Nanog organizes transcription bodies

Kuznetsova, Ksenia; Chabot, Noémie M.; Ugolini, Martino; Wu, Edlyn; Lalit, Manan; Oda, Hirotaka; Sato, Yuko; Kimura, Hiroshi; Jug, Florian; Vastenhouw, Nadine L.

doi:10.1016/j.cub.2022.11.015

Cited by 13 publications

(20 citation statements)

References 68 publications

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“…Quantification of Nanog fluorescence revealed that these foci increased the local Nanog concentration 2.5- to 4-fold (fig. S1B), which is consistent with the occurrence of transcription factor and coactivator foci or hubs observed during embryogenesis and in cultured cells ( 19 – 28 ). We also observed that Nanog foci were associated with Pol II elongation, which is consistent with previous observations ( 16 , 17 , 22 , 25 , 27 – 30 ).…”

Section: Nanog Forms Dna-bound Foci Associated With Pol II Recruitmen...supporting

confidence: 87%

“…We used ChromExM to characterize the nanoscale organization of the pioneer factor Nanog and RNA Pol II as they activate transcription during genome activation. Although previous studies have shown how pioneer factors direct chromatin opening in vitro ( 51 , 52 ) and organize into hubs in vivo ( 19 , 28 , 53 , 54 ), the nanoscale organization of such hubs has remained unclear. ChromExM revealed that Pol II shows three types of organization during genome activation and is intimately associated with Nanog (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…In maternal-zygotic Nanog mutants (MZ nanog −/− ) ( 8 ), Pol II foci are lost and overall levels are reduced at the 256-cell stage, which confirms Nanog’s role in Pol II recruitment and transcriptional activation (fig. S1, D and E) ( 28 ). Mutating the Nanog homeodomain to prevent DNA binding abolished Nanog foci, which indicates that they form in a DNA-binding–dependent manner rather than strictly through protein–protein interactions (fig.…”

Section: Nanog Forms Dna-bound Foci Associated With Pol II Recruitmen...mentioning

confidence: 99%

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Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin

Pownall

Miao

Vejnar

et al. 2023

Science

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Nanoscale chromatin organization regulates gene expression. Although chromatin is notably reprogrammed during zygotic genome activation (ZGA), the organization of chromatin regulatory factors during this universal process remains unclear. In this work, we developed chromatin expansion microscopy (ChromExM) to visualize chromatin, transcription, and transcription factors in vivo. ChromExM of embryos during ZGA revealed how the pioneer factor Nanog interacts with nucleosomes and RNA polymerase II (Pol II), providing direct visualization of transcriptional elongation as string-like nanostructures. Blocking elongation led to more Pol II particles clustered around Nanog, with Pol II stalled at promoters and Nanog-bound enhancers. This led to a new model termed "kiss and kick", in which enhancer–promoter contacts are transient and released by transcriptional elongation. Our results demonstrate that ChromExM is broadly applicable to study nanoscale nuclear organization.

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Section: Nanog Forms Dna-bound Foci Associated With Pol II Recruitmen...supporting

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Section: Nanog Forms Dna-bound Foci Associated With Pol II Recruitmen...mentioning

confidence: 99%

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Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin

Pownall

Miao

Vejnar

et al. 2023

Science

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“…Transcription occurs in bursts, and bursting frequencies are regulated by developmental enhancers (Fukaya et al, 2016; Suter et al, 2011). Transcription factors occupy their binding sites only for short residence times (Chen et al, 2014; Dufourt et al, 2018; Huang et al, 2021; Kuznetsova et al, 2022). An increase of the residence time of transcriptional activators on enhancers was shown to increase transcription bursting frequency in yeast and mammalian cell culture (Donovan et al, 2019; Popp et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

Activator-blocker model of transcriptional regulation by pioneer-like factors

Riesle

Gao

Rosenblatt

et al. 2023

Preprint

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SummaryZygotic genome activation (ZGA) in the development of flies, fish, frogs and mammals depends on pioneer-like transcription factors (TFs). Those TFs create open chromatin regions, promote histone acetylation on enhancers, and activate transcription. Here, we use the panel of single, double and triple mutants for zebrafish genome activators Pou5f3, Sox19b and Nanog, multi-omics and mathematical modeling to investigate the combinatorial mechanisms of genome activation. We show that Pou5f3 and Nanog act differently on synergistic and antagonistic enhancer types. Pou5f3 and Nanog both bind as pioneers on synergistic enhancers, promote histone acetylation and activate transcription. Antagonistic enhancers are activated by pioneer binding of one of these factors. The other TF binds as non-pioneer, competes with the activator and blocks all its effects, partially or completely. This activator-blocker mechanism mutually restricts widespread transcriptional activation by Pou5f3 and Nanog and prevents premature expression of late developmental regulators in the early embryo.Pou5f3 and Nanog compete as pioneer-like and non-pioneer factors on common genomic sites.Pioneer-like binding activates transcription, non-pioneer binding blocks transcription.Competition between Pou5f3 and Nanog establishes the order of gene expression.

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“…These likely represent the priming of miR-430 transcription sites. The miR-430 locus is the first zygotically transcribed region in the zebrafish genome and can be detected as early as the 64 cell cycle [43][44][45] .…”

Section: Gears Illuminate the Native Behaviour Of Nanog During The Ea...mentioning

confidence: 99%

Genetically encoded affinity reagents (GEARs): A toolkit for visualizing and manipulating endogenous protein functionin vivo

Boswell,

Hoppe,

Sherrard

et al. 2023

Preprint

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Probing endogenous protein localization and function in vivo remains challenging due to laborious gene targeting and monofunctional alleles. Here, we develop a multifunctional, universal, and adaptable toolkit based on genetically encoded affinity reagents (GEARs). GEARs use nanobodies and single chain variable fragments (scFv), which recognize small epitopes, enabling fluorescent visualization and selective degradation of protein targets in vivo. Furthermore, we delineate a CRISPR/Cas9-based epitope tagging pipeline to demonstrate its utility for producing knock-in alleles that have broad multifunctionality. We use GEARs to examine the native behaviour of the pioneer transcription factor Nanog and the planar cell polarity protein Vangl2 during early zebrafish development. Together, this toolkit provides a versatile system for probing and perturbing endogenous protein function while circumventing challenges associated with conventional gene targeting and is broadly available to the model organism community.

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Nanog organizes transcription bodies

Cited by 13 publications

References 68 publications

Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin

Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin

Activator-blocker model of transcriptional regulation by pioneer-like factors

Genetically encoded affinity reagents (GEARs): A toolkit for visualizing and manipulating endogenous protein functionin vivo

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