title: Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin.
abstract: The nucleus of eukaryotes is organized into functional compartments, the two most prominent being heterochromatin and nucleoli. These structures are highly enriched in DNA, proteins or RNA, and thus thought to be crowded. In vitro, molecular crowding induces volume exclusion, hinders diffusion and enhances association, but whether these effects are relevant in vivo remains unclear. Here, we establish that volume exclusion and diffusive hindrance occur in dense nuclear compartments by probing the diffusive behaviour of inert fluorescent tracers in living cells. We also demonstrate that chromatin-interacting proteins remain transiently trapped in heterochromatin due to crowding induced enhanced affinity. The kinetic signatures of these crowding consequences allow us to derive a fractal model of chromatin organization, which explains why the dynamics of soluble nuclear proteins are affected independently of their size. This model further shows that the fractal architecture differs between heterochromatin and euchromatin, and predicts that chromatin proteins use different target-search strategies in the two compartments. We propose that fractal crowding is a fundamental principle of nuclear organization, particularly of heterochromatin maintenance.
authors.affiliation: Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany.
authors.forename: Aurélien
authors.initials: A
authors.lastname: Bancaud
authors.forename: Sébastien
authors.initials: S
authors.lastname: Huet
authors.forename: Nathalie
authors.initials: N
authors.lastname: Daigle
authors.forename: Julien
authors.initials: J
authors.lastname: Mozziconacci
authors.forename: Joël
authors.initials: J
authors.lastname: Beaudouin
authors.forename: Jan
authors.initials: J
authors.lastname: Ellenberg
mesh_terms: D000818:Animals; D002466:Cell Nucleolus / Q000378:metabolism; D002467:Cell Nucleus / Q000378:metabolism*; D002843:Chromatin / Q000737:chemistry*; D004247:DNA / Q000378:metabolism; D017709:Fractals; D006570:Heterochromatin / Q000737:chemistry*; D007668:Kidney / Q000166:cytology; D007700:Kinetics; D051379:Mice; D008856:Microscopy, Fluorescence / Q000379:methods; D008954:Models, Biological; D012313:RNA / Q000378:metabolism; D051381:Rats; D013050:Spectrometry, Fluorescence / Q000379:methods
chemical_list: D002843:Chromatin; D006570:Heterochromatin; D012313:RNA; D004247:DNA