Chromatin Binding Regulates Phase Behavior and Morphology of Condensates Formed by Prion-like Domains.

Anushka Supakar, Richoo B Davis, Subhadip Biswas, Sean Yang, Davit A Potoyan, Priya R Banerjee

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Article in Journal of molecular biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

6 authors.

Anushka SupakarDepartment of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY 14260, USA.

Richoo B DavisDepartment of Physics, The State University of New York at Buffalo, Buffalo, NY 14260, USA.

Subhadip BiswasDepartment of Chemistry, Iowa State University, Ames, IA 50011, USA.

Sean YangDepartment of Chemistry, Iowa State University, Ames, IA 50011, USA.

Davit A PotoyanDepartment of Chemistry, Iowa State University, Ames, IA 50011, USA. Electronic address: potoyan@iastate.edu.

Priya R BanerjeeDepartment of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY 14260, USA; Department of Physics, The State University of New York at Buffalo, Buffalo, NY 14260, USA. Electronic address: prbanerj@buffalo.edu.

Funding

Multi-scale computational investigation of functions and mechanisms of protein-RNA phase separation.R35GM138243 · NIGMS · IOWA STATE UNIVERSITY · PI Davit POTOYAN · 2020 to 2026

$2.4M

NIGMS NIH HHS R35 GM138243

6 · The paper itself

Abstract

Many transcription factors (TFs) contain intrinsically disordered regions (IDRs) and are thought to form biomolecular condensates in the cell nucleus. These proteins can be conceptualized as block co-polymers, with the IDRs driving both homotypic and heterotypic protein-protein interactions and the DNA-binding domain (DBD) mediating heterotypic interactions with chromatin. While in vitro studies have predominantly reported micron-scale, spherical condensates in the absence of chromatin, TF condensates in live cells exhibit strikingly different behavior, adopting diverse, nanoscale, often aspherical morphologies and displaying sub-diffusive dynamics. Here, using engineered fusion proteins with tunable IDR-DBD architectures, we show that this distinct phase behavior can arise from TF-chromatin interactions. Specifically, we fused the prion-like domain (PLD) of the SS18 subunit from the mammalian SWI/SNF complex, a domain known to drive homotypic phase separation, to the DBD of the pioneer factor FOXA1. While SS18

Indexed as

ChromatinPrionsCell NucleusCell SurvivalComputer SimulationDNAHEK293 CellsHepatocyte Nuclear Factor 3-alphaHumansIntrinsically Disordered ProteinsModels, MolecularProtein ConformationProto-Oncogene ProteinsRepressor ProteinsChromatinDNAHepatocyte Nuclear Factor 3-alphaIntrinsically Disordered ProteinsPrionsProto-Oncogene ProteinsRepressor ProteinsDNA-binding proteinsintrinsically disordered proteinsnucleoprotein condensatestranscription factorviscoelastic condensates

Identifiers

PMID40848932

DOI10.1016/j.jmb.2025.169398

PMCPMC13504605

What OpenQuestion holds

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.