title: Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation.
abstract: Chromosome Conformation Capture (3C) and 3C-based technologies are constantly evolving in order to probe nuclear organization with higher depth and resolution. One such method is 4C-technology that allows the investigation of the nuclear environment of a locus of choice. The use of Illumina next generation sequencing as a detection platform for the analysis of 4C data has further improved the sensitivity and resolution of this method. Here we provide a step-by-step protocol for 4C-seq, describing the procedure from the initial template preparation until the final data analysis, interchanged with background information and considerations.
authors.affiliation: Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht 3584 CT, The Netherlands.
authors.forename: Erik
authors.initials: E
authors.lastname: Splinter
authors.forename: Elzo
authors.initials: E
authors.lastname: de Wit
authors.forename: Harmen J G
authors.initials: HJ
authors.lastname: van de Werken
authors.forename: Petra
authors.initials: P
authors.lastname: Klous
authors.forename: Wouter
authors.initials: W
authors.lastname: de Laat
mesh_terms: D000465:Algorithms; D000818:Animals; D002478:Cells, Cultured; D002843:Chromatin / Q000737:chemistry / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D053837:DNA Cleavage; D011088:DNA Ligases / Q000737:chemistry; D017931:DNA Primers / Q000235:genetics; D004262:DNA Restriction Enzymes / Q000737:chemistry; D003627:Data Interpretation, Statistical; D004843:Epistasis, Genetic; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017422:Sequence Analysis, DNA; D016707:Tissue Fixation / Q000379:methods
chemical_list: D002843:Chromatin; D017931:DNA Primers; D004247:DNA; D004262:DNA Restriction Enzymes; D011088:DNA Ligases