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Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription

View ORCID ProfileHaitham A. Shaban, Roman Barth, Kerstin Bystricky
doi: https://doi.org/10.1101/230789
Haitham A. Shaban
Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS; University of Toulouse, UPS; 31062 Toulouse; France
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  • ORCID record for Haitham A. Shaban
  • For correspondence: haitham.shaban@ibcg.biotoul.fr kerstin.bystricky@ibcg.biotoul.fr
Roman Barth
Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS; University of Toulouse, UPS; 31062 Toulouse; France
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Kerstin Bystricky
Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS; University of Toulouse, UPS; 31062 Toulouse; France
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  • For correspondence: haitham.shaban@ibcg.biotoul.fr kerstin.bystricky@ibcg.biotoul.fr
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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, we introduce an approach called Dense Flow reConstruction and Correlation (DFCC) to quantify correlation of chromatin motion with sub-pixel sensitivity at the level of the whole nucleus. DFCC is based on reconstructing dense global flow fields of fluorescent images acquired in real-time. By simulating variations in microscopic and dynamic parameters, we demonstrate that our approach is robust and more accurate than other methods to estimate flow fields and spatial correlations of dense structures such as chromatin. We applied our approach to analyze stochastic movements of DNA and histones based on direction and magnitude at different time lags in human cells. We observe long-range correlations extending over several μm between coherently moving regions over the entire nucleus. Spatial correlation of global chromatin dynamics was reduced by inhibiting elongation by RNA polymerase II and abolished in quiescent cells. Furthermore, quantification of spatial smoothness over time intervals up to 30 seconds points to clear-cut boundaries between distinct regions, while smooth transitions in small (<1 μm) neighborhoods dominate for short time intervals. Clear transitions between regions of coherent motion indicate directed squeezing or stretching of chromatin boundaries suggestive of changes in local concentrations of actors regulating gene expression. The DFCC approach hence allows characterizing stochastically forming domains of specific nuclear activity.

Significance Statement Control 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted December 07, 2017.
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Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription
Haitham A. Shaban, Roman Barth, Kerstin Bystricky
bioRxiv 230789; doi: https://doi.org/10.1101/230789
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Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription
Haitham A. Shaban, Roman Barth, Kerstin Bystricky
bioRxiv 230789; doi: https://doi.org/10.1101/230789

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