About

Professor Justin Brumbaugh is a researcher at the University of Colorado Boulder, leading the Brumbaugh Lab within the College of Arts and Sciences. His research focuses on understanding the molecular mechanisms that regulate cell fate during development, with particular emphasis on the processes of self-renewal and differentiation in complex organisms. His work explores how intricate and dynamic regulatory mechanisms operate largely without changes to the genomic content of cells, which is crucial for both basic science and medical applications. The lab develops and applies innovative tools to study the determinants of cell identity, including the mechanisms of reprogramming and transdifferentiation, which allow differentiated cells to revert to pluripotency or convert into different cell types. Professor Brumbaugh's research also investigates chromatin modifications, especially histone methylation at specific sites on histone H3, to understand their roles during development and homeostasis. Additionally, his work examines RNA processing, particularly alternative polyadenylation (APA), as a regulatory mechanism controlling gene expression and cell fate transitions. His research aims to elucidate how proteins controlling APA influence stem cell function and differentiation, contributing to the broader understanding of developmental biology and regenerative medicine.

Research topics

• Genetics
• Biology
• Cell biology
• Chemistry
• Molecular biology
• Cancer research
• Medicine
• Neuroscience
• Immunology

Selected publications

• Modulation of Nudt21 levels reveals dose-dependent roles of alternative polyadenylation in tissue regeneration

  Nature Communications · 2026-01-24

  articleOpen access

  Stem cells continually self-renew and differentiate to sustain tissue homeostasis, yet the role of post-transcriptional mechanisms in guiding these processes remains incompletely understood. Here, we demonstrate that the regulation of 3'UTR length via alternative mRNA polyadenylation (APA) is essential for stem cell function across diverse tissues. Modulating the APA regulator Nudt21 reveals that stem cell self-renewal and differentiation depend on distinct dosage thresholds and thus can be uncoupled. Specifically, moderate Nudt21 suppression elicits a maturation arrest of stem cells due to 3'UTR-shortening of differentiation-associated mRNAs that escape miRNA regulation and perturb ceRNA networks. By contrast, complete Nudt21 suppression additionally shortens the 3'UTRs of mRNAs encoding essential multiprotein complexes, including the nuclear pore, leading to complex destabilization, proteotoxic stress, DNA damage, and cell cycle arrest. Critically, deletion of the alternative 3'UTRs of individual nucleoporins recapitulates defects observed with Nudt21 loss. We further demonstrate that the co-translational assembly of dozens of protein complexes is impaired in Nudt21-deficient cells, providing a mechanistic framework for compromised complex integrity. Collectively, our results show that APA plays distinct, dose-dependent roles in stem cell homeostasis by fine-tuning the expression of differentiation-associated genes and coordinating the biogenesis of multiprotein complexes essential for cell cycle progression.

  PublisherDOI

• Structure-guided design and development of cyclic peptide allosteric activators of Polycomb Repressive Complex 2

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-26

  preprintOpen access

  Dysregulation of the histone methyltransferase Polycomb repressive complex 2 (PRC2) results in aberrant silencing of tumor suppressors and activation of oncogenes. Targeting PRC2 with compounds holds significant potential for both basic research and therapeutic applications. Here, we leveraged extensive structural studies of PRC2 to design a cyclic peptide that robustly activates PRC2. Structure-activity relationship studies guided the functional optimization of this cyclic peptide, yielding a Phenylalanine-type (Phe-type) cyclic peptide with approximately eight-fold activation compared to that of the poised state of PRC2. A 3.3Å cryo-electron microscopy structure of the PRC2-peptide complex, combined with biochemical analyses, revealed a shift in the H3K27 methylation from mono- (me1) and dimethylation (me2) to trimethylation (me3). Finally, we demonstrated that the cyclic peptide exhibits improved mouse plasma stability and can also be readily taken up by cells which results in a shift of the H3K27 methylation landscape to trimethylation, similar to the observed effects in vitro. These findings support the utility of such molecules for probing PRC2 activation and targeting dysregulated H3K27 methylation in cancer.

  PublisherOA PDFDOI

• H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium

  Nature Cell Biology · 2025-01-08 · 14 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Selective RNA sequestration in biomolecular condensates directs cell fate transitions

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-10 · 1 citations

  preprintOpen access

  Recent studies have emphasized the significance of biomolecular condensates in modulating gene expression through RNA processing and translational control. However, the functional roles of RNA condensates in cell fate specification remains poorly understood. Here, we profiled the coding and non-coding transcriptome within intact biomolecular condensates, specifically P-bodies, in diverse developmental contexts, spanning multiple vertebrate species. Our analyses revealed the conserved, cell type-specific sequestration of untranslated RNAs encoding key cell fate regulators. Notably, P-body contents did not directly reflect active gene expression profiles for a given cell type, but rather were enriched for translationally repressed transcripts characteristic of the preceding developmental stage. Mechanistically, microRNAs (miRNAs) direct the selective sequestration of RNAs into P-bodies in a context-dependent manner, and perturbing AGO2 or alternative polyadenylation profoundly reshapes P-body RNA content. Building on these mechanistic insights, we demonstrate that modulating P-body assembly or miRNA activity dramatically enhances both activation of a totipotency transcriptional program in naïve pluripotent stem cells as well as the programming of primed human embryonic cells towards the germ cell lineage. Collectively, our findings establish a direct link between biomolecular condensates and cell fate decisions across vertebrate species and provide a novel framework for harnessing condensate biology to expand clinically relevant cell populations.

  PublisherOA PDFDOI

• Selective RNA sequestration in biomolecular condensates directs cell fate transitions

  Nature Biotechnology · 2025-10-28 · 6 citations

  articleOpen accessCorresponding

  Controlling stem cell differentiation is a longstanding goal in biomedical research. Here we explore how cell fate is influenced by RNA condensates, specifically P-bodies, which modulate gene expression posttranscriptionally. We profiled the transcriptomes of biomolecular condensates in diverse developmental contexts spanning multiple vertebrate species. Our analyses revealed conserved, cell type-specific sequestration of untranslated RNAs encoding cell fate regulators. P-body RNA contents do not reflect active gene expression in each cell type but are enriched for translationally repressed transcripts characteristic of the preceding developmental stage. Mechanistically, P-body contents are controlled by microRNAs and can be profoundly reshaped by perturbing AGO2 or polyadenylation site usage. Applying these insights to stem cell differentiation, we show that manipulating P-body assembly or microRNA activity can direct naive mouse and human pluripotent stem cells toward totipotency or primed human embryonic cells toward the germ cell lineage. Our findings link cell fate decisions to RNA condensates across vertebrates and provide a means of controlling cell identity.

  PublisherDOI

• Transposable element activity captures human pluripotent cell states

  EMBO Reports · 2024-12-12 · 3 citations

  articleOpen access

  Human pluripotent stem cells (hPSCs) exist in multiple, transcriptionally distinct states and serve as powerful models for studying human development. Despite their significance, the molecular determinants and pathways governing these pluripotent states remain incompletely understood. Here, we demonstrate that transposable elements act as sensitive indicators of distinct pluripotent cell states. We engineered hPSCs with fluorescent reporters to capture the temporal expression dynamics of two state-specific transposable elements, LTR5_Hs, and MER51B. This dual reporter system enables real-time monitoring and isolation of stem cells transitioning from naïve to primed pluripotency and further towards differentiation, serving as a more accurate readout of pluripotency states compared to conventional systems. Unexpectedly, we identified a rare, metastable cell population within primed hPSCs, marked by transcripts related to preimplantation embryo development and which is associated with a DNA damage response. Moreover, our system establishes the chromatin factor NSD1 and the RNA-binding protein FUS as potent molecular safeguards of primed pluripotency. Our study introduces a novel system for investigating cellular potency and provides key insights into the regulation of embryonic development.

  PublisherDOI

• Mechanical memory stored through epigenetic remodeling reduces cell therapeutic potential

  Biophysical Journal · 2023 · 39 citations

  • Cell biology
  • Chemistry
  • Neuroscience
  PublisherOA PDFDOI

• Leveraging dominant-negative histone H3 K-to-M mutations to study chromatin during differentiation and development

  Development · 2023-10-17 · 10 citations

  articleOpen accessSenior author

  Histone modifications are associated with regulation of gene expression that controls a vast array of biological processes. Often, these associations are drawn by correlating the genomic location of a particular histone modification with gene expression or phenotype; however, establishing a causal relationship between histone marks and biological processes remains challenging. Consequently, there is a strong need for experimental approaches to directly manipulate histone modifications. A class of mutations on the N-terminal tail of histone H3, lysine-to-methionine (K-to-M) mutations, was identified as dominant-negative inhibitors of histone methylation at their respective and specific residues. The dominant-negative nature of K-to-M mutants makes them a valuable tool for studying the function of specific methylation marks on histone H3. Here, we review recent applications of K-to-M mutations to understand the role of histone methylation during development and homeostasis. We highlight important advantages and limitations that require consideration when using K-to-M mutants, particularly in a developmental context.

  PublisherOA PDFDOI

• Human fetal tissue is critical for biomedical research

  Stem Cell Reports · 2023-11-16 · 12 citations

  reviewOpen access1st authorCorresponding

  Human fetal tissue and cells derived from fetal tissue are crucial for biomedical research. Fetal tissues and cells are used to study both normal development and developmental disorders. They are broadly applied in vaccine development and production. Further, research using cells from fetal tissue is instrumental for studying many infectious diseases, including a broad range of viruses. These widespread applications underscore the value of fetal tissue research and reflect an important point: cells derived from fetal tissues have capabilities that cells from other sources do not. In many cases, increased functionality of cells derived from fetal tissues arises from increased proliferative capacity, ability to survive in culture, and developmental potential that is attenuated in adult tissues. This review highlights important, representative applications of fetal tissue for science and medicine.

  PublisherOA PDFDOI

• NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia

  Nature Immunology · 2022 · 53 citations

  • Immunology
  • Biology
  • Cancer research
  PublisherOA PDFDOI

Recent grants

• The regulatory role of chromatin interaction in pluripotency and differentiation

  NIH · $120k · 2014–2017

• DEFINING REGULATORY ROLES FOR HISTONE H3 METHYLATION IN DEVELOPMENT

  NIH · $2.1M · 2021–2027

• The regulatory role of chromatin interaction in pluripotency and differentiation

  NIH · $55k · 2014–2017

Frequent coauthors

• Konrad Hochedlinger

  Harvard Stem Cell Institute

  111 shared

• Aaron J. Huebner

  Massachusetts General Hospital

  40 shared

• Bruno Di Stefano

  Baylor College of Medicine

  40 shared

• Ori Bar‐Nur

  ETH Zurich

  37 shared

• Benjamin A. Schwarz

  Massachusetts General Hospital

  26 shared

• Marti Borkent

  Massachusetts General Hospital

  25 shared

• Inna Lipchina

  Massachusetts General Hospital

  25 shared

• Alexander Meissner

  Max Planck Institute for Molecular Genetics

  24 shared

Education

• Postdoctoral Fellow, Molecular Biology

  Massachusetts General Hospital

  2018

• Postdoctoral Fellow, Regenerative Biology

  Morgridge Institute for Research

  2012

• PhD, Biochemistry

  University of Wisconsin Madison

  2011

• Visiting Scholar

  Max-Planck-Institut für Biochemie

  2011

• Fulbright Scholar, Gene Expression

  European Molecular Biology Laboratory

  2006

• BS, Biochemistry and Molecular Biology

  Penn State

  2004

• Study Abroad

  University of Melbourne

  2002