Mitotic chromosome binding predicts transcription factor properties in interphase

Raccaud, Mahé; Friman, Elias T; Alber, Andrea Brigitta; Agarwal, Harsha; Deluz, Cédric; Kühn, Timo; Gebhardt, Christof; Suter, David M.

doi:10.1038/s41467-019-08417-5

Cited by 89 publications

(113 citation statements)

References 84 publications

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“…Cells were cultured and prepared as described in 25 . Cells with stable integration of Halo-CDX2 under doxycycline-induced expression control (kind gift from the lab of David Suter, EFPL, Lausanne, Switzerland) were seeded one day before the measurement on a Delta-T glass bottom dish (Bioptechs, Pennsylvania, USA).…”

Section: Cell Culture and Preparationmentioning

confidence: 99%

Inferring quantity and qualities of superimposed reaction rates in single molecule survival time distributions

Reisser

Hettich

Kühn

et al. 2019

Preprint

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Actions of molecular species, for example binding of transcription factors to chromatin, are intrinsically stochastic and may comprise several mutually exclusive pathways. Inverse Laplace transformation in principle resolves the rate constants and frequencies of superimposed reaction processes, however current approaches are challenged by single molecule fluorescence time series prone to photobleaching. Here, we present a genuine rate identification method (GRID) that infers the quantity, rates and frequencies of dissociation processes from single molecule fluorescence survival time distributions using a dense grid of possible decay rates. In particular, GRID is able to resolve broad clusters of rate constants not accessible to common models of one to three exponential decay rates. We validate GRID by simulations and apply it to the problem of in-vivo TF-DNA dissociation, which recently gained interest due to novel single molecule imaging technologies. We consider dissociation of the transcription factor CDX2 from chromatin. GRID resolves distinct, decay rates and identifies residence time classes overlooked by other methods. We confirm that such sparsely distributed decay rates are compatible with common models of TF sliding on DNA.

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Section: Cell Culture and Preparationmentioning

confidence: 99%

Inferring quantity and qualities of superimposed reaction rates in single molecule survival time distributions

Reisser

Hettich

Kühn

et al. 2019

Preprint

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“…We then aimed to identify the molecular mechanisms by which small and transient endogenous fluctuations of SOX2 and OCT4 result in major biases in differentiation potential. As SOX2 and OCT4 were shown to regulate chromatin accessibility (King & Klose, 2017;Raccaud et al, 2019), we reasoned that small changes in their expression level could prime cells for different fates by altering the chromatin accessibility landscape. We thus performed ATAC-seq in G1-sorted SHOH, SHOL, SLOH and SLOL cells.…”

Section: Oct4-high Cells Open Differentiation Enhancersmentioning

confidence: 99%

Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions

Strebinger

Friman

Deluz

et al. 2018

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SOX2 and OCT4 are pioneer transcription factors playing a key role in embryonic stem (ES) cell self-renewal and differentiation. However, how temporal fluctuations in their expression levels bias lineage commitment is unknown. Here we generated knock-in reporter fusion ES cell lines allowing to monitor endogenous SOX2 and OCT4 protein fluctuations in living cells and to determine their impact on mesendodermal and neuroectodermal commitment. We found that small differences in SOX2 and OCT4 levels impact cell fate commitment in G1 but not in S phase. Elevated SOX2 levels modestly increased neuroectodermal commitment and decreased mesendodermal commitment upon directed differentiation. In contrast, elevated OCT4 levels strongly biased ES cell towards both neuroectodermal and mesendodermal fates. Using ATAC-seq on ES cells gated for different endogenous SOX2 and OCT4 levels, we found that high OCT4 levels increased chromatin accessibility at differentiation-associated enhancers. This suggests that small endogenous fluctuations of pioneer transcription factors can bias cell fate decisions by concentration-dependent priming of differentiation-associated enhancers. KeywordsEmbryonic stem cells/Endogenous fluctuations/SOX2/OCT4/Differentiation

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“…Proliferating cells show a global downregulation of transcription during mitosis. This results from the 2 combination of three main processes: 1) nuclear envelope breakdown leading to an increase of the volume 3 that transcription factors (TFs) and the RNA polymerases II (RNAPII) can explore and therefore 4 a decrease of their local concentration around gene promoters; 2) major reorganization of chromatin 5 architecture characterized by chromosome condensation, repositioning of nucleosomes in some regulatory 6 regions, loss of long-range interaction between enhancers and promoters and disassembling of topological 7 associated domains (TADs); and, 3) TF-DNA binding inactivation through postranscriptionally regulated 8 phosphorylation. As a consequence, most TFs and the RNAPII are evicted from mitotic chromosomes 9 and RNA synthesis is drastically reduced [1].…”

Section: Introductionmentioning

confidence: 99%

Regulation of transcription reactivation dynamics exiting mitosis

Sarnataro¹,

Riba²,

Molina³

2020

Preprint

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Proliferating cells experience a global reduction of transcription during mitosis, yet their cell identity is maintained and regulatory information is propagated from mother to daughter cells. Mitotic bookmarking by transcription factors has been proposed as a potential mechanism to ensure the reactivation of transcription at the proper set of genes exiting mitosis. Recently, mitotic transcription and waves of transcription reactivation have been observed in synchronized populations of human hepatoma cells.However, the study did not consider that mitotic-arrested cell populations progressively desynchronize leading to measurements of gene expression on a mixture of cells at different internal cell-cycle times.Moreover, it is not well understood yet what is the precise role of mitotic bookmarking on mitotic transcription as well as on the transcription reactivation waves. Ultimately, the core gene regulatory network driving the precise transcription reactivation dynamics remains to be identified. To address these questions, we developed a mathematical model to correct for the progressive desynchronization of cells and estimate gene expression dynamics with respect to a cell-cycle pseudotime. Furthermore, we used a multiple linear regression model to infer transcription factor activity dynamics. Our analysis allows us to characterize waves of transcription factor activities exiting mitosis and identify a core gene regulatory network responsible of the transcription reactivation dynamics. Moreover, we identified more than 60 transcription factors that are highly active during mitosis and represent new candidates of mitotic bookmarking factors which could represent relevant therapeutic targets to control cell proliferation.

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Mitotic chromosome binding predicts transcription factor properties in interphase

Cited by 89 publications

References 84 publications

Inferring quantity and qualities of superimposed reaction rates in single molecule survival time distributions

Inferring quantity and qualities of superimposed reaction rates in single molecule survival time distributions

Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions

Regulation of transcription reactivation dynamics exiting mitosis

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