Dynamic properties of independent chromatin domains measured by correlation spectroscopy in living cells. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Wachsmuth, Malte; Knoch, Tobias; Rippe, Karsten
• Is Part Of: Epigenetics & chromatin. Volume 9:Issue 1(2016)
• Page Start: 1
• Page End: 20
• Publication Date: 2016-12
• Subjects: Chromatin structure -- Polymer model -- Chromatin conformation capture carbon copy (5C) -- Targeted chromatin capture (T2C) -- Fluorescence correlation spectroscopy (FCS) -- Quantitative microscopy; Epigenesis -- Periodicals; Chromatin -- Periodicals; 572.8
• DOI: 10.1186/s13072-016-0093-1
• Languages: English
• ISSNs: 1756-8935

Abstract

Abstract Background Genome organization into subchromosomal topologically associating domains (TADs) is linked to cell-type-specific gene expression programs. However, dynamic properties of such domains remain elusive, and it is unclear how domain plasticity modulates genomic accessibility for soluble factors. Results Here, we combine and compare a high-resolution topology analysis of interacting chromatin loci with fluorescence correlation spectroscopy measurements of domain dynamics in single living cells. We identify topologically and dynamically independent chromatin domains of ~1 Mb in size that are best described by a loop-cluster polymer model. Hydrodynamic relaxation times and gyration radii of domains are larger for open (161 ± 15 ms, 297 ± 9 nm) than for dense chromatin (88 ± 7 ms, 243 ± 6 nm) and increase globally upon chromatin hyperacetylation or ATP depletion. Conclusions Based on the domain structure and dynamics measurements, we propose a loop-cluster model for chromatin domains. It suggests that the regulation of chromatin accessibility for soluble factors displays a significantly stronger dependence on factor concentration than search processes within a static network.