Nucleosome allostery in pioneer transcription factor binding

Tan, Cheng; Takada, Shoji

doi:10.1073/pnas.2005500117

Cited by 81 publications

(92 citation statements)

References 67 publications

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“…Our findings on nucleosomes unraveling by NF-κB is significant in that, coupled with the unravelling effect observed, binding to condensed chromatin is a trait reserved for pioneer transcription factors(Cirillo et al, 2002; Tan and Takada, 2020; Zaret, 2020). While NF-κB is not currently categorized as a pioneer factor, the results in this study suggest that it is capable of acting as one.…”

Section: Discussionmentioning

confidence: 68%

Transcription Factor NF-κB Unravels Nucleosomes

Stormberg

Filliaux

Baughman

et al. 2021

Preprint

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NF-κB is a transcription factor responsible for activating hundreds of genes in mammalian organisms. To accomplish its function, NF-κB must interact with DNA occupied by nucleosomes, but how this interaction occurs is unclear. Here we used Atomic Force Microscopy to characterize complexes of NF-κB with nucleosomes assembled on different DNA templates. The assembly of NF-κB-nucleosome complexes leads to a substantial decrease of DNA wrapping efficiency. Mapping of the nucleosomes did not reveal displacement of under-wrapped nucleosomes from their original position, suggesting that unravelling involves dissociation of one or both flanks of the nucleosomes. We discovered two binding modes of NF-κB associated with nucleosome unraveling - NF-κB bound to the nucleosome core and to the DNA flanks and propose models explaining the interaction of NF-κB with the nucleosome. We speculate that NF-κB can function as a pioneer factor enhancing its ability to facilitate rapid transcriptional response to cell stress.

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Section: Discussionmentioning

confidence: 68%

Transcription Factor NF-κB Unravels Nucleosomes

Stormberg

Filliaux

Baughman

et al. 2021

Preprint

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“…Sox19b protein is highly abundant in the early embryo 9 , and it is possible that high frequency of non-specific Sox19b–DNA interactions may, for instance, increase nucleosome turnover and facilitate Pou5f3 access to chromatin. It is also possible that Sox19b facilitates Pou5f3 binding at the distance, by allosteric mechanism which was recently proposed for Sox2 66 .…”

Section: Discussionmentioning

confidence: 92%

Pluripotency factors determine gene expression repertoire at zygotic genome activation

Gao

Veil

Rosenblatt

et al. 2020

Preprint

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PouV and SoxB1 family transcription factors (TFs) have emerged as master regulators of cell fate transitions. To investigate the genetic interactions between Pou5f3 and Sox19b in zebrafish embryos passing through Zygotic Genome Activation (ZGA), we combined time-resolved mutant transcription analysis using the novel tool RNA-sense, chromatin state and phenotypic assays. We distinguish four types of embryonic enhancers, differentially regulated by the two TFs. Pou5f3 is critical for activation of enhancer types 1 and 2, which are responsible for transcription of genes involved in gastrulation and ventral genes. Pou5f3 or Sox19b prevent premature activation of type 3 and 4 enhancers, which are responsible for transcription of organogenesis regulators, differentiation factors and dorsal genes. We also show that the balance between Sox19b and Pou5f3 is important for bulk ZGA timing. Our results uncover how independent activities of maternal Pou5f3 and Sox19b add up or antagonize to determine the early gene expression repertoire. Bullet points:• Pou5f3 and Sox19b bind independently to DNA • Disbalance between maternal Pou5f3 and Sox19b delays ZGA • Pou5f3 suppresses premature transcription of neural patterning genes, activated by SoxB1 factors • Pou5f3 and Sox19b synergistically suppress premature transcription of a wide range of differentiation genes • Pou5f3 and Sox19b restrict the dorsal organizer

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“…In this study, as the physical interaction part of

, we used a well-tested coarse-grained model for proteins and DNAs, which have been extensively used in many recent studies, including simulations for nucleosomes ( Niina et al, 2017 ; Brandani et al, 2018 ; Tan and Takada, 2020 ). Briefly, proteins are represented by chains of beads, each of which represents an amino acid.…”

Section: Methodsmentioning

confidence: 99%

Case Report: Bayesian Statistical Inference of Experimental Parameters via Biomolecular Simulations: Atomic Force Microscopy

Fuchigami

Niina

Takada

2021

Front. Mol. Biosci.

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The atomic force microscopy (AFM) is a powerful tool for imaging structures of molecules bound on surfaces. To gain high-resolution structural information, one often superimposes structure models on the measured images. Motivated by high flexibility of biomolecules, we previously developed a flexible-fitting molecular dynamics (MD) method that allows protein structural changes upon superimposing. Since the AFM image largely depends on the AFM probe tip geometry, the fitting process requires accurate estimation of the parameters related to the tip geometry. Here, we performed a Bayesian statistical inference to estimate a tip radius of the AFM probe from a given AFM image via flexible-fitting molecular dynamics (MD) simulations. We first sampled conformations of the nucleosome that fit well the reference AFM image by the flexible-fitting with various tip radii. We then estimated an optimal tip parameter by maximizing the conditional probability density of the AFM image produced from the fitted structure.

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Nucleosome allostery in pioneer transcription factor binding

Cited by 81 publications

References 67 publications

Transcription Factor NF-κB Unravels Nucleosomes

Transcription Factor NF-κB Unravels Nucleosomes

Pluripotency factors determine gene expression repertoire at zygotic genome activation

Case Report: Bayesian Statistical Inference of Experimental Parameters via Biomolecular Simulations: Atomic Force Microscopy

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