Dynamic properties of independent chromatin domains measured by correlation spectroscopy in living cells

Abstract

BackgroundGenome 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.ResultsHere, 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.ConclusionsBased 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-016-0093-1) contains supplementary material, which is available to authorized users.

The Detailed 3D Multi-Loop Aggregate/Rosette Chromatin Architecture and Functional Dynamic Organization of the Human and Mouse Genomes

“…2e; see below) where the nucleosome composition transitions to an average fibre for 4-6 nucleosomes per 11 nm, L p ranges from ~80 to 120 nm, respectively. This is in agreement with earlier values (see introduction; [32,33]), with values derivable from spatial distance measurements between genetic markers [5,7,8,87], and again with values for L p extractable from genome-wide in vivo FCS measurements [11]. Importantly, this average stiffness predicts that the average loop sizes will have to be on the scale seen above to ensure e.g.…”

“…This would also be the case for an unstable architecture, which would not leave a defined footprint within the sequence. Once more this agrees with our simulations of the dynamics as well as the genomewide in vivo FCS measurements [11]. Moreover, thus the 3D architecture and DNA sequence organization are indeed co-evolutionary tightly entangled (review of previous notions in [5,16]).…”

“…Between the subchromosomal domains, the architecture obviously varies more than within domains in agreement with the FCS in vivo measurements [11], where differences were found for different genomic regions or functional states such as eu-and hetero chromatin, or during massive changes by (de-)compacting the chromatin quasi-fibre by Trichostatin A or Azide treatment. The dynamics of the chromatin quasi-fibre on the millisecond scale in comparison with the size of the differences stresses again how stable this architecture is (see also simulations below; Additional file 11: Movie S1, Additional file 12: Movie S2, Additional file 13: Movie S3 and Additional file 14: Movie S4; and [11]). Hence, this illustrates the notion of the variation of a theme and points to the evolutionary balance between flexibility and stability of genome architecture in agreement with other findings/predictions [4-10, 15-17, 51-54, 59-61].…”

“…These led to a number of suggestions, such as the fractal globule model [71], the loop array architecture in mitotic chromosomes [73], and the highly dynamic loop formation based on single cell ( [74]; compatible with a switch and binder model [75]), or cell population experiments [76]. However, these suggestions are based on experimental (raw) data that are open to other interpretations (this publication [5,11,37,62,64], Imam et al, in prep.) and are in contrast to previous observations (see above).…”

“…However, the dynamic three-dimensional higher-order architecture of genomes, their spatial and temporal modifications and/or relation to functional multi-dimensional interaction and regulatory networks have yet to be determined in detail (e.g. [4][5][6][7][8][9][10][11]). The DNA double helix and the nucleosome [12][13][14] have been determined in general structurally at the very highest level of detail including genome sequences and histone modifications.…”