title: 4C technology: protocols and data analysis.
abstract: Chromosome conformation capture (3C) technology and its genome-wide derivatives have revolutionized our knowledge on chromatin folding and nuclear organization. 4C-seq Technology combines 3C principles with high-throughput sequencing (4C-seq) to enable for unbiased genome-wide screens for DNA contacts made by single genomic sites of interest. Here, we discuss in detail the design, application, and data analysis of 4C-seq experiments. Based on many hundreds of different 4C-seq experiments, we define criteria to assess data quality and show how different restriction enzymes and cross-linking conditions affect results. We describe in detail the mapping strategy of 4C-seq reads and show advanced strategies for data analysis.
authors.affiliation: Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Harmen J G
authors.initials: HJ
authors.lastname: van de Werken
authors.forename: Paula J P
authors.initials: PJ
authors.lastname: de Vree
authors.forename: Erik
authors.initials: E
authors.lastname: Splinter
authors.forename: Sjoerd J B
authors.initials: SJ
authors.lastname: Holwerda
authors.forename: Petra
authors.initials: P
authors.lastname: Klous
authors.forename: Elzo
authors.initials: E
authors.lastname: de Wit
authors.forename: Wouter
authors.initials: W
authors.lastname: de Laat
mesh_terms: D002843:Chromatin / Q000737:chemistry*; D042002:Chromatin Assembly and Disassembly; D002874:Chromosome Mapping / Q000379:methods*; D003432:Cross-Linking Reagents; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D004262:DNA Restriction Enzymes / Q000737:chemistry; D005557:Formaldehyde / Q000737:chemistry; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D013223:Statistics as Topic / Q000379:methods*; D055544:beta-Globins / Q000737:chemistry / Q000235:genetics
chemical_list: D002843:Chromatin; D003432:Cross-Linking Reagents; D055544:beta-Globins; D005557:Formaldehyde; D004247:DNA; D004262:DNA Restriction Enzymes