title: Restraint-based three-dimensional modeling of genomes and genomic domains.
abstract: Chromosomes are large polymer molecules composed of nucleotides. In some species, such as humans, this polymer can sum up to meters long and still be properly folded within the nuclear space of few microns in size. The exact mechanisms of how the meters long DNA is folded into the nucleus, as well as how the regulatory machinery can access it, is to a large extend still a mystery. However, and thanks to newly developed molecular, genomic and computational approaches based on the Chromosome Conformation Capture (3C) technology, we are now obtaining insight on how genomes are spatially organized. Here we review a new family of computational approaches that aim at using 3C-based data to obtain spatial restraints for modeling genomes and genomic domains.
authors.affiliation: Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain.
authors.forename: François
authors.initials: F
authors.lastname: Serra
authors.affiliation: Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain.
authors.forename: Marco
authors.initials: M
authors.lastname: Di Stefano
authors.affiliation: Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain.
authors.forename: Yannick G
authors.initials: YG
authors.lastname: Spill
authors.affiliation: Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain.
authors.forename: Yasmina
authors.initials: Y
authors.lastname: Cuartero
authors.affiliation: Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain.
authors.forename: Michael
authors.initials: M
authors.lastname: Goodstadt
authors.affiliation: Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain.
authors.forename: Davide
authors.initials: D
authors.lastname: Baù
authors.affiliation: Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain. Electronic address: mmarti@pcb.ub.cat.
authors.forename: Marc A
authors.initials: MA
authors.lastname: Marti-Renom
mesh_terms: D000818:Animals; D002875:Chromosomes / Q000235:genetics / Q000648:ultrastructure*; D003198:Computer Simulation; D005786:Gene Expression Regulation; D016678:Genome; D006801:Humans; D008957:Models, Genetic; D009690:Nucleic Acid Conformation
keywords: 3D genome reconstruction; Chromosome Conformation Capture; Genome architecture; Restraint-based modeling