title: The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility.
abstract: The eukaryotic cell nucleus harbours the DNA genome that is organized in a dynamic chromatin network and embedded in a viscous crowded fluid. This environment directly affects enzymatic reactions and target search processes that access the DNA sequence information. However, its physical properties as a reaction medium are poorly understood. Here, we exploit mobility measurements of differently sized inert green fluorescent tracer proteins to characterize the viscoelastic properties of the nuclear interior of a living human cell. We find that it resembles a viscous fluid on small and large scales but appears viscoelastic on intermediate scales that change with protein size. Our results are consistent with simulations of diffusion through polymers and suggest that chromatin forms a random obstacle network rather than a self-similar structure with fixed fractal dimensions. By calculating how long molecules remember their previous position in dependence on their size, we evaluate how the nuclear environment affects search processes of chromatin targets.
authors.affiliation: Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
authors.forename: Fabian
authors.initials: F
authors.lastname: Erdel
authors.forename: Michael
authors.initials: M
authors.lastname: Baum
authors.forename: Karsten
authors.initials: K
authors.lastname: Rippe
mesh_terms: D002460:Cell Line; D002470:Cell Survival; D002843:Chromatin / Q000378:metabolism*; D000090266:Chromobox Protein Homolog 5; D002868:Chromosomal Proteins, Non-Histone / Q000737:chemistry / Q000378:metabolism; D003593:Cytoplasm / Q000378:metabolism; D004058:Diffusion; D004548:Elasticity; D049452:Green Fluorescent Proteins / Q000378:metabolism; D006801:Humans; D009068:Movement; D016062:Porosity; D017434:Protein Structure, Tertiary; D013050:Spectrometry, Fluorescence; D014783:Viscosity
chemical_list: D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D000090266:Chromobox Protein Homolog 5; D049452:Green Fluorescent Proteins