Statistical analysis of protein ensembles

Máté, Gabriell; Heermann, Dieter W.

doi:10.3389/fphy.2014.00020

Cited by 1 publication

(2 citation statements)

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“…The "separation of the sub-components" [98] and the size of the holes can be obtained by considering the endpoints of the bars of components and holes. Hence, for each point cloud defined by the H3K9me3 blinking events detected in a nucleus, a normalized histogram showing the distribution of endpoints of the bars (=the highest α value of a bar) of components and holes was computed.…”

Section: Clustering and Persistent Homologies Of γH2ax Foci And Heterochromatinmentioning

confidence: 99%

“…The average distribution of the endpoints of bars within all nuclei of the given sample is shown in Figure 9 for non-irradiated cells in comparison to irradiated cells analyzed at different times PI. The "separation of the sub-components" [98] and the size of the holes can be obtained by considering the endpoints of the bars of components and holes. Hence, for each point cloud defined by the H3K9me3 blinking events detected in a nucleus, a normalized histogram showing the distribution of endpoints of the bars (=the highest α value of a bar) of components and holes was computed.…”

Section: Clustering and Persistent Homologies Of γH2ax Foci And Heterochromatinmentioning

confidence: 99%

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Elucidation of the Clustered Nano-Architecture of Radiation-Induced DNA Damage Sites and Surrounding Chromatin in Cancer Cells: A Single Molecule Localization Microscopy Approach

Hausmann

Falk

Neitzel

et al. 2021

IJMS

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In cancer therapy, the application of (fractionated) harsh radiation treatment is state of the art for many types of tumors. However, ionizing radiation is a “double-edged sword”—it can kill the tumor but can also promote the selection of radioresistant tumor cell clones or even initiate carcinogenesis in the normal irradiated tissue. Individualized radiotherapy would reduce these risks and boost the treatment, but its development requires a deep understanding of DNA damage and repair processes and the corresponding control mechanisms. DNA double strand breaks (DSBs) and their repair play a critical role in the cellular response to radiation. In previous years, it has become apparent that, beyond genetic and epigenetic determinants, the structural aspects of damaged chromatin (i.e., not only of DSBs themselves but also of the whole damage-surrounding chromatin domains) form another layer of complex DSB regulation. In the present article, we summarize the application of super-resolution single molecule localization microscopy (SMLM) for investigations of these structural aspects with emphasis on the relationship between the nano-architecture of radiation-induced repair foci (IRIFs), represented here by γH2AX foci, and their chromatin environment. Using irradiated HeLa cell cultures as an example, we show repair-dependent rearrangements of damaged chromatin and analyze the architecture of γH2AX repair clusters according to topological similarities. Although HeLa cells are known to have highly aberrant genomes, the topological similarity of γH2AX was high, indicating a functional, presumptively genome type-independent relevance of structural aspects in DSB repair. Remarkably, nano-scaled chromatin rearrangements during repair depended both on the chromatin domain type and the treatment. Based on these results, we demonstrate how the nano-architecture and topology of IRIFs and chromatin can be determined, point to the methodological relevance of SMLM, and discuss the consequences of the observed phenomena for the DSB repair network regulation or, for instance, radiation treatment outcomes.

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Section: Clustering and Persistent Homologies Of γH2ax Foci And Heterochromatinmentioning

confidence: 99%

Section: Clustering and Persistent Homologies Of γH2ax Foci And Heterochromatinmentioning

confidence: 99%

Elucidation of the Clustered Nano-Architecture of Radiation-Induced DNA Damage Sites and Surrounding Chromatin in Cancer Cells: A Single Molecule Localization Microscopy Approach

Hausmann

Falk

Neitzel

et al. 2021

IJMS

Self Cite

View full text Add to dashboard Cite

show abstract

Statistical analysis of protein ensembles

Cited by 1 publication

References 12 publications

Elucidation of the Clustered Nano-Architecture of Radiation-Induced DNA Damage Sites and Surrounding Chromatin in Cancer Cells: A Single Molecule Localization Microscopy Approach

Elucidation of the Clustered Nano-Architecture of Radiation-Induced DNA Damage Sites and Surrounding Chromatin in Cancer Cells: A Single Molecule Localization Microscopy Approach

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