High-Throughput Flow Cytometry Combined with Genetic Analysis Brings New Insights into the Understanding of Chromatin Regulation of Cellular Quiescence

Zahedi, Yasaman; Durand-Dubief, Mickaël; Ekwall, Karl

doi:10.3390/ijms21239022

Cited by 15 publications

(17 citation statements)

References 38 publications

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“…These histone tails modulate charge, hydrophobicity, and steric access to chromatin (Ghoneim et al, 2021). Histone PTMs Allen et al, 2006 Fission yeast Cell culture Nitrogen-induced starvation; Glucose deprivation Hayashi et al, 2018;Zahedi et al, 2020 Human dermal fibroblasts Cell culture Serum-starvation; Contact-inhibition Evertts et al, 2013a;Mitra et al, 2018a Human lung fibroblasts Cell culture Mitogen withdrawal; Contact inhibition; Loss of adhesion are added and removed by enzymatic proteins referred to as "writers" and "erasers, " respectively (Soshnev et al, 2016;Hyun et al, 2017;Husmann and Gozani, 2019). Histone PTMs serve as recognition sites for proteins ("readers") that site-specifically bind to chromatin.…”

Section: Histone Post-translational Modifications As a Possible Biological Code Nucleosome Structure And Histone Marksmentioning

confidence: 99%

Is There a Histone Code for Cellular Quiescence?

Bonitto

Sarathy

Atai

et al. 2021

Front. Cell Dev. Biol.

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Many of the cells in our bodies are quiescent, that is, temporarily not dividing. Under certain physiological conditions such as during tissue repair and maintenance, quiescent cells receive the appropriate stimulus and are induced to enter the cell cycle. The ability of cells to successfully transition into and out of a quiescent state is crucial for many biological processes including wound healing, stem cell maintenance, and immunological responses. Across species and tissues, transcriptional, epigenetic, and chromosomal changes associated with the transition between proliferation and quiescence have been analyzed, and some consistent changes associated with quiescence have been identified. Histone modifications have been shown to play a role in chromatin packing and accessibility, nucleosome mobility, gene expression, and chromosome arrangement. In this review, we critically evaluate the role of different histone marks in these processes during quiescence entry and exit. We consider different model systems for quiescence, each of the most frequently monitored candidate histone marks, and the role of their writers, erasers and readers. We highlight data that support these marks contributing to the changes observed with quiescence. We specifically ask whether there is a quiescence histone “code,” a mechanism whereby the language encoded by specific combinations of histone marks is read and relayed downstream to modulate cell state and function. We conclude by highlighting emerging technologies that can be applied to gain greater insight into the role of a histone code for quiescence.

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Section: Histone Post-translational Modifications As a Possible Biological Code Nucleosome Structure And Histone Marksmentioning

confidence: 99%

Is There a Histone Code for Cellular Quiescence?

Bonitto

Sarathy

Atai

et al. 2021

Front. Cell Dev. Biol.

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“…Dam1 possesses a highly variable length for different fungi and whereas its C-terminus has been shown to interact with the globular head of ndc80 HEC1 in S. cerevisiae , it is predicted to be too short (155 aa in S. pombe , 343 aa in S. cerevisiae ) to do so in S. pombe ( Jenni and Harrison, 2018 ). Furthermore, deleting dam1 is viable for S. pombe ( Zahedi et al, 2020 ) but inviable for S. cerevisiae ( Giaever et al, 2002 ). Consistent with these observations, we hypothesize that S. pombe dam1 indeed interacts and colocalizes with the ndc80 HEC1 -loop region.…”

Section: Resultsmentioning

confidence: 99%

Unraveling the kinetochore nanostructure in Schizosaccharomyces pombe using multi-color SMLM imaging

Virant

Vojnovic

Winkelmeier

et al. 2023

Journal of Cell Biology

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The key to ensuring proper chromosome segregation during mitosis is the kinetochore (KT), a tightly regulated multiprotein complex that links the centromeric chromatin to the spindle microtubules and as such leads the segregation process. Understanding its architecture, function, and regulation is therefore essential. However, due to its complexity and dynamics, only its individual subcomplexes could be studied in structural detail so far. In this study, we construct a nanometer-precise in situ map of the human-like regional KT of Schizosaccharomyces pombe using multi-color single-molecule localization microscopy. We measure each protein of interest (POI) in conjunction with two references, cnp1CENP-A at the centromere and sad1 at the spindle pole. This allows us to determine cell cycle and mitotic plane, and to visualize individual centromere regions separately. We determine protein distances within the complex using Bayesian inference, establish the stoichiometry of each POI and, consequently, build an in situ KT model with unprecedented precision, providing new insights into the architecture.

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“…Whereas the dam1 C-terminus has been shown to interact with the globular head of ndc80 HEC1 in S. cerevisiae , it is predicted to be too short (only 155 aa in S. pombe in comparison to 343 aa in S. cerevisiae ) to do so in S. pombe (Jenni and Harrison, 2018). Furthermore, deleting dam1 is viable for S. pombe (Zahedi et al, 2020) but inviable for S. cerevisiae (Giaever et al, 2002). Consistent with these observations, we deduct from our data that S. pombe dam1 indeed interacts and colocalizes with the ndc80 HEC1 -loop region.…”

Section: Resultsmentioning

confidence: 99%

Unraveling the kinetochore nanostructure in Schizosaccharomyces pombe using multi-color single-molecule localization microscopy

Virant

Vojnovic

Winkelmeier

et al. 2021

Preprint

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The key to ensuring proper chromosome segregation during mitosis is the kinetochore complex. This large and tightly regulated multi-protein complex links the centromeric chromatin to the microtubules attached to the spindle pole body and as such leads the segregation process. Understanding the architecture, function and regulation of this vital complex is therefore essential. However, due to its complexity and dynamics, only its individual subcomplexes could be studied in high-resolution structural detail so far.In this study we construct a nanometer-precise in situ map of the human-like regional kinetochore of Schizosaccharomyces pombe (S. pombe) using multi-color single-molecule localization microscopy (SMLM). We measure each kinetochore protein of interest (POI) in conjunction with two reference proteins, cnp1CENP-A at the centromere and sad1 at the spindle pole. This arrangement allows us to determine the cell cycle and in particularly the mitotic plane, and to visualize individual centromere regions separately. From these data, we determine protein distances within the complex using Bayesian inference, establish the stoichiometry of each POI for individual chromosomes and, consequently, build an in situ kinetochore model for S.pombe with so-far unprecedented precision. Being able to quantify the kinetochore proteins within the full in situ kinetochore structure, we provide valuable new insights in the S.pombe kinetochore architecture.

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High-Throughput Flow Cytometry Combined with Genetic Analysis Brings New Insights into the Understanding of Chromatin Regulation of Cellular Quiescence

Cited by 15 publications

References 38 publications

Is There a Histone Code for Cellular Quiescence?

Is There a Histone Code for Cellular Quiescence?

Unraveling the kinetochore nanostructure in Schizosaccharomyces pombe using multi-color SMLM imaging

Unraveling the kinetochore nanostructure in Schizosaccharomyces pombe using multi-color single-molecule localization microscopy

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