Dataset Information

Selective RNA sequestration in P-bodies regulates cell identity

ABSTRACT: Post-transcriptional regulation is pivotal in guiding the gene expression programs that instruct cell fate decisions. Recent studies emphasize the significance of biomolecular condensates in modulating gene expression through RNA processing and translational control. However, the functional roles of RNA condensates in the context of cell fate specification are unknown. In this study, we profiled the coding and non-coding transcriptome within intact biomolecular condensates known as P-bodies in diverse developmental contexts and vertebrate species. Our analyses revealed the conserved, cell type-specific sequestration of RNAs encoding key cell fate specifiers. Notably, P-body contents did not directly reflect gene expression profiles for a given cell type, but rather were enriched for transcripts characteristic of the preceding developmental stage, which are translationally suppressed and stored within P-bodies. We demonstrate that the forced degradation of P-bodies stimulates the translation of transcripts encoding fate-instructive factors, ultimately re-activating a totipotency transcriptional program in human and mouse pluripotent cells. Mechanistically, microRNAs (miRNAs) facilitate the sequestration of specific RNAs into P-bodies in a context-dependent manner. Accordingly, perturbing AGO2, alternative polyadenylation, and miRNA function profoundly reshapes the RNA content of P-bodies and alters cell fate. Furthermore, we show that adding a miRNA target sequence is sufficient to redirect transcripts to P-bodies and influence stem cell self-renewal. Collectively, our findings establish a direct link between biomolecular condensates and cell fate decisions across vertebrate species.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Embryonic Stem Cell

SUBMITTER: Alicia Richards

LAB HEAD: DanielleL Swaney

PROVIDER: PXD058827 | Pride | 2025-05-07

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	20240924_172432_exLewis006283.sne	Other
	20240924_172432_exLewis006283_Report.tsv	Tabular
	JBB1_GPF_092424.tsv	Tabular
	checksum.txt	Txt
	exLewis006274.raw	Raw

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Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus MPro inhibitors with potent in vivo efficacy.

Detomasi Tyler C TC Degotte Gilles G Huang Sijie S Suryawanshi Rahul K RK Diallo Amy A Lizzadro Luca L Zapatero-Belinchón Francisco J FJ Taha Taha Y TY Li Jiapeng J Richards Alicia L AL Hantz Eric R ER Alam Zain Z Montano Mauricio M McCavitt-Malvido Maria M Gumpena Rajesh R Partridge James R JR Correy Galen J GJ Matsui Yusuke Y Charvat Annemarie F AF Glenn Isabella S IS Rosecrans Julia J Revalde Jezrael L JL Anderson Dashiell D Hultquist Judd F JF Arkin Michelle R MR Neitz R Jeffrey RJ Swaney Danielle L DL Krogan Nevan J NJ Shoichet Brian K BK Verba Kliment A KA Ott Melanie M Renslo Adam R AR Craik Charles S CS

Science advances 20250423 17

The main protease (MPro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a validated drug target. Starting with a lead-like dihydrouracil chemotype identified in a large-library docking campaign, we improved MPro inhibition >1000-fold by engaging additional MPro subsites and using a latent electrophile to engage Cys145. Advanced leads from this series show pan-coronavirus antiviral activity, low clearance in mice, and for AVI-4773 ...[more]

PMID: 40267184

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Project description:The cellular stress response plays a vital role in regulating homeostasis by modulating cell survival and death. Stress granules (referred to as SGs) are cytoplasmic compartments that allow cells to survive various stressors. Defects in SG assembly and disassembly have been found to play important roles in neurodegenerative diseases, antiviral responses and cancer1–5. Inflammasomes are multi-protein heteromeric complexes that sense intracellular pathogen- and damage-associated molecular patterns and assemble into cytosolic compartments called ASC specks to facilitate caspase-1 (CASP1) activation. This activation of inflammasomes induces secretion of the leaderless proinflammatory cytokines IL-1β and IL-18 and also drives cell fate towards pyroptosis, a form of programmed inflammatory cell death that plays major role in health and disease6–12. Cellular stress sensing can trigger both SGs and inflammasomes; however, they drive contrasting cell fate decisions during stress conditions. Crosstalk between SGs and inflammasomes to decide cell fate has not been well studied. Here we show that the induction of SGs specifically inhibits NLRP3 inflammasome activation, ASC speck formation and pyroptosis. The SG protein DDX3X interacts with NLRP3 to drive inflammasome activation in the absence of SGs. Assembly of SGs leads to the sequestration of DDX3X to inhibit NLRP3 inflammasome function. SGs and the NLRP3 inflammasome compete for DDX3X molecules to coordinate the activation of innate responses and subsequent cell fate decisions under stress conditions. Induction of SGs or loss of DDX3X in the myeloid compartment leads to decreased production of inflammasome-dependent cytokines in vivo. Our findings suggest that macrophages utilize DDX3X availability to interpret stress signals and choose between pro-survival SGs and pyroptotic ASC specks. Together, our data show the role of DDX3X in driving NLRP3 inflammasome and SG assembly, informing a new rheostat-like mechanistic paradigm for regulating live or die cell fate decisions under stress conditions.

Project description:Biomolecular condensates are implicated in many cellular processes, and are thought to create subcellular microenvironments that regulate specific biochemical activities. For example, in vitro experiments suggest that condensates enable non-stoichiometric enrichment of small molecules within condensates. However, probing the microenvironments of condensates in cells is a major challenge, because tools to selectively manipulate specific condensates in living cells are limited. Here we developed a non-natural micropeptide (i.e., the “killswitch”) and a Nanobody-based recruitment system as a universal approach to probe endogenous condensates, and demonstrate direct links between condensate microenvironments and function in cells. The killswitch is a hydrophobic, aromatic-rich sequence with an ability to self-associate, and no homology to human proteins. When recruited to endogenous and disease-specific condensates in human cells, the killswitch arrested the dynamics of the condensate-forming proteins, which led to predicted and unexpected effects. Targeting the killswitch to the nucleolar protein NPM1 altered nucleolar composition, and inhibited the dynamics of a ribosomal protein within nucleoli. Targeting the killswitch to fusion oncoprotein condensates inhibited the dynamics of effector proteins in the condensates, altered condensate composition, and inhibited proliferation of condensate-driven leukemia cells. In adenoviral nuclear condensates, the killswitch inhibited partitioning of capsid protein into condensates, and suppressed viral particle assembly. The results suggest that the microenvironment within cellular condensates has an essential contribution to non-stoichiometric enrichment and the dynamics of effector proteins. The killswitch is a widely applicable tool to alter the material properties of endogenous condensates, and as a consequence, to probe functions of condensates linked to diverse physiological and pathological processes in living systems.

Dataset Information

Selective RNA sequestration in P-bodies regulates cell identity

Dataset's files

Publications

Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus M<sup>Pro</sup> inhibitors with potent in vivo efficacy.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

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Dataset Information

Selective RNA sequestration in P-bodies regulates cell identity

Dataset's files

Publications

Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus M&lt;sup&gt;Pro&lt;/sup&gt; inhibitors with potent in vivo efficacy.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus M<sup>Pro</sup> inhibitors with potent in vivo efficacy.