Publications

My lab has identified regulated protein self-assembly as a physiological system for cellular memory, epigenetic information transmission, gene regulation, and adaptive genome plasticity. We have established that this form of biochemical inheritance is widespread, controlling fundamental cellular decisions such as whether to proliferate or differentiate. We have also characterized the structures and stability of the proteinaceous particles and their self-templating properties. Most do not form amyloid fibers but instead form gel-like assemblies that can be replicated and inherited over many cell divisions. In genetic screens, we have identified dozens such protein-based epigenetic switches in eukaryotic proteomes. Many are transcription factors and RNA-binding proteins that influence gene regulation, stress responses, and drug resistance.

Preprint

A Molecular Mechanism for Environmental Context in Protein-Based Epigenetic Memory

Theodore S. Yang, Anupam K. Chakravarty, Thomas M. Lozanoski, Richard She, Livia S. Wyss, Jialing Fang, Isabel Larus, Elizabeth L. Hinks, William J. Greenleaf, Jian Qin, Roseanna N. Zia, and Daniel F. Jarosz

Cell Press SSRN/Sneak Peek. posted January 28, 2026.

DOI

Reveals how a folded RNA-binding domain forms polymorphic, self-templating [SMAUG+] particles and how specific combinations of target RNAs shape distinct inherited states, establishing a colloidal-physics mechanism for contextual cellular memory and adaptation.

Research article

A Prion Epigenetic Switch Establishes an Active Chromatin State

Zachary H. Harvey, Anupam K. Chakravarty, Raymond A. Futia, and Daniel F. Jarosz

Cell. 2020;180(5):928–940.e14.

DOI PubMed PMC

Connects self-templating protein assembly to inducible and persistent chromatin activation as well as heritable epigenetic changes in transcriptional control

Research article

A Non-amyloid Prion Particle that Activates a Heritable Gene Expression Program

Anupam K. Chakravarty, Tina Smejkal, Alan K. Itakura, David M. Garcia, and Daniel F. Jarosz

Molecular Cell. 2020;77(2):251–265.e9.

DOI PubMed PMC

Together with its sister paper (Itakura et al., 2020), this study identifies a widespread self-templating protein assembly that activates a post-transcriptional regulatory mechanism to control a fundamental cell biological decision

Research article

Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits

Sohini Chakrabortee, James S. Byers, Sandra K. Jones, David M. Garcia, Bhupinder Bhullar, Amelia Chang, Richard She, Laura Lee, Brayon J. Fremin, Susan Lindquist, and Daniel F. Jarosz

Cell. 2016;167(2):369–381.e12.

DOI PubMed PMC

Established the broad capacity of intrinsically disordered proteins to generate and transmit alternative biological states, transforming the prion concept beyond inactivation linked to amyloid transitions

Research article

Cross-Kingdom Chemical Communication Drives a Heritable, Mutually Beneficial Prion-Based Transformation of Metabolism

Daniel F. Jarosz, Jessica C. S. Brown, Gordon A. Walker, Manoshi S. Datta, W. Lloyd Ung, Alex K. Lancaster, Assaf Rotem, Amelia Chang, Gregory A. Newby, David A. Weitz, Linda F. Bisson, and Susan Lindquist

Cell. 2014;158(5):1083–1093.

DOI PubMed PMC

Demonstrates that bacterial signals induce [GAR+] in yeast, creating a heritable metabolic shift that benefits both organisms and alters the dynamics of microbial communities and fermentations

Our studies reveal how environmental stress and protein homeostasis reshape genotype-to-phenotype relationships, developing nucleotide-resolution and genome-to-proteome approaches that make those effects mechanistically understandable, reveal new regulatory principles, and increasingly enable the prediction of cellular adaptation and even future evolutionary trajectories.

Research article

Prion-based protein self-assembly tunes mutagenesis to enable rapid adaptation

Alexandria Van Elgort, Christopher M. Jakobson, Yiwen R. Chen, James S. Byers, Raymond A. Futia, Thomas M. Lozanoski, Zachary H. Harvey, Jinglin L. Xie, David M. Garcia, and Daniel F. Jarosz

Cell. 2026;189(17):5232–5249.e29.

DOI PubMed PMC

Demonstrates that regulated protein self-assembly can reversibly reprogram genome-maintenance pathways, regulating mutation supply, adaptation, and the emergence of drug resistance

Research article

A genome-to-proteome map reveals how natural variants drive proteome diversity and shape fitness

Christopher M. Jakobson, Johannes Hartl, Pauline Trébulle, Michael Mülleder, Daniel F. Jarosz, and Markus Ralser

Science. 2025;390(6769):eadu3198.

DOI PubMed PMC

Defined principles of how natural genetic variation drives proteome remodeling, discovered evidence of pervasive directional selection in protein levels across pathways, and revealed that genetic control of latent variability in protein levels forecasts fitness in new environments

Research article

Molecular Origins of Complex Heritability in Natural Genotype-to-Phenotype Relationships

Christopher M. Jakobson and Daniel F. Jarosz

Cell Systems. 2019;8(5):363–379.e3.

DOI PubMed PMC

Charts 90 comprehensive genotype-to-phenotype maps to expose the molecular origins of complex heritability, including environment-dependent pleiotropy, distinct signatures of causal regulatory and synonymous variants, and strong phenotypic effects from variants in disordered regions of signaling proteins

Our work in this area, using models from yeast to vertebrates and human patient samples, distinguishes regulated, functional protein assembly from pathological aggregation and reveals how proteostasis is organized across the cell cycle, tissues, and the lifespan.

Research article

DNA binding and mitotic phosphorylation protect polyglutamine proteins from assembly formation

Shady Saad, Tomek Swigut, Saman Tabatabaee, Pranav Lalgudi, Daniel F. Jarosz, and Joanna Wysocka

Cell. 2025;188(11):2974–2991.e20.

DOI PubMed PMC

Reveals how DNA binding and cell-cycle regulation suppress aggregation of polyglutamine-containing transcription factors, suggests that this principle influenced the function of human-specific variation in the ‘speech gene’ FOXP2, and posits that these mechanisms can be repurposed to dissipate assemblies formed by pathological polyglutamine expansions linked to Huntington’s Disease.

Research article

Identification of protein aggregates in the aging vertebrate brain with prion-like and phase-separation properties

Itamar Harel, Yiwen R. Chen, Inbal Ziv, Param Priya Singh, Daniel Heinzer, Paloma Navarro Negredo, Uri Goshtchevsky, Wei Wang, Gwendoline Astre, Eitan Moses, Andrew McKay, Ben E. Machado, Katja Hebestreit, Sifei Yin, Alejandro Sánchez Alvarado, Daniel F. Jarosz, and Anne Brunet

Cell Reports. 2024;43(6):112787.

DOI PubMed PMC

Identifies proteins that aggregate in the aging vertebrate brain and showed that the prion-like RNA helicase DDX5 forms enzymatically active condensates that can mature into transmissible aggregates.

All Publications

Complete public record of research articles, methods, reviews and commentary, invited chapters, educational work, public preprints, and a patent application. Featured publications are repeated here so the chronological record remains complete.

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2025–present

Research article

DNA binding and mitotic phosphorylation protect polyglutamine proteins from assembly formation

Shady Saad, Tomek Swigut, Saman Tabatabaee, Pranav Lalgudi, Daniel F. Jarosz, and Joanna Wysocka

Cell. 2025;188(11):2974–2991.e20.

DOI PubMed PMC Coverage

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2020–2024

Research article

Tissue-specific landscape of protein aggregation and quality control in an aging vertebrate

Yiwen R. Chen, Itamar Harel, Param Priya Singh, Inbal Ziv, Eitan Moses, Uri Goshtchevsky, Ben E. Machado, Anne Brunet, and Daniel F. Jarosz

Developmental Cell. 2024;59(14):1892–1911.e13.

DOI PubMed PMC Coverage

Research article

Defining the condensate landscape of fusion oncoproteins

Swarnendu Tripathi, Hazheen K. Shirnekhi, Scott D. Gorman, Bappaditya Chandra, David W. Baggett, Cheon-Gil Park, Ramiz Somjee, Benjamin Lang, Seyed Mohammad Hadi Hosseini, Brittany J. Pioso, Yongsheng Li, Ilaria Iacobucci, Qingsong Gao, Michael N. Edmonson, Stephen V. Rice, Xin Zhou, John Bollinger, Diana M. Mitrea, Michael R. White, Daniel J. McGrail, Daniel F. Jarosz, S. Stephen Yi, M. Madan Babu, Charles G. Mullighan, Jinghui Zhang, Nidhi Sahni, and Richard W. Kriwacki

Nature Communications. 2023;14:6008.

DOI PubMed PMC

Research article

Massive QTL analysis identifies pleiotropic genetic determinants for stress resistance, aroma formation, and ethanol, glycerol and isobutanol production in Saccharomyces cerevisiae

Ping-Wei Ho, Supinya Piampongsant, Brigida Gallone, Andrea Del Cortona, Pieter-Jan Peeters, Frank Reijbroek, Jules Verbaet, Beatriz Herrera, Jeroen Cortebeeck, Robbe Nolmans, Veerle Saels, Jan Steensels, Daniel F. Jarosz, and Kevin J. Verstrepen

Biotechnology for Biofuels. 2021;14:211.

DOI PubMed PMC

Research article

A Prion Epigenetic Switch Establishes an Active Chromatin State

Zachary H. Harvey, Anupam K. Chakravarty, Raymond A. Futia, and Daniel F. Jarosz

Cell. 2020;180(5):928–940.e14.

DOI PubMed PMC Coverage

Research article

Widespread Prion-Based Control of Growth and Differentiation Strategies in Saccharomyces cerevisiae

Alan K. Itakura, Anupam K. Chakravarty, Christopher M. Jakobson, and Daniel F. Jarosz

Molecular Cell. 2020;77(2):266–278.e6.

DOI PubMed PMC Coverage

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2015–2019

Book chapter

Amyloid Prions in Fungi

Sven J. Saupe, Daniel F. Jarosz, and Heather L. True

The Fungal Kingdom. 2017;673–685. ASM Press.

DOI

Research article

Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits

Sohini Chakrabortee, James S. Byers, Sandra K. Jones, David M. Garcia, Bhupinder Bhullar, Amelia Chang, Richard She, Laura Lee, Brayon J. Fremin, Susan Lindquist, and Daniel F. Jarosz

Cell. 2016;167(2):369–381.e12.

DOI PubMed PMC Coverage

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2010–2014

Research article

Cross-Kingdom Chemical Communication Drives a Heritable, Mutually Beneficial Prion-Based Transformation of Metabolism

Daniel F. Jarosz, Jessica C. S. Brown, Gordon A. Walker, Manoshi S. Datta, W. Lloyd Ung, Alex K. Lancaster, Assaf Rotem, Amelia Chang, Gregory A. Newby, David A. Weitz, Linda F. Bisson, and Susan Lindquist

Cell. 2014;158(5):1083–1093.

DOI PubMed PMC Coverage

Research article

Cryptic Variation in Morphological Evolution: HSP90 as a Capacitor for Loss of Eyes in Cavefish

Nicolas Rohner, Daniel F. Jarosz, Johanna E. Kowalko, Masato Yoshizawa, William R. Jeffery, Richard L. Borowsky, Susan Lindquist, and Clifford J. Tabin

Science. 2013;342(6164):1372–1375.

DOI PubMed PMC Coverage

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2005–2009

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Meeting abstracts and invited presentations

These records are listed separately and are not research articles.

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