About

Clifford P. Brangwynne is a Principal Investigator at Princeton University, focusing on the field of soft living matter. His research involves understanding the physical principles underlying the organization and behavior of biological systems, particularly at the cellular and molecular levels. His work contributes to the broader understanding of biomolecular condensates, phase separation, and the biophysical mechanisms that govern cellular organization. Brangwynne's background includes extensive research in molecular biology and biophysics, and he has made significant contributions to elucidating how phase separation influences cellular function and disease. His laboratory employs interdisciplinary approaches combining biology, physics, and engineering to explore the emergent properties of biological materials, aiming to uncover fundamental principles that can inform the development of novel therapeutic strategies and biomaterials.

Research topics

• Cell biology
• Biology
• Biophysics
• Chemistry
• Physics
• Statistical physics
• Nanotechnology
• Astrobiology
• Chemical physics
• Environmental science
• Genetics
• Materials science

Selected publications

• Metabolism of Epigenetic Ribonucleosides Leads to Nucleolar Stress and Cytotoxicity

  ACS Chemical Biology · 2026-03-06

  articleOpen access

  Post-transcriptional RNA modifications are ubiquitous in biology, but the fate of epigenetic ribonucleotides after RNA turnover and the consequences of their metabolism and misincorporation into nucleic acids are largely unknown. Here, we explore epigenetic ribonucleoside metabolism in human cells by studying effects on cell growth, quantifying RNA misincorporation and identifying metabolic regulators, and exploring phenotypes associated with cytotoxicity. We find that bulky N6-modified adenosines (i.e., i6A) exhibit high levels of cytotoxicity and RNA misincorporation, whereas cells dramatically restrict the misincorporation of small N6-modified adenosines (i.e., m6A), partly through sanitization by enzymatic deamination, consistent with a recent report. Epigenetic ribopyrimidines also exhibit cytotoxicity, dependent on nucleoside kinase UCK2, but only at much higher concentrations than ribopurines. We further characterize the effects of cytotoxic ribonucleoside metabolism on nucleolar morphology and protein translation. Taken together, our work provides new insights into the metabolism of epigenetic ribonucleosides and mechanisms underlying their cytotoxicity to cells.

  PublisherDOI

• Kinase KEY1 controls pyrenoid condensate size throughout the cell cycle by disrupting phase separation interactions

  Nature Cell Biology · 2026-03-17

  articleOpen access

  Abstract Biomolecular condensates spatially organize cellular functions, but the regulation of their size, number, dissolution and re-condensation is poorly understood. The pyrenoid, an algal biomolecular condensate that mediates one-third of global CO 2 fixation, typically exists as one large condensate per chloroplast, but during cell division it transiently dissolves and reconfigures into multiple smaller condensates. Here, we identify a kinase, KEY1, in the model alga Chlamydomonas reinhardtii that regulates pyrenoid condensate size and number dynamics throughout the cell cycle and is necessary for normal pyrenoid function and growth. Unlike the wild type, key1 mutant cells have multiple smaller condensates throughout the cell cycle that fail to dissolve during cell division. We show that KEY1 localizes to the condensates and promotes their dissolution by disrupting interactions between their core constituents, the CO 2 -fixing enzyme Rubisco and its linker protein EPYC1, through EPYC1 phosphorylation. We develop a biophysical model that recapitulates KEY1-mediated condensate size and number regulation and suggests a mechanism for controlling condensate position. These data provide a foundation for the mechanistic understanding of the regulation of size, number, position and dissolution in pyrenoids and other biomolecular condensates.

  PublisherDOI

• Enhanced GPP synthesis by Erg20p-peptide fusions and biomolecular condensates boosts monoterpene production in yeast

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-30

  article

  Abstract Monoterpenes are a diverse class of natural products with broad industrial and pharmaceutical applications. While there is great interest in transitioning their production from chemical synthesis and natural source extraction to yeast bioprocesses, this approach remains limited by the dual functionality of the endogenous farnesyl diphosphate synthase Erg20p, which produces the monoterpene precursor geranyl diphosphate (GPP) but favors its subsequent conversion to farnesyl diphosphate (FPP). To address this limitation, we recruited Erg20p and monoterpene synthases into synthetic membraneless organelles, improving production. In doing so, we found that short C-terminal peptide fusions used for recruitment also significantly enhance GPP synthase activity relative to FPP synthase activity. The combined effects of metabolic spatial organization and GPP synthase activity enhancement significantly boost production of different monoterpenes, including geraniol titers exceeding 4 g/L. The strategies presented here can be readily integrated with other traditional metabolic engineering approaches to build yeast strains with high levels of monoterpene production.

  PublisherDOI

• Ribosome biogenesis bottlenecks reveal vulnerabilities in cancer

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-21

  articleOpen accessSenior authorCorresponding

  Summary Cell growth requires elevated protein synthesis, which depends on the production of ribosomes. Ribosome biogenesis is a complex, multi-step pathway in which newly transcribed precursor ribosomal RNA (rRNA) undergoes coordinated processing and assembly in the nucleolus to produce the small and large ribosomal subunits (SSU and LSU). 1–3 Oncogene activation stimulates rRNA transcription and processing, giving rise to enlarged nucleoli that produce thousands of ribosomes every minute. 4,5 However, efficient ribosome production requires tight coordination across numerous maturation steps, and it remains unclear if elevated rDNA transcription is proportionally converted into mature ribosomes, or whether imperfect coordination constrains the output yield. Here, we quantify pre-rRNA transcription (input) and compare it with newly-assembled cytoplasmic ribosomes (output), revealing that oncogene activation reduces the efficiency of ribosome production. Using a quantitative pulse-chase sequencing approach with mathematical modeling to resolve rRNA maturation kinetics, we found that oncogene activation creates late-stage processing bottlenecks, characterized by delayed precursor maturation and increased degradation. Perturbation of late-stage ribosome biogenesis factors preferentially impaired oncogene-driven cell growth, and limited tumor growth in mouse models, suggesting that these bottlenecks represent selective vulnerabilities in cancer, created by imbalanced biosynthetic flux. Together, these findings reveal that oncogene-driven ribosome production is imperfectly coordinated across maturation steps, and suggest that capacity limits in multi-step assembly pathways may be therapeutically exploitable in cancer and other diseases.

  PublisherOA PDFDOI

• BPS2026 – Condensate-driven chromatin organization via elastocapillary interactions

  Biophysical Journal · 2026-02-01

  articleSenior author
  PublisherDOI

• Condensate-driven chromatin organization via elastocapillary interactions

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-15 · 3 citations

  preprintOpen accessSenior authorCorresponding

  Summary Biomolecular condensates are ubiquitous structures found throughout eukaryotic cells, with nuclear condensates playing a key role in the mesoscale organization and functionality of the genome 1,2 . Protein- and RNA-rich liquid-like condensates form through phase separation on and around chromatin, driving diverse condensate morphologies with varying sphericity and intra-condensate chromatin density 3,4 . However, a unifying set of physical principles underlying these varied interactions and their implications for chromatin organization remains elusive. Here, we develop and experimentally validate a mesoscopic model that bridges the physics of phase separation and chromatin mechanics. Specifically, by integrating computational modeling with experiments using two canonical condensate proteins, the heterochromatin protein HP1α, and the euchromatin protein BRD4, we demonstrate that wetting properties and chromatin stiffness shape condensate morphology, while condensates remodel chromatin mechanics and organization. This two-way interplay is governed by elastocapillarity—the deformation of chromatin by condensate interfacial tension — and resolves discrepancies in nuclear condensate behavior, with emergent behaviors that deviate from the simplest liquid-liquid phase separation (LLPS) models 5–8 . Our findings underscore that nuclear condensates and chromatin cannot be studied in isolation, as they are fundamentally interdependent, impacted by biomolecularly-defined wetting properties, with implications for genome organization, transcriptional regulation, and epigenetic control in diverse phenotypes, including cancer 2,9,10 . Beyond the nucleus, the methodologies we present offer a generalizable platform for exploring multiphase, multicomponent soft matter systems across a broad range of biological and synthetic contexts 11 .

  PublisherOA PDFDOI

• Protocol for the isolation, culture, and transfection of squid primary cells

  STAR Protocols · 2025-08-06 · 1 citations

  articleOpen accessSenior authorCorresponding

  We present a protocol for the isolation, culture, and transfection of squid primary cells from various tissues and ages by including steps for squid dissection, cell isolation, maintenance in culture, and expression of exogenous genes. We also highlight life-stage tractability in Euprymna berryi squids for future aging studies. This protocol enables molecular- and cellular-level investigations into processes specific to squids, including their complex behaviors, rapid color change mechanisms, and RNA editing capabilities, with broader implications in basic cell physiology. • Procedures for isolating primary cells from various tissues from any age of the squid • Step-by-step instructions for maintaining squid cells in culture • Protocol for transfecting primary squid cells with mRNAs • Steps for visualizing expression with fixed- or live-cell imaging Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. We present a protocol for the isolation, culture, and transfection of squid primary cells from various tissues and ages by including steps for squid dissection, cell isolation, maintenance in culture, and expression of exogenous genes. We also highlight life-stage tractability in Euprymna berryi squids for future aging studies. This protocol enables molecular- and cellular-level investigations into processes specific to squids, including their complex behaviors, rapid color change mechanisms, and RNA editing capabilities, with broader implications in basic cell physiology.

  PublisherDOI

• Metabolism of epigenetic ribonucleosides leads to nucleolar stress and cytotoxicity

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-13

  preprint

  ABSTRACT Post-transcriptional RNA modifications are ubiquitous in biology, but the fate of epigenetic ribonucleotides after RNA turnover and the consequences of their metabolism and misincorporation into nucleic acids are largely unknown. Here we explore the metabolism of epigenetic ribonucleosides in human cells by studying effects on cell growth, quantifying misincorporation into cellular RNAs and identifying metabolic regulators, and exploring phenotypes associated with cytotoxicity. We find that bulky N 6 -modified adenosines (i.e. i 6 A) exhibit high levels of cytotoxicity and RNA misincorporation, whereas cells dramatically restrict the misincorporation of small N 6 -modified adenosines (i.e. m 6 A), partly through sanitization by enzymatic deamination. Epigenetic ribopyrimidines also exhibit cytotoxicity, mediated primarily by nucleoside kinase UCK2, but only at much higher concentrations than ribopurines. We further characterize the effects of cytotoxic ribonucleoside metabolism on nucleolar morphology and protein translation. Taken together, our work provides new insights into the metabolism of epigenetic ribonucleosides and mechanisms underlying their cytotoxicity to cells.

  PublisherDOI

• Sequestration of ribosome biogenesis factors in HSV-1 nuclear aggregates revealed by spatially resolved thermal profiling

  Science Advances · 2025-06-27 · 4 citations

  articleOpen access

  Viruses exploit host cell reliance on compartmentalization to facilitate their replication. Herpes simplex virus type 1 (HSV-1) modulates the subcellular localization of host proteins to suppress immune activation, license viral gene expression, and achieve translational shutoff. To spatially resolve dynamic protein-protein interaction (PPI) networks during infection with an immunostimulatory HSV-1 strain, we integrated nuclear/cytoplasmic fractionation with thermal proximity coaggregation analysis (N/C-TPCA). The resulting expanded depth and spatial resolution of PPIs charted compartment-specific assemblies of protein complexes throughout infection. We find that a broader suite of host chaperones than previously anticipated exhibits nuclear recruitment to form condensates known as virus-induced chaperone-enriched (VICE) domains. Monitoring protein and RNA constituents and ribosome activity, we establish that VICE domains sequester ribosome biogenesis factors from ribosomal RNA, accompanying a cell-wide defect in ribosome supply. These findings highlight infection-driven VICE domains as nodes of translational remodeling and demonstrate the utility of N/C-TPCA to study dynamic biological contexts.

  PublisherDOI

• Genome-wide mapping of mesoscale neuronal RNA organization and condensation

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-20 · 4 citations

  preprintOpen accessSenior authorCorresponding

  SUMMARY Subcellular RNA organization can affect critical cellular functions. However, our understanding of RNA microenvironments, particularly biomolecular condensates, remains limited, largely due to a lack of technologies to comprehensively interrogate mesoscale RNA organization. Here, we adapt Split-Pool Recognition of Interactions by Tag Extension to map micron-scale RNA-RNA spatial proximity genome-wide across cell regions (RNA-SPRITE). Deploying RNA-SPRITE, we find extensive, conserved organization of mature mRNAs, with increased colocalization between mRNAs that share RNA-binding protein (RBP) motifs or encode functionally related proteins. Both effects are especially strong in dendrites and axons, suggesting prevalent mRNA co-regulation. Moreover, mRNAs with less compact folding, lower translation efficiency, and specific RBP motifs are more likely to be in RNA-rich condensates. However, perturbations that broadly dissolve or enhance condensation reveal that RBP motif and encoded protein-mediated colocalizations largely remain intact, independent of condensation. These results demonstrate the power of RNA-SPRITE in revealing critical aspects of RNA’s functional organization. In Brief Unbiased, genome-wide maps of RNA-RNA mesoscale spatial proximity uncover extensive subcellular organization and its governing principles. Highlights RNA-SPRITE reveals micron-scale RNA colocalization genome-wide across cell regions mRNA colocalization specificity is driven by shared motifs and encoded protein function mRNAs with less compact folding, lower translation efficiency, and distinct protein-binding motifs are more likely to be in condensates Neurites have a particularly high degree of sequence and function-dependent mRNA organization

  PublisherOA PDFDOI

Recent grants

• Optogenetic Droplets: Using Light to Control Nucleoplasmic Phase Separation

  NIH · $1.4M · 2015–2021

• CAREER: Non-Equilibrium RNA/Protein Liquids and Intracellular Phase Transitions

  NSF · $700k · 2013–2018

• NIH Grant DP2GM10543701

  NIH · $2.4M · 2017

Frequent coauthors

• Amy R. Strom

  Princeton University

  34 shared

• Ned S. Wingreen

  Princeton University

  32 shared

• Jorine M. Eeftens

  Radboud University Nijmegen

  30 shared

• Daniel S.W. Lee

  Berkeley College

  29 shared

• Yaojun Zhang

  Johns Hopkins University

  26 shared

• Joshua A. Riback

  University of Chicago

  23 shared

• David W. Sanders

  Princeton University

  23 shared

• Anthony A. Hyman

  Max Planck Institute of Molecular Cell Biology and Genetics

  20 shared

Labs

• Soft Living Matter GroupPI

  The Soft Living Matter Group at Princeton University focuses on the study of soft materials and their biological applications.

Awards & honors

• National Academy of Sciences, 2026
• Keio Medical Science Prize, 2025
• Raymond and Beverly Sackler International Prize in Biophysic…
• Breakthrough Prize for Life Sciences, 2023
• Tsuneko & Reiji Okazaki Award, 2021