Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription

Abstract

Intrinsic dynamics of chromatin contribute to gene regulation. How chromatin mobility responds to genomic processes and whether this response relies on coordinated movement is still unclear. Here, CC-BY-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was . http://dx.doi.org/10.1101/230789 doi: bioRxiv preprint first posted online Dec. 7, 2017; Significance StatementControl of gene expression relies on modifications of chromatin structure and activity of the transcription machinery. However, how chromatin responds dynamically to this genomic process and whether this response is coordinated in space is still unclear. We introduce a novel approach called Dense Flow reConstruction and Correlation (DFCC) to characterize spatially correlated dynamics of chromatin in living cells at nanoscale resolution. DFCC allows us to detect chromatin domains in living cells with long range correlations over the entire nucleus. Furthermore, transitions between domains can be quantified by the newly introduced smoothness parameter of local chromatin motion. The DFCC approach permits characterizing stochastically forming domains of other DNA dependent activity in any cell type in real time imaging.

Coupling chromatin structure and dynamics by live super-resolution imaging

“…The flow magnitude is positively correlated for all time lags, while the correlation displays a slight increase for time lags ≤20 s [ Fig. 5A (vi)], which has also been observed previously (8,12,22). The spatial autocorrelation of dynamic and structural properties of chromatin are in stark contrast.…”

“…To quantify the experimentally observed chromatin dynamics at the nanoscale, down to the size of one pixel (13.5 nm), we used a dense reconstruction of flow fields, optical flow ( Fig. 4A; see Materials and Methods), which was previously used to analyze images taken on confocal (12,14), and structured illumination microscopes (8). We examined the suitability of optical flow for super-resolution on the basis of single-molecule localization images using simulations.…”

The rich inner life of the cell nucleus: dynamic organization, active flows, and emergent rheology

“…Domains of coherent motion ( 3–5μm) reach across chromosome territories, suggesting some types of coupling of motion over scales that are huge compared to individual genes (Zidovska et al 2013 ). The discovery of coherent chromatin motion was later corroborated by high-resolution imaging of the local motion of single nucleosomes and replication domains and DCS-like spectroscopy analysis in U2OS cells (Nozaki et al 2017 ; Xiang et al 2018 ; Shaban et al 2018 ). While the biological role of coherent motion is yet to be uncovered, it leads to physical motion of the entire genome, thus likely impacting gene regulation via local changes in rates and molecular transport in the nucleus.…”

“…These large-scale coupled motions were ATP-dependent and independent of the cytoplasmic cytoskeleton (Zidovska et al 2013 ). Perturbation of major nuclear ATPases such as DNA polymerase, RNA polymerase II, and topoisomerase II caused local displacements to increase, but eliminated coherence, i.e., local motions became uncoupled (Zidovska et al 2013 ; Shaban et al 2018 ). These observations revealed coherent motions to be an emergent property of the active chromatin dynamics, suggesting that gene-level activity might lead to the nucleus-wide motions (Zidovska 2020 ).…”

Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes

“…Experiments suggest that genomic loci do not diffuse freely but instead follow a random walk that has a scaling exponent that differs from that predicted by the simplest polymer dynamics models ( 2 ). In addition to the observed subdiffusivity of the trajectories of individual loci, collective motions of chromatin are seen to be coherent beyond the boundaries of chromosome territories, over micrometer-scale regions; this suggests that there is some sort of mechanical coupling between loci very far apart along the polymer or even belonging to two different polymers ( 4 , 5 ). The medium surrounding the chromosomes is also believed to be viscoelastic on the basis of the velocity autocorrelation functions of fluorescently labeled loci, which show a characteristic negative dip ( 3 ).…”