1
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Ziogas A, Novakovic B, Ventriglia L, Galang N, Tran KA, Li W, Matzaraki V, van Unen N, Schlüter T, Ferreira AV, Moorlag SJCFM, Koeken VACM, Moyo M, Li X, Baltissen MPA, Martens JHA, Li Y, Divangahi M, Joosten LAB, Mhlanga MM, Netea MG. Long-term histone lactylation connects metabolic and epigenetic rewiring in innate immune memory. Cell 2025; 188:2992-3012.e16. [PMID: 40318634 DOI: 10.1016/j.cell.2025.03.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 01/08/2025] [Accepted: 03/31/2025] [Indexed: 05/07/2025]
Abstract
Trained immunity, a de facto innate immune memory characterized by enhanced responsiveness to future challenges, is underpinned by epigenetic and metabolic rewiring. In individuals vaccinated with Bacille Calmette-Guérin (BCG), lactate release was associated with enhanced cytokine responsiveness upon restimulation. Trained monocytes/macrophages are characterized by lactylation of histone H3 at lysine residue 18(H3K18la), mainly at distal regulatory regions. Histone lactylation was positively associated with active chromatin and gene transcription, persisted after the elimination of the training stimulus, and was strongly associated with "trained" gene transcription in response to a secondary stimulus. Increased lactate production upon induction of trained immunity led to enhanced production of proinflammatory cytokines, a process associated with histone lactylation. Pharmacological inhibition of lactate production or histone lactylation blocked trained immunity responses, while polymorphisms of LDHA and EP300 genes modulated trained immunity. Long-term histone lactylation persisted in vivo 90 days after vaccination with BCG, highlighting H3K18la as an epigenetic mark of innate immune memory.
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Affiliation(s)
- Athanasios Ziogas
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands.
| | - Boris Novakovic
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Australia
| | - Lorenzo Ventriglia
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Hepatogastroenterology Division, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Noriko Galang
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Kim A Tran
- Department of Medicine, Department of Pathology, Department of Microbiology & Immunology, Research Institute of the McGill University Health Centre, McGill International TB Centre, Meakins-Christie Laboratories, McGill University, Montreal, QC, Canada
| | - Wenchao Li
- Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Vasiliki Matzaraki
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nienke van Unen
- Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Titus Schlüter
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Anaísa V Ferreira
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Simone J C F M Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Valerie A C M Koeken
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Research Centre Innovations in Care, Rotterdam University of Applied Sciences, Rotterdam, the Netherlands
| | - Mthabisi Moyo
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Xiaolin Li
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marijke P A Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Yang Li
- Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hanover Medical School, Hannover, Germany; Lower Saxony center for artificial intelligence and causal methods in medicine (CAIMed), Hannover, Germany
| | - Maziar Divangahi
- Department of Medicine, Department of Pathology, Department of Microbiology & Immunology, Research Institute of the McGill University Health Centre, McGill International TB Centre, Meakins-Christie Laboratories, McGill University, Montreal, QC, Canada
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Musa M Mhlanga
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department for Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany.
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2
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Playter C, Golloshi R, Garretson JH, Rodriguez Gonzalez A, Olajide TH, Saad A, Benson SJ, McCord RP. Deciphering pre-existing and induced 3D genome architecture changes involved in constricted melanoma migration. iScience 2025; 28:112346. [PMID: 40292313 PMCID: PMC12032941 DOI: 10.1016/j.isci.2025.112346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 01/22/2025] [Accepted: 03/31/2025] [Indexed: 04/30/2025] Open
Abstract
Metastatic cancer cells traverse constricted spaces that exert forces on their nucleus and the genomic contents within. Cancerous tumors are highly heterogeneous and not all cells within them can achieve such a feat. Here, we investigated what initial genome architecture characteristics favor the constricted migratory ability of cancer cells and which arise only after passage through multiple constrictions. We identified a cell surface protein (ITGB4) whose expression correlates with increased initial constricted migration ability in human melanoma A375 cells. Sorting out this subpopulation allowed us to identify cellular and nuclear features that pre-exist and favor migration, as well as alterations that only appear after cells have passed through constrictions. We identified specific genomic regions that experienced altered genome spatial compartment profiles only after constricted migration. Our study reveals 3D genome structure contributions to both selection and induction mechanisms of cell fate change during cancer metastasis.
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Affiliation(s)
- Christopher Playter
- Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Rosela Golloshi
- Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Joshua H. Garretson
- Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Alvaro Rodriguez Gonzalez
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
| | - Taiwo Habeeb Olajide
- Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Ahmed Saad
- Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Samuel John Benson
- Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Rachel Patton McCord
- Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
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3
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Pellon A, Palacios A, Abecia L, Rodríguez H, Anguita J. Friends to remember: innate immune memory regulation by the microbiota. Trends Microbiol 2025; 33:510-520. [PMID: 39794207 DOI: 10.1016/j.tim.2024.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Revised: 11/28/2024] [Accepted: 12/11/2024] [Indexed: 01/13/2025]
Abstract
Innate immune memory (IIM) is the process by which, upon a primary challenge, innate immune cells alter their epigenetic, transcriptional, and immunometabolic profiles, resulting in modified secondary responses. Unlike infections or other immune-system-related diseases, the role of IIM in nonpathogenic contexts is less understood. An increasing body of research has shown that normal microbiota members or their metabolic byproducts induce alternative memory phenotypes, suggesting that memory cells contribute to homeostasis in mucosal areas. In this review, we discuss the newest insights in the emerging field of IIM to the microbiota and the potential of manipulating these long-term responses to promote better mucosal health.
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Affiliation(s)
- Aize Pellon
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA, Derio, Spain.
| | - Ainhoa Palacios
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA, Derio, Spain; Present address: Research Unit, Basque Center for Blood Transfusion and Human Tissues, Osakidetza; Galdakao, Spain and Cell Therapy, Stem Cells and Tissues Group, BioBizkaia Health Research Institute; Barakaldo, Spain
| | - Leticia Abecia
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA, Derio, Spain; Department of Immunology, Microbiology, and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Héctor Rodríguez
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA, Derio, Spain
| | - Juan Anguita
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA, Derio, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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4
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Vinayak V, Basir R, Golloshi R, Toth J, Sant'Anna L, Lakadamyali M, McCord RP, Shenoy VB. Polymer model integrates imaging and sequencing to reveal how nanoscale heterochromatin domains influence gene expression. Nat Commun 2025; 16:3816. [PMID: 40268925 PMCID: PMC12019571 DOI: 10.1038/s41467-025-59001-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Accepted: 04/08/2025] [Indexed: 04/25/2025] Open
Abstract
Chromatin organization regulates gene expression, with nanoscale heterochromatin domains playing a fundamental role. Their size varies with microenvironmental stiffness and epigenetic interventions, but how these factors regulate their formation and influence transcription remains unclear. To address this, we developed a sequencing-informed copolymer model that simulates chromatin evolution through diffusion and active epigenetic reactions. Our model predicts the formation of nanoscale heterochromatin domains and quantifies how domain size scales with epigenetic reaction rates, showing that epigenetic and compaction changes primarily occur at domain boundaries. We validated these predictions via Hi-C and super-resolution imaging of hyperacetylated melanoma cells and identified differential expression of metastasis-related genes through RNA-seq. We validated our findings in hMSCs, where epigenetic reaction rates respond to microenvironmental stiffness. Conclusively, our simulations reveal that heterochromatin domain boundaries regulate gene expression and epigenetic memory. These findings demonstrate how external cues drive chromatin organization and transcriptional memory in development and disease.
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Affiliation(s)
- Vinayak Vinayak
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Ramin Basir
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Rosela Golloshi
- Departments of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Giovanis Institute for Translational Cell Biology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Joshua Toth
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Lucas Sant'Anna
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Melike Lakadamyali
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel Patton McCord
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Vivek B Shenoy
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Paldi F, Cavalli G. 3D genome folding in epigenetic regulation and cellular memory. Trends Cell Biol 2025:S0962-8924(25)00065-0. [PMID: 40221344 DOI: 10.1016/j.tcb.2025.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Revised: 03/07/2025] [Accepted: 03/11/2025] [Indexed: 04/14/2025]
Abstract
The 3D folding of the genome is tightly linked to its epigenetic state which maintains gene expression programmes. Although the relationship between gene expression and genome organisation is highly context dependent, 3D genome organisation is emerging as a novel epigenetic layer to reinforce and stabilise transcriptional states. Whether regulatory information carried in genome folding could be transmitted through mitosis is an area of active investigation. In this review, we discuss the relationship between epigenetic state and nuclear organisation, as well as the interplay between transcriptional regulation and epigenetic genome folding. We also consider the architectural remodelling of nuclei as cells enter and exit mitosis, and evaluate the potential of the 3D genome to contribute to cellular memory.
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Affiliation(s)
- Flora Paldi
- Institute of Human Genetics, CNRS and University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS and University of Montpellier, Montpellier, France.
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6
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Mikulski P, Tehrani SSH, Kogan A, Abdul-Zani I, Shell E, James L, Ryan BJ, Jansen LET. Heritable maintenance of chromatin modifications confers transcriptional memory of interferon-γ signaling. Nat Struct Mol Biol 2025:10.1038/s41594-025-01522-8. [PMID: 40186025 DOI: 10.1038/s41594-025-01522-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/20/2025] [Indexed: 04/07/2025]
Abstract
Interferon-γ (IFNγ) transiently activates genes related to inflammation and innate immunity. A subset of targets retain a mitotically heritable memory of prior IFNγ exposure, resulting in hyperactivation upon re-exposure through poorly understood mechanisms. Here, we discover that the transcriptionally permissive chromatin marks H3K4me1, H3K14ac and H4K16ac are established during IFNγ priming and are selectively maintained on a cluster of guanylate-binding protein (GBP) genes in dividing human cells in the absence of transcription. The histone acetyltransferase KAT7 is required for H3K14ac deposition at GBP genes and for accelerated GBP reactivation upon re-exposure to IFNγ. In naive cells, the GBP cluster is maintained in a low-level repressive chromatin state, marked by H3K27me3, limiting priming through a PRC2-dependent mechanism. Unexpectedly, IFNγ priming results in transient accumulation of this repressive mark despite active gene expression. However, during the memory phase, H3K27 methylation is selectively depleted from primed GBP genes, facilitating hyperactivation. Furthermore, we identified a cis-regulatory element that forms transient, long-range contacts across the GBP cluster and acts as a repressor, curbing hyperactivation of previously IFNγ-primed cells. Our results provide insight into the chromatin basis for the long-term transcriptional memory of IFNγ signaling, which might contribute to enhanced innate immunity.
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Affiliation(s)
- Pawel Mikulski
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The International Institute of Molecular Mechanisms and Machines PAS, Warsaw, Poland.
| | - Sahar S H Tehrani
- Department of Biochemistry, University of Oxford, Oxford, UK
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Anna Kogan
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Izma Abdul-Zani
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Emer Shell
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Louise James
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Brent J Ryan
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Lars E T Jansen
- Department of Biochemistry, University of Oxford, Oxford, UK.
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7
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Smaruj PN, Xiao Y, Fudenberg G. Recipes and ingredients for deep learning models of 3D genome folding. Curr Opin Genet Dev 2025; 91:102308. [PMID: 39862604 PMCID: PMC11867851 DOI: 10.1016/j.gde.2024.102308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 12/19/2024] [Accepted: 12/31/2024] [Indexed: 01/27/2025]
Abstract
Three-dimensional genome folding plays roles in gene regulation and disease. In this review, we compare and contrast recent deep learning models for predicting genome contact maps. We survey preprocessing, architecture, training, evaluation, and interpretation methods, highlighting the capabilities and limitations of different models. In each area, we highlight challenges, opportunities, and potential future directions for genome-folding models.
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Affiliation(s)
- Paulina N Smaruj
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Yao Xiao
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Geoffrey Fudenberg
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
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8
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Wang B, Bian Q. Regulation of 3D genome organization during T cell activation. FEBS J 2025; 292:1833-1852. [PMID: 38944686 DOI: 10.1111/febs.17211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/23/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024]
Abstract
Within the three-dimensional (3D) nuclear space, the genome organizes into a series of orderly structures that impose important influences on gene regulation. T lymphocytes, crucial players in adaptive immune responses, undergo intricate transcriptional remodeling upon activation, leading to differentiation into specific effector and memory T cell subsets. Recent evidence suggests that T cell activation is accompanied by dynamic changes in genome architecture at multiple levels, providing a unique biological context to explore the functional relevance and molecular mechanisms of 3D genome organization. Here, we summarize recent advances that link the reorganization of genome architecture to the remodeling of transcriptional programs and conversion of cell fates during T cell activation and differentiation. We further discuss how various chromatin architecture regulators, including CCCTC-binding factor and several transcription factors, collectively modulate the genome architecture during this process.
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Affiliation(s)
- Bao Wang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
| | - Qian Bian
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
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9
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Stepanova D, Brunet Guasch M, Byrne HM, Alarcón T. Understanding How Chromatin Folding and Enzyme Competition Affect Rugged Epigenetic Landscapes. Bull Math Biol 2025; 87:59. [PMID: 40153141 DOI: 10.1007/s11538-025-01434-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Accepted: 03/03/2025] [Indexed: 03/30/2025]
Abstract
Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without altering the DNA sequence. Epigenetic regulation occurs within the context of hierarchically folded chromatin, yet the interplay between the dynamics of epigenetic modifications and chromatin architecture remains poorly understood. In addition, it remains unclear what mechanisms drive the formation of rugged epigenetic patterns, characterised by alternating genomic regions enriched in activating and repressive marks. In this study, we focus on post-translational modifications of histone H3 tails, particularly H3K27me3, H3K4me3, and H3K27ac. We introduce a mesoscopic stochastic model that incorporates chromatin architecture and competition of histone-modifying enzymes into the dynamics of epigenetic modifications in small genomic loci comprising several nucleosomes. Our approach enables us to investigate the mechanisms by which epigenetic patterns form on larger scales of chromatin organisation, such as loops and domains. Through bifurcation analysis and stochastic simulations, we demonstrate that the model can reproduce uniform chromatin states (open, closed, and bivalent) and generate previously unexplored rugged profiles. Our results suggest that enzyme competition and chromatin conformations with high-frequency interactions between distant genomic loci can drive the emergence of rugged epigenetic landscapes. Additionally, we hypothesise that bivalent chromatin can act as an intermediate state, facilitating transitions between uniform and rugged landscapes. This work offers a powerful mathematical framework for understanding the dynamic interactions between chromatin architecture and epigenetic regulation, providing new insights into the formation of complex epigenetic patterns.
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Affiliation(s)
- Daria Stepanova
- Centre de Recerca Matemàtica, Campus de Bellaterra, Edifici C, 08193, Bellaterra, Barcelona, Spain.
| | - Meritxell Brunet Guasch
- School of Mathematics and Maxwell Institute for Mathematical Sciences, University of Edinburgh, James Clerk Maxwell Building, Mayfield Rd, Edinburgh, EH9 3FD, Scotland, UK
| | - Helen M Byrne
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe, Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, England, UK
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, England, UK
| | - Tomás Alarcón
- Centre de Recerca Matemàtica, Campus de Bellaterra, Edifici C, 08193, Bellaterra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Passeig de Lluís Companys, 23, 08010, Barcelona, Barcelona, Spain
- Departament de Matemàtiques, Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193, Bellaterra, Barcelona, Spain
- Barcelona Collaboratorium for Predictive and Theoretical Biology, Wellington, 30, 08005, Barcelona, Barcelona, Spain
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10
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Falk MJ, Strupp AT, Scellier B, Murugan A. Temporal Contrastive Learning through implicit non-equilibrium memory. Nat Commun 2025; 16:2163. [PMID: 40038254 PMCID: PMC11880436 DOI: 10.1038/s41467-025-57043-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 02/10/2025] [Indexed: 03/06/2025] Open
Abstract
The backpropagation method has enabled transformative uses of neural networks. Alternatively, for energy-based models, local learning methods involving only nearby neurons offer benefits in terms of decentralized training, and allow for the possibility of learning in computationally-constrained substrates. One class of local learning methods contrasts the desired, clamped behavior with spontaneous, free behavior. However, directly contrasting free and clamped behaviors requires explicit memory. Here, we introduce 'Temporal Contrastive Learning', an approach that uses integral feedback in each learning degree of freedom to provide a simple form of implicit non-equilibrium memory. During training, free and clamped behaviors are shown in a sawtooth-like protocol over time. When combined with integral feedback dynamics, these alternating temporal protocols generate an implicit memory necessary for comparing free and clamped behaviors, broadening the range of physical and biological systems capable of contrastive learning. Finally, we show that non-equilibrium dissipation improves learning quality and determine a Landauer-like energy cost of contrastive learning through physical dynamics.
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Affiliation(s)
- Martin J Falk
- Department of Physics, University of Chicago, Chicago, IL, USA
| | - Adam T Strupp
- Department of Physics, University of Chicago, Chicago, IL, USA
| | | | - Arvind Murugan
- Department of Physics, University of Chicago, Chicago, IL, USA.
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11
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Lin H, Wang D, Wang Q, Mao J, Yang L, Bai Y, Qu J. Epigenetic modifications and metabolic gene mutations drive resistance evolution in response to stimulatory antibiotics. Mol Syst Biol 2025; 21:294-314. [PMID: 39820016 PMCID: PMC11876630 DOI: 10.1038/s44320-025-00087-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 12/29/2024] [Accepted: 01/07/2025] [Indexed: 01/19/2025] Open
Abstract
The antibiotic resistance crisis, fueled by misuse and bacterial evolution, is a major global health threat. Traditional perspectives tie resistance to drug target mechanisms, viewing antibiotics as mere growth inhibitors. New insights revealed that low-dose antibiotics may also serve as signals, unexpectedly promoting bacterial growth. Yet, the development of resistance under these conditions remains unknown. Our study investigated resistance evolution under stimulatory antibiotics and uncovered new genetic mechanisms of resistance linked to metabolic remodeling. We documented a shift from a fast, reversible mechanism driven by methylation in central metabolic pathways to a slower, stable mechanism involving mutations in key metabolic genes. Both mechanisms contribute to a metabolic profile transition from glycolysis to rapid gluconeogenesis. In addition, our findings demonstrated that rising environmental temperatures associated with metabolic evolution accelerated this process, increasing the prevalence of metabolic gene mutations, albeit with a trade-off in interspecific fitness. These findings expand beyond the conventional understanding of resistance mechanisms, proposing a broader metabolic mechanism within the selective window of stimulatory sub-MIC antibiotics, particularly in the context of climate change.
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Affiliation(s)
- Hui Lin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Donglin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
| | - Qiaojuan Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jie Mao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
| | - Lutong Yang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yaohui Bai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China.
| | - Jiuhui Qu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
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12
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Mimura I, Chen Z, Natarajan R. Epigenetic alterations and memory: key players in the development/progression of chronic kidney disease promoted by acute kidney injury and diabetes. Kidney Int 2025; 107:434-456. [PMID: 39725223 DOI: 10.1016/j.kint.2024.10.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 09/20/2024] [Accepted: 10/08/2024] [Indexed: 12/28/2024]
Abstract
Chronic kidney disease (CKD) is a highly prevalent global public health issue and can progress to kidney failure. Survivors of acute kidney injury (AKI) have an increased risk of progressing to CKD by 8.8-fold and kidney failure by 3.1-fold. Further, 20% to 40% of individuals with diabetes will develop CKD, also known as diabetic kidney disease (DKD). Thus, preventing these kidney diseases can positively impact quality-of-life and life-expectancy outcomes for affected individuals. Frequent episodes of hyperglycemia and renal hypoxia are implicated in the pathophysiology of CKD. Prior periods of hyperglycemia/uncontrolled diabetes can result in development/progression of DKD even after achieving normoglycemia, a phenomenon known as metabolic memory or legacy effect. Similarly, in AKI, hypoxic memory is stored in renal cells even after recovery from the initial AKI episode and can transition to CKD. Epigenetic mechanisms involving DNA methylation, chromatin histone post-translational modifications, and noncoding RNAs are implicated in both metabolic and hypoxic memory, collectively known as "epigenetic memory." This epigenetic memory is generally reversible and provides a therapeutic avenue to ameliorate persistent disease progression due to hyperglycemia and hypoxia and prevent/ameliorate CKD progression. Indeed, therapeutic strategies targeting epigenetic memory are effective at preventing CKD development/progression in experimental models of AKI and DKD. Here, we review the latest in-depth evidence for epigenetic features in DKD and AKI, and in epigenetic memories of AKI-to-CKD transition or DKD development and progression, followed by translational and clinical implications of these epigenetic changes for the treatment of these widespread kidney disorders.
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Affiliation(s)
- Imari Mimura
- Division of Nephrology and Endocrinology, the University of Tokyo School of Medicine, Tokyo Japan.
| | - Zhuo Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA.
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13
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Kollenstart L, Biran A, Alcaraz N, Reverón-Gómez N, Solis-Mezarino V, Völker-Albert M, Jenkinson F, Flury V, Groth A. Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability. SCIENCE ADVANCES 2025; 11:eadr1453. [PMID: 39970210 PMCID: PMC11837984 DOI: 10.1126/sciadv.adr1453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 01/15/2025] [Indexed: 02/21/2025]
Abstract
In the process of DNA replication, the first steps in restoring the chromatin landscape involve parental histone recycling and new histone deposition. Disrupting histone recycling to either the leading or lagging strand induces asymmetric histone inheritance, affecting epigenome maintenance and cellular identity. However, the order and kinetics of these effects remain elusive. Here, we use inducible mutants to dissect the early and late consequences of impaired histone recycling. Simultaneous disruption of both leading (POLE4) and lagging strand (MCM2-2A) recycling pathways impairs the transmission of parental histones to newly synthesized DNA, releasing some parental histones to the soluble pool. Subsequently, H3K27me3 accumulates aberrantly during chromatin restoration in a manner preceding gene expression changes. Loss of histone inheritance and the ensuing chromatin restoration defects alter gene expression in embryonic stem cells and challenge differentiation programs and cell viability. Our findings demonstrate the importance of efficient transmission of histone-based information during DNA replication for maintaining chromatin landscapes, differentiation potential, and cellular viability.
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Affiliation(s)
- Leonie Kollenstart
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Alva Biran
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Nicolas Alcaraz
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Nazaret Reverón-Gómez
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
| | | | | | - Fion Jenkinson
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Valentin Flury
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen 2200, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark
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14
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Tsukamoto S, Mofrad MRK. Bridging scales in chromatin organization: Computational models of loop formation and their implications for genome function. J Chem Phys 2025; 162:054122. [PMID: 39918128 DOI: 10.1063/5.0232328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Accepted: 11/18/2024] [Indexed: 05/08/2025] Open
Abstract
Chromatin loop formation plays a crucial role in 3D genome interactions, with misfolding potentially leading to irregular gene expression and various diseases. While experimental tools such as Hi-C have advanced our understanding of genome interactions, the biophysical principles underlying chromatin loop formation remain elusive. This review examines computational approaches to chromatin folding, focusing on polymer models that elucidate chromatin loop mechanics. We discuss three key models: (1) the multi-loop-subcompartment model, which investigates the structural effects of loops on chromatin conformation; (2) the strings and binders switch model, capturing thermodynamic chromatin aggregation; and (3) the loop extrusion model, revealing the role of structural maintenance of chromosome complexes. In addition, we explore advanced models that address chromatin clustering heterogeneity in biological processes and disease progression. The review concludes with an outlook on open questions and current trends in chromatin loop formation and genome interactions, emphasizing the physical and computational challenges in the field.
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Affiliation(s)
- Shingo Tsukamoto
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, 208A Stanley Hall, Berkeley, California 94720-1762, USA
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, 208A Stanley Hall, Berkeley, California 94720-1762, USA
- Molecular Biophysics and Integrative BioImaging Division, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
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15
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Bell CC, Faulkner GJ, Gilan O. Chromatin-based memory as a self-stabilizing influence on cell identity. Genome Biol 2024; 25:320. [PMID: 39736786 DOI: 10.1186/s13059-024-03461-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 12/16/2024] [Indexed: 01/01/2025] Open
Abstract
Cell types are traditionally thought to be specified and stabilized by gene regulatory networks. Here, we explore how chromatin memory contributes to the specification and stabilization of cell states. Through pervasive, local, feedback loops, chromatin memory enables cell states that were initially unstable to become stable. Deeper appreciation of this self-stabilizing role for chromatin broadens our perspective of Waddington's epigenetic landscape from a static surface with islands of stability shaped by evolution, to a plasticine surface molded by experience. With implications for the evolution of cell types, stabilization of resistant states in cancer, and the widespread plasticity of complex life.
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Affiliation(s)
- Charles C Bell
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD, 4102, Australia.
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD, 4102, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, 4169, Australia
| | - Omer Gilan
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, 3004, Australia
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16
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Pease NA, Denecke KM, Chen L, Gerges PH, Kueh HY. A timed epigenetic switch balances T and ILC lineage proportions in the thymus. Development 2024; 151:dev203016. [PMID: 39655434 PMCID: PMC11664168 DOI: 10.1242/dev.203016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 11/04/2024] [Indexed: 01/11/2025]
Abstract
How multipotent progenitors give rise to multiple cell types in defined numbers is a central question in developmental biology. Epigenetic switches, acting at single gene loci, can generate extended delays in the activation of lineage-specifying genes and impact lineage decisions and cell type output. Here, we analyzed a timed epigenetic switch controlling expression of mouse Bcl11b, a transcription factor that drives T-cell commitment, but only after a multi-day delay. To investigate roles for this delay in controlling lineage decision making, we analyzed progenitors with a deletion in a distal Bcl11b enhancer, which extends this delay by ∼3 days. Strikingly, delaying Bcl11b activation reduces T-cell output but enhances innate lymphoid cell (ILC) generation in the thymus by redirecting uncommitted progenitors to the ILC lineages. Mechanistically, delaying Bcl11b activation promoted ILC redirection by enabling upregulation of the ILC-specifying transcription factor PLZF. Despite the upregulation of PLZF, committed ILC progenitors could subsequently express Bcl11b, which is also needed for type 2 ILC differentiation. These results show that epigenetic switches can control the activation timing and order of lineage-specifying genes to modulate cell type numbers and proportions.
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Affiliation(s)
- Nicholas A. Pease
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98105, USA
| | - Kathryn M. Denecke
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Lihua Chen
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Peter Habib Gerges
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98105, USA
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17
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Song A, Wang Y, Liu C, Yu J, Zhang Z, Lan L, Lin H, Zhao J, Li G. Replication-coupled inheritance of chromatin states. CELL INSIGHT 2024; 3:100195. [PMID: 39391004 PMCID: PMC11462216 DOI: 10.1016/j.cellin.2024.100195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 08/05/2024] [Accepted: 08/05/2024] [Indexed: 10/12/2024]
Abstract
During the development of eukaryote, faithful inheritance of chromatin states is central to the maintenance of cell fate. DNA replication poses a significant challenge for chromatin state inheritance because every nucleosome in the genome is disrupted as the replication fork passes. It has been found that many factors including DNA polymerases, histone chaperones, as well as, RNA Pol II and histone modifying enzymes coordinate spatially and temporally to maintain the epigenome during this progress. In this review, we provide a summary of the detailed mechanisms of replication-coupled nucleosome assembly and post-replication chromatin maturation, highlight the inheritance of chromatin states and epigenome during these processes, and discuss the future directions and challenges in this field.
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Affiliation(s)
- Aoqun Song
- New Cornerstone Science Laboratory, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunting Wang
- New Cornerstone Science Laboratory, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, 100101, China
| | - Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zixu Zhang
- New Cornerstone Science Laboratory, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liting Lan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiyan Lin
- New Cornerstone Science Laboratory, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jicheng Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Guohong Li
- New Cornerstone Science Laboratory, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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18
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Movilla Miangolarra A, Howard M. Theory of epigenetic switching due to stochastic histone mark loss during DNA replication. Phys Biol 2024; 22:016005. [PMID: 39556945 PMCID: PMC11605279 DOI: 10.1088/1478-3975/ad942c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Revised: 11/12/2024] [Accepted: 11/18/2024] [Indexed: 11/20/2024]
Abstract
How much information does a cell inherit from its ancestors beyond its genetic sequence? What are the epigenetic mechanisms that allow this? Despite the rise in available epigenetic data, how such information is inherited through the cell cycle is still not fully understood. Often, epigenetic marks can display bistable behaviour and their bistable state is transmitted to daughter cells through the cell cycle, providing the cell with a form of memory. However, loss-of-memory events also take place, where a daughter cell switches epigenetic state (with respect to the mother cell). Here, we develop a framework to compute these epigenetic switching rates, for the case when they are driven by DNA replication, i.e. the frequency of loss-of-memory events due to replication. We consider the dynamics of histone modifications during the cell cycle deterministically, except at DNA replication, where nucleosomes are randomly distributed between the two daughter DNA strands, which is therefore implemented stochastically. This hybrid stochastic-deterministic approach enables an analytic derivation of the replication-driven switching rate. While retaining great simplicity, this framework can explain experimental switching rate data, establishing its biological importance as a framework to quantitatively study epigenetic inheritance.
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Affiliation(s)
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
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19
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Dekker J, Mirny LA. The chromosome folding problem and how cells solve it. Cell 2024; 187:6424-6450. [PMID: 39547207 PMCID: PMC11569382 DOI: 10.1016/j.cell.2024.10.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2024] [Revised: 10/15/2024] [Accepted: 10/15/2024] [Indexed: 11/17/2024]
Abstract
Every cell must solve the problem of how to fold its genome. We describe how the folded state of chromosomes is the result of the combined activity of multiple conserved mechanisms. Homotypic affinity-driven interactions lead to spatial partitioning of active and inactive loci. Molecular motors fold chromosomes through loop extrusion. Topological features such as supercoiling and entanglements contribute to chromosome folding and its dynamics, and tethering loci to sub-nuclear structures adds additional constraints. Dramatically diverse chromosome conformations observed throughout the cell cycle and across the tree of life can be explained through differential regulation and implementation of these basic mechanisms. We propose that the first functions of chromosome folding are to mediate genome replication, compaction, and segregation and that mechanisms of folding have subsequently been co-opted for other roles, including long-range gene regulation, in different conditions, cell types, and species.
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Affiliation(s)
- Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Leonid A Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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20
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Li H, Playter C, Das P, McCord RP. Chromosome compartmentalization: causes, changes, consequences, and conundrums. Trends Cell Biol 2024; 34:707-727. [PMID: 38395734 PMCID: PMC11339242 DOI: 10.1016/j.tcb.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
The spatial segregation of the genome into compartments is a major feature of 3D genome organization. New data on mammalian chromosome organization across different conditions reveal important information about how and why these compartments form and change. A combination of epigenetic state, nuclear body tethering, physical forces, gene expression, and replication timing (RT) can all influence the establishment and alteration of chromosome compartments. We review the causes and implications of genomic regions undergoing a 'compartment switch' that changes their physical associations and spatial location in the nucleus. About 20-30% of genomic regions change compartment during cell differentiation or cancer progression, whereas alterations in response to a stimulus within a cell type are usually much more limited. However, even a change in 1-2% of genomic bins may have biologically relevant implications. Finally, we review the effects of compartment changes on gene regulation, DNA damage repair, replication, and the physical state of the cell.
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Affiliation(s)
- Heng Li
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Christopher Playter
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Priyojit Das
- University of Tennessee-Oak Ridge National Laboratory (UT-ORNL) Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Rachel Patton McCord
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA.
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21
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Chen Z, Malek V, Natarajan R. Update: the role of epigenetics in the metabolic memory of diabetic complications. Am J Physiol Renal Physiol 2024; 327:F327-F339. [PMID: 38961840 PMCID: PMC11460341 DOI: 10.1152/ajprenal.00115.2024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024] Open
Abstract
Diabetes, a chronic disease characterized by hyperglycemia, is associated with significantly accelerated complications, including diabetic kidney disease (DKD), which increases morbidity and mortality. Hyperglycemia and other diabetes-related environmental factors such as overnutrition, sedentary lifestyles, and hyperlipidemia can induce epigenetic changes. Working alone or with genetic factors, these epigenetic changes that occur without alterations in the underlying DNA sequence, can alter the expression of pathophysiological genes and impair functions of associated target cells/organs, leading to diabetic complications like DKD. Notably, some hyperglycemia-induced epigenetic changes persist in target cells/tissues even after glucose normalization, leading to sustained complications despite glycemic control, so-called metabolic memory. Emerging evidence from in vitro and in vivo animal models and clinical trials with subjects with diabetes identified clear associations between metabolic memory and epigenetic changes including DNA methylation, histone modifications, chromatin structure, and noncoding RNAs at key loci. Targeting such persistent epigenetic changes and/or molecules regulated by them can serve as valuable opportunities to attenuate, or erase metabolic memory, which is crucial to prevent complication progression. Here, we review these cell/tissue-specific epigenetic changes identified to-date as related to diabetic complications, especially DKD, and the current status on targeting epigenetics to tackle metabolic memory. We also discuss limitations in current studies, including the need for more (epi)genome-wide studies, integrative analysis using multiple epigenetic marks and Omics datasets, and mechanistic evaluation of metabolic memory. Considering the tremendous technological advances in epigenomics, genetics, sequencing, and availability of genomic datasets from clinical cohorts, this field is likely to see considerable progress in the upcoming years.
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Affiliation(s)
- Zhuo Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, California
| | - Vajir Malek
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, California
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, California
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22
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Playter C, Golloshi R, Garretson JH, Gonzalez AR, Olajide TH, Saad A, Benson SJ, McCord RP. Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.21.609017. [PMID: 39229109 PMCID: PMC11370405 DOI: 10.1101/2024.08.21.609017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Metastatic cancer cells traverse constricted spaces that exert forces on their nucleus and the genomic contents within. Cancerous tumors are highly heterogeneous and not all cells within them can achieve such a feat. Here, we investigated what initial genome architecture characteristics favor the constricted migratory ability of cancer cells and which arise only after passage through multiple constrictions. We identified a cell surface protein (ITGB4) whose expression correlates with increased initial constricted migration ability in human melanoma A375 cells. Sorting out this subpopulation allowed us to identify cellular and nuclear features that pre-exist and favor migration, as well as alterations that only appear after cells have passed through constrictions. We identified specific genomic regions that experienced altered genome spatial compartment profiles only after constricted migration. Our study reveals 3D genome structure contributions to both selection and induction mechanisms of cell fate change during cancer metastasis.
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23
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Stephens RK, Miroshnikova YA. Nuclear periphery and its mechanical regulation in cell fate transitions. Curr Opin Struct Biol 2024; 87:102867. [PMID: 38889500 DOI: 10.1016/j.sbi.2024.102867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/20/2024]
Abstract
Cell fate changes require rewiring of transcriptional programs to generate functionally specialized cell states. Reconfiguration of transcriptional networks requires overcoming epigenetic barriers imposed by silenced heterochromatin in order to activate lineage-specific genes. Further, cell fate decisions are made in a tissue-specific context, where cells are physically linked to each other as well as to the connective tissue environment. Here, cells are continuously exposed to a multitude of mechanical forces emanating from cellular dynamics in their local microenvironments, for example through cell movements, cell divisions, tissue contractions, or fluid flow. Through their ability to deform cellular structures and activate receptors, mechanical forces can be sensed at the plasma membrane, but also at the nuclear periphery through direct or cytoskeleton-mediated deformation of the nuclear envelope. This deformation and the associated signaling is capable of triggering changes in the mechanical state of the nuclear membranes, the organization and rigidity of the underlying nuclear lamina, compaction state of chromatin, and ultimately transcription. This review focuses on the role of nuclear architecture, particularly the nuclear lamina-chromatin interface, and its mechanical regulation in cell fate decisions as well as its physiological role in development and cellular reprogramming.
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Affiliation(s)
- Rebecca K Stephens
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA. https://twitter.com/BecKateStephens
| | - Yekaterina A Miroshnikova
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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24
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Ames A, Seman M, Larkin A, Raiymbek G, Chen Z, Levashkevich A, Kim B, Biteen JS, Ragunathan K. Epigenetic memory is governed by an effector recruitment specificity toggle in Heterochromatin Protein 1. Nat Commun 2024; 15:6276. [PMID: 39054315 PMCID: PMC11272775 DOI: 10.1038/s41467-024-50538-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
HP1 proteins are essential for establishing and maintaining transcriptionally silent heterochromatin. They dimerize, forming a binding interface to recruit diverse chromatin-associated factors. Although HP1 proteins are known to rapidly evolve, the extent of variation required to achieve functional specialization is unknown. To investigate how changes in amino acid sequence impacts heterochromatin formation, we performed a targeted mutagenesis screen of the S. pombe HP1 homolog, Swi6. Substitutions within an auxiliary surface adjacent to the HP1 dimerization interface produce Swi6 variants with divergent maintenance properties. Remarkably, substitutions at a single amino acid position lead to the persistent gain or loss of epigenetic inheritance. These substitutions increase Swi6 chromatin occupancy in vivo and altered Swi6-protein interactions that reprogram H3K9me maintenance. We show how relatively minor changes in Swi6 amino acid composition in an auxiliary surface can lead to profound changes in epigenetic inheritance providing a redundant mechanism to evolve HP1-effector specificity.
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Affiliation(s)
- Amanda Ames
- Department of Biology, Brandeis University, Waltham, MA, 02453, USA
| | - Melissa Seman
- Department of Biology, Brandeis University, Waltham, MA, 02453, USA
| | - Ajay Larkin
- Department of Biology, Brandeis University, Waltham, MA, 02453, USA
| | - Gulzhan Raiymbek
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ziyuan Chen
- Department of Biophysics, University of Michigan, Ann Arbor, MI, 48104, USA
| | | | - Bokyung Kim
- Department of Biochemistry, Brandeis University, Waltham, MA, 02453, USA
| | - Julie Suzanne Biteen
- Department of Biophysics, University of Michigan, Ann Arbor, MI, 48104, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48104, USA
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25
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Liberali P, Schier AF. The evolution of developmental biology through conceptual and technological revolutions. Cell 2024; 187:3461-3495. [PMID: 38906136 DOI: 10.1016/j.cell.2024.05.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Developmental biology-the study of the processes by which cells, tissues, and organisms develop and change over time-has entered a new golden age. After the molecular genetics revolution in the 80s and 90s and the diversification of the field in the early 21st century, we have entered a phase when powerful technologies provide new approaches and open unexplored avenues. Progress in the field has been accelerated by advances in genomics, imaging, engineering, and computational biology and by emerging model systems ranging from tardigrades to organoids. We summarize how revolutionary technologies have led to remarkable progress in understanding animal development. We describe how classic questions in gene regulation, pattern formation, morphogenesis, organogenesis, and stem cell biology are being revisited. We discuss the connections of development with evolution, self-organization, metabolism, time, and ecology. We speculate how developmental biology might evolve in an era of synthetic biology, artificial intelligence, and human engineering.
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Affiliation(s)
- Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland.
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26
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Manivannan V, Inamdar MM, Padinhateeri R. Role of diffusion and reaction of the constituents in spreading of histone modification marks. PLoS Comput Biol 2024; 20:e1012235. [PMID: 38991050 PMCID: PMC11265668 DOI: 10.1371/journal.pcbi.1012235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 07/23/2024] [Accepted: 06/06/2024] [Indexed: 07/13/2024] Open
Abstract
Cells switch genes ON or OFF by altering the state of chromatin via histone modifications at specific regulatory locations along the chromatin polymer. These gene regulation processes are carried out by a network of reactions in which the histone marks spread to neighboring regions with the help of enzymes. In the literature, this spreading has been studied as a purely kinetic, non-diffusive process considering the interactions between neighboring nucleosomes. In this work, we go beyond this framework and study the spreading of modifications using a reaction-diffusion (RD) model accounting for the diffusion of the constituents. We quantitatively segregate the modification profiles generated from kinetic and RD models. The diffusion and degradation of enzymes set a natural length scale for limiting the domain size of modification spreading, and the resulting enzyme limitation is inherent in our model. We also demonstrate the emergence of confined modification domains without the explicit requirement of a nucleation site. We explore polymer compaction effects on spreading and show that single-cell domains may differ from averaged profiles. We find that the modification profiles from our model are comparable with existing H3K9me3 data of S. pombe.
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Affiliation(s)
- Vinoth Manivannan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Mandar M. Inamdar
- Department of Civil Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Mumbai, India
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27
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Akilli N, Cheutin T, Cavalli G. Phase separation and inheritance of repressive chromatin domains. Curr Opin Genet Dev 2024; 86:102201. [PMID: 38701672 DOI: 10.1016/j.gde.2024.102201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 05/05/2024]
Abstract
Polycomb-associated chromatin and pericentromeric heterochromatin form genomic domains important for the epigenetic regulation of gene expression. Both Polycomb complexes and heterochromatin factors rely on 'read and write' mechanisms, which, on their own, are not sufficient to explain the formation and the maintenance of these epigenetic domains. Microscopy has revealed that they form specific nuclear compartments separated from the rest of the genome. Recently, some subunits of these molecular machineries have been shown to undergo phase separation, both in vitro and in vivo, suggesting that phase separation might play important roles in the formation and the function of these two kinds of repressive chromatin. In this review, we will present the recent advances in the field of facultative and constitutive heterochromatin formation and maintenance through phase separation.
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Affiliation(s)
- Nazli Akilli
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France. https://twitter.com/@sinmerank
| | - Thierry Cheutin
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
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28
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Movilla Miangolarra A, Saxton DS, Yan Z, Rine J, Howard M. Two-way feedback between chromatin compaction and histone modification state explains Saccharomyces cerevisiae heterochromatin bistability. Proc Natl Acad Sci U S A 2024; 121:e2403316121. [PMID: 38593082 PMCID: PMC11032488 DOI: 10.1073/pnas.2403316121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/02/2024] [Indexed: 04/11/2024] Open
Abstract
Compact chromatin is closely linked with gene silencing in part by sterically masking access to promoters, inhibiting transcription factor binding and preventing polymerase from efficiently transcribing a gene. However, a broader hypothesis suggests that chromatin compaction can be both a cause and a consequence of the locus histone modification state, with a tight bidirectional interaction underpinning bistable transcriptional states. To rigorously test this hypothesis, we developed a mathematical model for the dynamics of the HMR locus in Saccharomyces cerevisiae, that incorporates activating histone modifications, silencing proteins, and a dynamic, acetylation-dependent, three-dimensional locus size. Chromatin compaction enhances silencer protein binding, which in turn feeds back to remove activating histone modifications, leading to further compaction. The bistable output of the model was in good agreement with prior quantitative data, including switching rates from expressed to silent states (and vice versa), and protein binding/histone modification levels within the locus. We then tested the model by predicting changes in switching rates as the genetic length of the locus was increased, which were then experimentally verified. Such bidirectional feedback between chromatin compaction and the histone modification state may be a widespread and important regulatory mechanism given the hallmarks of many heterochromatic regions: physical chromatin compaction and dimerizing (or multivalent) silencing proteins.
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Affiliation(s)
| | - Daniel S. Saxton
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Zhi Yan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
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29
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Daniel B, Chen AY, Sandor K, Zhang W, Miao Z, Lareau CA, Yost KE, Chang HY, Satpathy AT. Regulation of immune signal integration and memory by inflammation-induced chromosome conformation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582872. [PMID: 38496446 PMCID: PMC10942375 DOI: 10.1101/2024.02.29.582872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
3-dimensional (3D) genome conformation is central to gene expression regulation, yet our understanding of its contribution to rapid transcriptional responses, signal integration, and memory in immune cells is limited. Here, we study the molecular regulation of the inflammatory response in primary macrophages using integrated transcriptomic, epigenomic, and chromosome conformation data, including base pair-resolution Micro-Capture C. We demonstrate that interleukin-4 (IL-4) primes the inflammatory response in macrophages by stably rewiring 3D genome conformation, juxtaposing endotoxin-, interferon-gamma-, and dexamethasone-responsive enhancers in close proximity to their cognate gene promoters. CRISPR-based perturbations of enhancer-promoter contacts or CCCTC-binding factor (CTCF) boundary elements demonstrated that IL-4-driven conformation changes are indispensable for enhanced and synergistic endotoxin-induced transcriptional responses, as well as transcriptional memory following stimulus removal. Moreover, transcriptional memory mediated by changes in chromosome conformation often occurred in the absence of changes in chromatin accessibility or histone modifications. Collectively, these findings demonstrate that rapid and memory transcriptional responses to immunological stimuli are encoded in the 3D genome.
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Affiliation(s)
- Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- These authors contributed equally to this work
- Present address: Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA, USA
| | - Andy Y. Chen
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- These authors contributed equally to this work
| | - Katalin Sandor
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- These authors contributed equally to this work
| | - Wenxi Zhang
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Zhuang Miao
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Caleb A. Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Present address: Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathryn E. Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Present address: Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Ansuman T. Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
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30
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Murphy SE, Boettiger AN. Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition. Nat Genet 2024; 56:493-504. [PMID: 38361032 DOI: 10.1038/s41588-024-01661-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Polycomb group proteins have a critical role in silencing transcription during development. It is commonly proposed that Polycomb-dependent changes in genome folding, which compact chromatin, contribute directly to repression by blocking the binding of activating complexes. Recently, it has also been argued that liquid-liquid demixing of Polycomb proteins facilitates this compaction and repression by phase-separating target genes into a membraneless compartment. To test these models, we used Optical Reconstruction of Chromatin Architecture to trace the Hoxa gene cluster, a canonical Polycomb target, in thousands of single cells. Across multiple cell types, we find that Polycomb-bound chromatin frequently explores decompact states and partial mixing with neighboring chromatin, while remaining uniformly repressed, challenging the repression-by-compaction or phase-separation models. Using polymer simulations, we show that these observed flexible ensembles can be explained by 'spatial feedback'-transient contacts that contribute to the propagation of the epigenetic state (epigenetic memory), without inducing a globular organization.
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Affiliation(s)
- Sedona Eve Murphy
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
- Department of Cell Biology, Yale University, New Haven, CT, USA
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