scholarly journals Coupling chromatin structure and dynamics by live super-resolution imaging

2019 ◽  
Author(s):  
R. Barth ◽  
K. Bystricky ◽  
H. A. Shaban
Keyword(s):  
Chromatin Structure ◽  
Cell Function ◽  
Super Resolution ◽  
Temporal Correlation ◽  
Temporal Organization ◽  
Chromatin Dynamics ◽  
Structure And Dynamics ◽  
Resolution Imaging ◽  
Spatio Temporal ◽  
Chromatin Structure And Dynamics

AbstractChromatin conformation regulates gene expression and thus constant remodeling of chromatin structure is essential to guarantee proper cell function. To gain insight into the spatio-temporal organization of the genome, we employ high-density photo-activated localization microscopy and deep learning to obtain temporally resolved super-resolution images of chromatin in living cells. In combination with high-resolution dense motion reconstruction, we confirm the existence of elongated ~ 45 to 90 nm wide chromatin ‘blobs’. A computational chromatin model suggests that these blobs are dynamically associating chromatin fragments in close physical and genomic proximity and adopt TAD-like interactions in the time-average limit. Experimentally, we found that chromatin exhibits a spatio-temporal correlation over ~ 4 μm in space and tens of seconds in time, while chromatin dynamics are correlated over ~ 6 μm and last 40 s. Notably, chromatin structure and dynamics are closely related, which may constitute a mechanism to grant access to regions with high local chromatin concentration.

scholarly journals Coupling chromatin structure and dynamics by live super-resolution imaging

2020 ◽  
Vol 6 (27) ◽  
pp. eaaz2196 ◽  
Author(s):  
R. Barth ◽  
K. Bystricky ◽  
H. A. Shaban
Keyword(s):  
Chromatin Structure ◽  
Cell Function ◽  
Super Resolution ◽  
Motion Reconstruction ◽  
Chromatin Dynamics ◽  
Structure And Dynamics ◽  
Photoactivated Localization Microscopy ◽  
Resolution Imaging ◽  
Insight Into ◽  
Chromatin Structure And Dynamics

Chromatin conformation regulates gene expression and thus, constant remodeling of chromatin structure is essential to guarantee proper cell function. To gain insight into the spatiotemporal organization of the genome, we use high-density photoactivated localization microscopy and deep learning to obtain temporally resolved super-resolution images of chromatin in living cells. In combination with high-resolution dense motion reconstruction, we find elongated ~45- to 90-nm-wide chromatin “blobs.” A computational chromatin model suggests that these blobs are dynamically associating chromatin fragments in close physical and genomic proximity and adopt topologically associated domain–like interactions in the time-average limit. Experimentally, we found that chromatin exhibits a spatiotemporal correlation over ~4 μm in space and tens of seconds in time, while chromatin dynamics are correlated over ~6 μm and last 40 s. Notably, chromatin structure and dynamics are closely related, which may constitute a mechanism to grant access to regions with high local chromatin concentration.

scholarly journals Characterization of Locus Specific Chromatin Structure and Dynamics using Correlative Conventional Super Resolution Crispr dCas9/Ms2 Imaging

2021 ◽  
Vol 120 (3) ◽  
pp. 9a
Author(s):  
Dushyant Mehra ◽  
Chiranjib Banerjee ◽  
Santosh Adhikari ◽  
Jacob M. Ritz ◽  
Angel Mancebo ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Super Resolution ◽  
Structure And Dynamics ◽  
Chromatin Structure And Dynamics

scholarly journals Characterizing Locus Specific Chromatin Structure and Dynamics with Correlative Conventional and Super Resolution imaging in living cells

2021 ◽  
Author(s):  
Dushyant Mehra ◽  
Santosh Adhikari ◽  
Chiranjib Banerjee ◽  
Elias M. Puchner
Keyword(s):  
Single Molecule ◽  
Chromatin Structure ◽  
Spatial Organization ◽  
Super Resolution ◽  
Living Cells ◽  
Diffraction Limit ◽  
Optical Diffraction ◽  
Acquisition Time ◽  
Structure And Dynamics ◽  
Chromatin Structure And Dynamics

The dynamic rearrangement of chromatin is critical for gene regulation, but mapping both the spatial organization of chromatin and its dynamics remains a challenge. Many structural conformations are too small to be resolved via conventional fluorescence microscopy and the long acquisition time of super-resolution PALM imaging precludes the structural characterization of chromatin below the optical diffraction limit in living cells due to chromatin motion. Here we develop a correlative conventional fluorescence and PALM imaging approach to quantitatively map time-averaged chromatin structure and dynamics below the optical diffraction limit in living cells. By assigning localizations to a locus as it moves, we reliably discriminate between bound and searching dCas9 molecules, whose mobility overlap. Our approach accounts for changes in DNA mobility and relates local chromatin motion to larger scale domain movement. In our experimental system, we show that compacted telomeres have a higher density of bound dCas9 molecules, but the relative motion of those molecules is more restricted than in less compacted telomeres. Correlative conventional and PALM imaging therefore improves the ability to analyze the mobility and time-averaged nanoscopic structural features of locus specific chromatin with single molecule precision and yields unprecedented insights across length and time scales.

scholarly journals Dynamics as a cause for the nanoscale organization of the genome

2020 ◽  
Author(s):  
R. Barth ◽  
G. Fourel ◽  
H. A. Shaban
Keyword(s):  
Local Density ◽  
Super Resolution ◽  
Active Motion ◽  
Chromatin Dynamics ◽  
Small Areas ◽  
Functional Implications ◽  
Causality Inference ◽  
A Cell ◽  
Resolution Imaging ◽  
Spatio Temporal

AbstractChromatin ‘blobs’ were recently identified by live super-resolution imaging as pervasive, but transient and dynamic structural entities consisting of a few associating nucleosomes. The origin and functional implications of these blobs are, however, unknown. Following these findings, we explore whether causal relationships exist between parameters characterizing the chromatin blob dynamics and structure, by adapting a framework for spatio-temporal Granger-causality inference. Our analysis reveals that chromatin dynamics is a key determinant of both blob area and local density. However, such causality can only be demonstrated in small areas (10 – 20%) of the nucleus, highlighting that chromatin dynamics and structure at the nanoscale is dominated by stochasticity. Pixels for which the inter-blob distance can be effectively demonstrated to depend on chromatin dynamics appears as clump in the nucleus, and display both a higher blob density and higher local dynamics as compared with the rest of the nucleus. Furthermore, we show that the theory of active semiflexible polymers can be invoked to provide potential mechanisms leading to the organization of chromatin into blobs. Based on active motion-inducing effectors, this framework qualitatively recapitulates experimental observations and predicts that chromatin blobs might be formed stochastically by a collapse of local polymer segments consisting of a few nucleosomes. Our results represent a first step towards elucidating the mechanisms that govern the dynamic and stochastic organization of chromatin in a cell nucleus.

Nucleosome dynamics

2006 ◽  
Vol 73 ◽  
pp. 109-119 ◽  
Author(s):  
Chris Stockdale ◽  
Michael Bruno ◽  
Helder Ferreira ◽  
Elisa Garcia-Wilson ◽  
Nicola Wiechens ◽  
...  
Keyword(s):  
High Resolution ◽  
Chromatin Structure ◽  
Current Knowledge ◽  
Dynamic Properties ◽  
Structure And Dynamics ◽  
Nucleosome Dynamics ◽  
Sharp Focus ◽  
Recent Advances ◽  
Insight Into ◽  
Chromatin Structure And Dynamics

In the 30 years since the discovery of the nucleosome, our picture of it has come into sharp focus. The recent high-resolution structures have provided a wealth of insight into the function of the nucleosome, but they are inherently static. Our current knowledge of how nucleosomes can be reconfigured dynamically is at a much earlier stage. Here, recent advances in the understanding of chromatin structure and dynamics are highlighted. The ways in which different modes of nucleosome reconfiguration are likely to influence each other are discussed, and some of the factors likely to regulate the dynamic properties of nucleosomes are considered.

Chromatin structure and dynamics

BioEssays ◽  
1994 ◽  
Vol 16 (9) ◽  
pp. 657-662 ◽  
Author(s):  
Andrew A. Travers
Keyword(s):  
Chromatin Structure ◽  
Structure And Dynamics ◽  
Chromatin Structure And Dynamics

scholarly journals Spatio-temporal correlation super-resolution optical fluctuation imaging

2019 ◽  
Vol 125 (2) ◽  
pp. 20005 ◽  
Author(s):  
A. Purohit ◽  
W. Vandenberg ◽  
T. Dertinger ◽  
D. Wöll ◽  
P. Dedecker ◽  
...  
Keyword(s):  
Super Resolution ◽  
Temporal Correlation ◽  
Spatio Temporal
Sign in / Sign up

Export Citation Format

Share Document