title: The 3D Genome as Moderator of Chromosomal Communication.
abstract: Proper expression of genes requires communication with their regulatory elements that can be located elsewhere along the chromosome. The physics of chromatin fibers imposes a range of constraints on such communication. The molecular and biophysical mechanisms by which chromosomal communication is established, or prevented, have become a topic of intense study, and important roles for the spatial organization of chromosomes are being discovered. Here we present a view of the interphase 3D genome characterized by extensive physical compartmentalization and insulation on the one hand and facilitated long-range interactions on the other. We propose the existence of topological machines dedicated to set up and to exploit a 3D genome organization to both promote and censor communication along and between chromosomes.
authors.affiliation: Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-0103, USA. Electronic address: job.dekker@umassmed.edu.
authors.forename: Job
authors.initials: J
authors.lastname: Dekker
authors.affiliation: Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, E25-526C, Cambridge, MA 02139, USA. Electronic address: leonid@mit.edu.
authors.forename: Leonid
authors.initials: L
authors.lastname: Mirny
mesh_terms: D000251:Adenosine Triphosphatases / Q000378:metabolism; D000818:Animals; D000076246:CCCTC-Binding Factor; D002875:Chromosomes / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism; D005260:Female; D016678:Genome; D006801:Humans; D008938:Mitosis; D046912:Multiprotein Complexes / Q000378:metabolism; D012097:Repressor Proteins; D049951:X Chromosome Inactivation
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D004268:DNA-Binding Proteins; D046912:Multiprotein Complexes; D012097:Repressor Proteins; C108312:condensin complexes; D000251:Adenosine Triphosphatases
keywords: CTCF; Hi-C; biophysics; cohesin; condensin; domains; enhancer; gene expression; gene regulation; polymers; promoter; simulations