Super-Resolution Imaging Reveals Spatio-Temporal Propagation of Human Replication Foci Mediated by CTCF-Organized Chromatin Structures

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.

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Terahertz Integration and Spatio-Temporal Super-Resolution Imaging on LiNbO3 Chip

Chinese Journal of Lasers ◽

10.3788/cjl201946.0508003 ◽

2019 ◽

Vol 46 (5) ◽

pp. 0508003

Author(s):

张琦 Zhang Qi ◽

吴强 Wu Qiang ◽

张斌 Zhang Bin ◽

潘崇佩 Pan Chongpei ◽

王日德 Wang Ride ◽

...

Keyword(s):

Super Resolution ◽

Resolution Imaging ◽

Spatio Temporal

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CTCF-mediated Chromatin Structures Dictate the Spatio-temporal Propagation of Replication Foci

10.1101/525915 ◽

2019 ◽

Cited By ~ 2

Author(s):

Qian Peter Su ◽

Ziqing Winston Zhao ◽

Luming Meng ◽

Miao Ding ◽

Weiwei Zhang ◽

...

Keyword(s):

Super Resolution ◽

S Phase ◽

Temporal Organization ◽

Replication Origins ◽

Stochastic Optical Reconstruction Microscopy ◽

Replication Foci ◽

Spatio Temporal ◽

Optical Reconstruction ◽

Epigenetic Signatures

ABSTRACTMammalian DNA replication is initiated at numerous replication origins, which are clustered into thousands of replication domains (RDs) across the genome. However, it remains unclear whether the replication origins within each RD are activated stochastically. To understand how replication is regulated at the sub-RD level, we directly visualized the spatio-temporal organization, morphology, and in situ epigenetic signatures of individual replication foci (RFi) across S-phase using super-resolution stochastic optical reconstruction microscopy (STORM). Importantly, we revealed a hierarchical radial pattern of RFi propagation that reverses its directionality from early to late S-phase, and is diminished upon caffeine treatment or CTCF knockdown. Together with simulation and bioinformatic analyses, our findings point to a ‘CTCF-organized REplication Propagation’ (CoREP) model. The CoREP model suggests a non-random selection mechanism for replication activation mediated by CTCF at the sub-RD level, as well as the critical involvement of local chromatin environment in regulating replication in space and time.

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Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments

10.1101/2020.03.04.976977 ◽

2020 ◽

Cited By ~ 1

Author(s):

Hajnalka L. Pálinkás ◽

Angéla Békési ◽

Gergely Róna ◽

Lőrinc Pongor ◽

Gergely Tihanyi ◽

...

Keyword(s):

Drug Treatment ◽

Human Cancer ◽

Super Resolution ◽

Cancer Cell Line ◽

Distribution Patterns ◽

Genome Wide ◽

Sequencing Method ◽

Anti Cancer ◽

Resolution Imaging ◽

Spatio Temporal

ABSTRACTNumerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug-treatment in human cancer cell-line HCT116. We developed a straightforward U-DNA sequencing method (U-DNA-Seq) that was combined with in situ super-resolution imaging. Using a novel robust analysis pipeline, we found broad regions with elevated probability of uracil occurrence both in treated and non-treated cells. Correlation with chromatin markers and other genomic features shows that non-treated cells possess uracil in the late replicating constitutive heterochromatic regions, while drug treatment induced a shift of incorporated uracil towards more active/functional segments. Data were corroborated by colocalization studies via dSTORM microscopy. This approach can also be applied to study the dynamic spatio-temporal nature of genomic uracil.

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Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments

eLife ◽

10.7554/elife.60498 ◽

2020 ◽

Vol 9 ◽

Author(s):

Hajnalka L Pálinkás ◽

Angéla Békési ◽

Gergely Róna ◽

Lőrinc Pongor ◽

Gábor Papp ◽

...

Keyword(s):

Human Cancer ◽

Super Resolution ◽

Cancer Cell Line ◽

Distribution Patterns ◽

Genome Wide ◽

Sequencing Method ◽

Anti Cancer ◽

Drug Treatments ◽

Resolution Imaging ◽

Spatio Temporal

Numerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug treatments in human cancer cell line models derived from HCT116. We developed a straightforward U-DNA sequencing method (U-DNA-Seq) that was combined with in situ super-resolution imaging. Using a novel robust analysis pipeline, we found broad regions with elevated probability of uracil occurrence both in treated and non-treated cells. Correlation with chromatin markers and other genomic features shows that non-treated cells possess uracil in the late replicating constitutive heterochromatic regions, while drug treatment induced a shift of incorporated uracil towards segments that are normally more active/functional. Data were corroborated by colocalization studies via dSTORM microscopy. This approach can be applied to study the dynamic spatio-temporal nature of genomic uracil.

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Single-molecule Photoswitching and Localization

Australian Journal of Chemistry ◽

10.1071/ch10284 ◽

2011 ◽

Vol 64 (5) ◽

pp. 503 ◽

Cited By ~ 18

Author(s):

Sebastian van de Linde ◽

Steve Wolter ◽

Markus Sauer

Keyword(s):

Single Molecule ◽

Optical Resolution ◽

Super Resolution ◽

Image Plane ◽

Localization Microscopy ◽

Stochastic Optical Reconstruction Microscopy ◽

Resolution Imaging ◽

Spatio Temporal ◽

Optical Reconstruction ◽

20 Nm

Within only a few years super-resolution fluorescence imaging based on single-molecule localization and image reconstruction has attracted considerable interest because it offers a comparatively simple way to achieve a substantially improved optical resolution down to ∼20 nm in the image plane. Since super-resolution imaging methods such as photoactivated localization microscopy, fluorescence photoactivation localization microscopy, stochastic optical reconstruction microscopy, and direct stochastic optical reconstruction microscopy rely critically on exact fitting of the centre of mass and the shape of the point-spread-function of isolated emitters unaffected by neighbouring fluorophores, controlled photoswitching or photoactivation of fluorophores is the key parameter for resolution improvement. This review will explain the principles and requirements of single-molecule based localization microscopy, and compare different super-resolution imaging concepts and highlight their strengths and limitations with respect to applications in fixed and living cells with high spatio-temporal resolution.

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Coupling chromatin structure and dynamics by live super-resolution imaging

10.1101/777482 ◽

2019 ◽

Cited By ~ 2

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.

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