q000737:chemistry / Q000235:genetics*; D004330:Drosophila / Q000235:genetics; D006657:Histones / Q000737:chemistry / Q000235:genetics; D051379:Mice; D046228:Microarray Analysis; D009690:Nucleic Acid Conformation
chemical_list: D002843:Chromatin; D006657:Histones
keywords: 4C; Bioinformatics; Chromatin; Chromosome Conformation Capture; Epigenetics; Microarray; Multi-resolution statistics; Normalization; Polycomb