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Tamburri S, Rustichelli S, Amato S, Pasini D. Navigating the complexity of Polycomb repression: Enzymatic cores and regulatory modules. Mol Cell 2024; 84:3381-3405. [PMID: 39178860 DOI: 10.1016/j.molcel.2024.07.030] [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: 05/18/2024] [Revised: 07/12/2024] [Accepted: 07/30/2024] [Indexed: 08/26/2024]
Abstract
Polycomb proteins are a fundamental repressive system that plays crucial developmental roles by orchestrating cell-type-specific transcription programs that govern cell identity. Direct alterations of Polycomb activity are indeed implicated in human pathologies, including developmental disorders and cancer. General Polycomb repression is coordinated by three distinct activities that regulate the deposition of two histone post-translational modifications: tri-methylation of histone H3 lysine 27 (H3K27me3) and histone H2A at lysine 119 (H2AK119ub1). These activities exist in large and heterogeneous multiprotein ensembles consisting of common enzymatic cores regulated by heterogeneous non-catalytic modules composed of a large number of accessory proteins with diverse biochemical properties. Here, we have analyzed the current molecular knowledge, focusing on the functional interaction between the core enzymatic activities and their regulation mediated by distinct accessory modules. This provides a comprehensive analysis of the molecular details that control the establishment and maintenance of Polycomb repression, examining their underlying coordination and highlighting missing information and emerging new features of Polycomb-mediated transcriptional control.
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Affiliation(s)
- Simone Tamburri
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via A. di Rudinì 8, 20142 Milan, Italy.
| | - Samantha Rustichelli
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Simona Amato
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Diego Pasini
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via A. di Rudinì 8, 20142 Milan, Italy.
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2
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Wong MMK, Hachmer S, Gardner E, Runfola V, Arezza E, Megeney LA, Emerson CP, Gabellini D, Dilworth FJ. SMCHD1 activates the expression of genes required for the expansion of human myoblasts. Nucleic Acids Res 2024; 52:9450-9462. [PMID: 38994563 PMCID: PMC11381350 DOI: 10.1093/nar/gkae600] [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: 11/22/2023] [Revised: 06/01/2024] [Accepted: 06/27/2024] [Indexed: 07/13/2024] Open
Abstract
SMCHD1 is an epigenetic regulatory protein known to modulate the targeted repression of large chromatin domains. Diminished SMCHD1 function in muscle fibers causes Facioscapulohumeral Muscular Dystrophy (FSHD2) through derepression of the D4Z4 chromatin domain, an event which permits the aberrant expression of the disease-causing gene DUX4. Given that SMCHD1 plays a broader role in establishing the cellular epigenome, we examined whether loss of SMCHD1 function might affect muscle homeostasis through additional mechanisms. Here we show that acute depletion of SMCHD1 results in a DUX4-independent defect in myoblast proliferation. Genomic and transcriptomic experiments determined that SMCHD1 associates with enhancers of genes controlling cell cycle to activate their expression. Amongst these cell cycle regulatory genes, we identified LAP2 as a key target of SMCHD1 required for the expansion of myoblasts, where the ectopic expression of LAP2 rescues the proliferation defect of SMCHD1-depleted cells. Thus, the epigenetic regulator SMCHD1 can play the role of a transcriptional co-activator for maintaining the expression of genes required for muscle progenitor expansion. This DUX4-independent role for SMCHD1 in myoblasts suggests that the pathology of FSHD2 may be a consequence of defective muscle regeneration in addition to the muscle wasting caused by spurious DUX4 expression.
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Affiliation(s)
- Matthew Man-Kin Wong
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute; Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa; Ottawa, ON K1H 8L6, Canada
| | - Sarah Hachmer
- Department of Cell and Regenerative Biology, University of Wisconsin; Madison, WI 53705, USA
| | - Ed Gardner
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute; Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa; Ottawa, ON K1H 8L6, Canada
| | - Valeria Runfola
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano 20132, Italy
| | - Eric Arezza
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute; Ottawa, ON K1H 8L6, Canada
| | - Lynn A Megeney
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute; Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa; Ottawa, ON K1H 8L6, Canada
| | - Charles P Emerson
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Davide Gabellini
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano 20132, Italy
| | - F Jeffrey Dilworth
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute; Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa; Ottawa, ON K1H 8L6, Canada
- Department of Cell and Regenerative Biology, University of Wisconsin; Madison, WI 53705, USA
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3
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Peraldi R, Kmita M. 40 years of the homeobox: mechanisms of Hox spatial-temporal collinearity in vertebrates. Development 2024; 151:dev202508. [PMID: 39167089 DOI: 10.1242/dev.202508] [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] [Indexed: 08/23/2024]
Abstract
Animal body plans are established during embryonic development by the Hox genes. This patterning process relies on the differential expression of Hox genes along the head-to-tail axis. Hox spatial collinearity refers to the relationship between the organization of Hox genes in clusters and the differential Hox expression, whereby the relative order of the Hox genes within a cluster mirrors the spatial sequence of expression in the developing embryo. In vertebrates, the cluster organization is also associated with the timing of Hox activation, which harmonizes Hox expression with the progressive emergence of axial tissues. Thereby, in vertebrates, Hox temporal collinearity is intimately linked to Hox spatial collinearity. Understanding the mechanisms contributing to Hox temporal and spatial collinearity is thus key to the comprehension of vertebrate patterning. Here, we provide an overview of the main discoveries pertaining to the mechanisms of Hox spatial-temporal collinearity.
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Affiliation(s)
- Rodrigue Peraldi
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
- Programme de Biologie Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Marie Kmita
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
- Programme de Biologie Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Département de Médecine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Department of Experimental Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
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4
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Raynal F, Sengupta K, Plewczynski D, Aliaga B, Pancaldi V. Global chromatin reorganization and regulation of genes of specific evolutionary age in differentiation and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.30.564438. [PMID: 39149250 PMCID: PMC11326123 DOI: 10.1101/2023.10.30.564438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Oncogenesis is accompanied by chromatin organization alterations and reactivation of unicellular phenotypes at the metabolic and transcriptional level. The mechanisms connecting these two observations are unexplored, despite its relevance in cancer biology. Assigning evolutionary ages to genes in the context of 3D chromatin structure, we characterize the epigenomic landscape, expression regulation and spatial organization of genes according to their evolutionary ages. We describe topological changes across differentiation and find some of the patterns, involving Polycomb repression and RNA Pol II pausing, being reversed during oncogenesis. Going beyond the evidence of non-random organization of genes and chromatin features in the 3D epigenome, we suggest that these patterns lead to preferential interactions of old, intermediate and young genes, mediated by respectively RNA Polymerase II, Polycomb and the lamina. Our results are in line and expand recent findings implicating loss of Polycomb repression and activation of embryonal and early evolutionary programs in cancer.
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Affiliation(s)
- Flavien Raynal
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Kaustav Sengupta
- Laboratory of Functional and Structural Genomics, Center of New Technologies (CeNT), University of Warsaw, Mazowieckie, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Dariusz Plewczynski
- Laboratory of Functional and Structural Genomics, Center of New Technologies (CeNT), University of Warsaw, Mazowieckie, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Benoît Aliaga
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Vera Pancaldi
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Barcelona Supercomputing Center, Barcelona, Spain
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5
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Zagirova D, Kononkova A, Vaulin N, Khrameeva E. From compartments to loops: understanding the unique chromatin organization in neuronal cells. Epigenetics Chromatin 2024; 17:18. [PMID: 38783373 PMCID: PMC11112951 DOI: 10.1186/s13072-024-00538-6] [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: 02/01/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
The three-dimensional organization of the genome plays a central role in the regulation of cellular functions, particularly in the human brain. This review explores the intricacies of chromatin organization, highlighting the distinct structural patterns observed between neuronal and non-neuronal brain cells. We integrate findings from recent studies to elucidate the characteristics of various levels of chromatin organization, from differential compartmentalization and topologically associating domains (TADs) to chromatin loop formation. By defining the unique chromatin landscapes of neuronal and non-neuronal brain cells, these distinct structures contribute to the regulation of gene expression specific to each cell type. In particular, we discuss potential functional implications of unique neuronal chromatin organization characteristics, such as weaker compartmentalization, neuron-specific TAD boundaries enriched with active histone marks, and an increased number of chromatin loops. Additionally, we explore the role of Polycomb group (PcG) proteins in shaping cell-type-specific chromatin patterns. This review further emphasizes the impact of variations in chromatin architecture between neuronal and non-neuronal cells on brain development and the onset of neurological disorders. It highlights the need for further research to elucidate the details of chromatin organization in the human brain in order to unravel the complexities of brain function and the genetic mechanisms underlying neurological disorders. This research will help bridge a significant gap in our comprehension of the interplay between chromatin structure and cell functions.
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Affiliation(s)
- Diana Zagirova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Build.1, Moscow, 121205, Russia
- Research and Training Center on Bioinformatics, Institute for Information Transmission Problems (Kharkevich Institute) RAS, Bolshoy Karetny per. 19, Build.1, Moscow, 127051, Russia
| | - Anna Kononkova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Build.1, Moscow, 121205, Russia
| | - Nikita Vaulin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Build.1, Moscow, 121205, Russia
| | - Ekaterina Khrameeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Build.1, Moscow, 121205, Russia.
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6
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Destain H, Prahlad M, Kratsios P. Maintenance of neuronal identity in C. elegans and beyond: Lessons from transcription and chromatin factors. Semin Cell Dev Biol 2024; 154:35-47. [PMID: 37438210 PMCID: PMC10592372 DOI: 10.1016/j.semcdb.2023.07.001] [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: 04/26/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/14/2023]
Abstract
Neurons are remarkably long-lived, non-dividing cells that must maintain their functional features (e.g., electrical properties, chemical signaling) for extended periods of time - decades in humans. How neurons accomplish this incredible feat is poorly understood. Here, we review recent advances, primarily in the nematode C. elegans, that have enhanced our understanding of the molecular mechanisms that enable post-mitotic neurons to maintain their functionality across different life stages. We begin with "terminal selectors" - transcription factors necessary for the establishment and maintenance of neuronal identity. We highlight new findings on five terminal selectors (CHE-1 [Glass], UNC-3 [Collier/Ebf1-4], LIN-39 [Scr/Dfd/Hox4-5], UNC-86 [Acj6/Brn3a-c], AST-1 [Etv1/ER81]) from different transcription factor families (ZNF, COE, HOX, POU, ETS). We compare the functions of these factors in specific neuron types of C. elegans with the actions of their orthologs in other invertebrate (D. melanogaster) and vertebrate (M. musculus) systems, highlighting remarkable functional conservation. Finally, we reflect on recent findings implicating chromatin-modifying proteins, such as histone methyltransferases and Polycomb proteins, in the control of neuronal terminal identity. Altogether, these new studies on transcription factors and chromatin modifiers not only shed light on the fundamental problem of neuronal identity maintenance, but also outline mechanistic principles of gene regulation that may operate in other long-lived, post-mitotic cell types.
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Affiliation(s)
- Honorine Destain
- Department of Neurobiology, University of Chicago, Chicago, IL, USA; Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, IL, USA; University of Chicago Neuroscience Institute, Chicago, IL, USA
| | - Manasa Prahlad
- Department of Neurobiology, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA; University of Chicago Neuroscience Institute, Chicago, IL, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, USA; Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA; University of Chicago Neuroscience Institute, Chicago, IL, USA.
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7
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Miller A, Dasen JS. Establishing and maintaining Hox profiles during spinal cord development. Semin Cell Dev Biol 2024; 152-153:44-57. [PMID: 37029058 PMCID: PMC10524138 DOI: 10.1016/j.semcdb.2023.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/18/2023] [Accepted: 03/30/2023] [Indexed: 04/09/2023]
Abstract
The chromosomally-arrayed Hox gene family plays central roles in embryonic patterning and the specification of cell identities throughout the animal kingdom. In vertebrates, the relatively large number of Hox genes and pervasive expression throughout the body has hindered understanding of their biological roles during differentiation. Studies on the subtype diversification of spinal motor neurons (MNs) have provided a tractable system to explore the function of Hox genes during differentiation, and have provided an entry point to explore how neuronal fate determinants contribute to motor circuit assembly. Recent work, using both in vitro and in vivo models of MN subtype differentiation, have revealed how patterning morphogens and regulation of chromatin structure determine cell-type specific programs of gene expression. These studies have not only shed light on basic mechanisms of rostrocaudal patterning in vertebrates, but also have illuminated mechanistic principles of gene regulation that likely operate in the development and maintenance of terminal fates in other systems.
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Affiliation(s)
- Alexander Miller
- NYU Neuroscience Institute and Developmental Genetics Programs, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA.
| | - Jeremy S Dasen
- NYU Neuroscience Institute and Developmental Genetics Programs, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA.
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8
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Parast SM, Yu D, Chen C, Dickinson AJ, Chang C, Wang H. Recognition of H2AK119ub plays an important role in RSF1-regulated early Xenopus development. Front Cell Dev Biol 2023; 11:1168643. [PMID: 37529237 PMCID: PMC10389277 DOI: 10.3389/fcell.2023.1168643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/07/2023] [Indexed: 08/03/2023] Open
Abstract
Polycomb group (PcG) proteins are key regulators of gene expression and developmental programs via covalent modification of histones, but the factors that interpret histone modification marks to regulate embryogenesis are less studied. We previously identified Remodeling and Spacing Factor 1 (RSF1) as a reader of histone H2A lysine 119 ubiquitination (H2AK119ub), the histone mark deposited by Polycomb Repressive Complex 1 (PRC1). In the current study, we used Xenopus laevis as a model to investigate how RSF1 affects early embryonic development and whether recognition of H2AK119ub is important for the function of RSF1. We showed that knockdown of Xenopus RSF1, rsf1, not only induced gastrulation defects as reported previously, but specific targeted knockdown in prospective neural precursors induced neural and neural crest defects, with reductions of marker genes. In addition, similar to knockdown of PRC1 components in Xenopus, the anterior-posterior neural patterning was affected in rsf1 knockdown embryos. Binding of H2AK119ub appeared to be crucial for rsf1 function, as a construct with deletion of the UAB domain, which is required for RSF1 to recognize the H2AK119ub nucleosomes, failed to rescue rsf1 morphant embryos and was less effective in interfering with early Xenopus development when ectopically expressed. Furthermore, ectopic deposition of H2AK119ub on the Smad2 target gene gsc using a ring1a-smad2 fusion protein led to ectopic recruitment of RSF1. The fusion protein was inefficient in inducing mesodermal markers in the animal region or a secondary axis when expressed in the ventral tissues. Taken together, our results reveal that rsf1 modulates similar developmental processes in early Xenopus embryos as components of PRC1 do, and that RSF1 acts at least partially through binding to the H2AK119ub mark via the UAB domain during development.
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Affiliation(s)
- Saeid Mohammad Parast
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Deli Yu
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Chunxu Chen
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Biomedical Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Amanda J. Dickinson
- Department of Biology, College of Humanities and Sciences, Virginia Commonwealth University, Richmond, VA, United States
| | - Chenbei Chang
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Hengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
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9
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Bredel M, Espinosa L, Kim H, Scholtens DM, McElroy JP, Rajbhandari R, Meng W, Kollmeyer TM, Malta TM, Quezada MA, Harsh GR, Lobo-Jarne T, Solé L, Merati A, Nagaraja S, Nair S, White JJ, Thudi NK, Fleming JL, Webb A, Natsume A, Ogawa S, Weber RG, Bertran J, Haque SJ, Hentschel B, Miller CR, Furnari FB, Chan TA, Grosu AL, Weller M, Barnholtz-Sloan JS, Monje M, Noushmehr H, Jenkins RB, Rogers CL, MacDonald DR, Pugh SL, Chakravarti A. Haploinsufficiency of NFKBIA reshapes the epigenome antipodal to the IDH mutation and imparts disease fate in diffuse gliomas. Cell Rep Med 2023; 4:101082. [PMID: 37343523 PMCID: PMC10314122 DOI: 10.1016/j.xcrm.2023.101082] [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: 04/22/2022] [Revised: 11/18/2022] [Accepted: 05/18/2023] [Indexed: 06/23/2023]
Abstract
Genetic alterations help predict the clinical behavior of diffuse gliomas, but some variability remains uncorrelated. Here, we demonstrate that haploinsufficient deletions of chromatin-bound tumor suppressor NFKB inhibitor alpha (NFKBIA) display distinct patterns of occurrence in relation to other genetic markers and are disproportionately present at recurrence. NFKBIA haploinsufficiency is associated with unfavorable patient outcomes, independent of genetic and clinicopathologic predictors. NFKBIA deletions reshape the DNA and histone methylome antipodal to the IDH mutation and induce a transcriptome landscape partly reminiscent of H3K27M mutant pediatric gliomas. In IDH mutant gliomas, NFKBIA deletions are common in tumors with a clinical course similar to that of IDH wild-type tumors. An externally validated nomogram model for estimating individual patient survival in IDH mutant gliomas confirms that NFKBIA deletions predict comparatively brief survival. Thus, NFKBIA haploinsufficiency aligns with distinct epigenome changes, portends a poor prognosis, and should be incorporated into models predicting the disease fate of diffuse gliomas.
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Affiliation(s)
- Markus Bredel
- Department of Radiation Oncology, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA.
| | - Lluís Espinosa
- Cancer Research Program, Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Institut Mar d'Investigacions Mèdiques, Hospital del Mar, 08003 Barcelona, Spain
| | - Hyunsoo Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Denise M Scholtens
- Division of Biostatistics-Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Joseph P McElroy
- Center for Biostatistics-Department of Biomedical Informatics, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Rajani Rajbhandari
- Department of Radiation Oncology, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Wei Meng
- Department of Radiation Oncology, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Thomas M Kollmeyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Tathiane M Malta
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI 48202, USA
| | - Michael A Quezada
- Department of Neurology & Neurological Sciences and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Griffith R Harsh
- Department of Neurological Surgery, University of California at Davis School of Medicine, Sacramento, CA 95817, USA
| | - Teresa Lobo-Jarne
- Cancer Research Program, Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Institut Mar d'Investigacions Mèdiques, Hospital del Mar, 08003 Barcelona, Spain
| | - Laura Solé
- Cancer Research Program, Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Institut Mar d'Investigacions Mèdiques, Hospital del Mar, 08003 Barcelona, Spain
| | - Aran Merati
- Department of Radiation Oncology, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Surya Nagaraja
- Department of Neurology & Neurological Sciences and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sindhu Nair
- Department of Radiation Oncology, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Jaclyn J White
- Department of Neurosurgery, Wake Forest University School of Medicine, Winston-Salem, NC 27103, USA
| | - Nanda K Thudi
- Department of Radiation Oncology, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Jessica L Fleming
- Department of Radiation Oncology, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Amy Webb
- Center for Biostatistics-Department of Biomedical Informatics, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Atsushi Natsume
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya 464-8601, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Ruthild G Weber
- Institute for Human Genetics, Hannover Medical School, 30625 Hannover, Germany
| | - Joan Bertran
- Biosciences Department, Faculty of Sciences, Technology, and Engineering. University of Vic-Central University of Catalonia, 08500 Vic, Spain
| | - S Jaharul Haque
- Department of Radiation Oncology, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Bettina Hentschel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107 Leipzig, Germany
| | - C Ryan Miller
- Division of Neuropathology-Department of Pathology, O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Frank B Furnari
- Laboratory of Tumor Biology, Division of Regenerative Medicine-Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Timothy A Chan
- Center for Immunotherapy and Precision Immuno-Oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Anca-Ligia Grosu
- Department of Radiation Oncology, Comprehensive Cancer Center, University of Freiburg, 79106 Freiburg, Germany
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, 8091 Zurich, Switzerland
| | - Jill S Barnholtz-Sloan
- Division of Cancer Epidemiology and Genetics-National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michelle Monje
- Department of Neurology & Neurological Sciences and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Houtan Noushmehr
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI 48202, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - David R MacDonald
- London Regional Cancer Program, Western University, London, ON N6A 5W9, Canada
| | - Stephanie L Pugh
- NRG Oncology Statistics and Data Management Center, Philadelphia, PA 19103, USA
| | - Arnab Chakravarti
- Department of Radiation Oncology, James Cancer Hospital and Solove Research Institute, The Ohio State University College of Medicine, Columbus, OH 43210, USA
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10
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Fedoseyeva VB, Novosadova EV, Nenasheva VV, Novosadova LV, Grivennikov IA, Tarantul VZ. Transcription of HOX Genes Is Significantly Increased during Neuronal Differentiation of iPSCs Derived from Patients with Parkinson's Disease. J Dev Biol 2023; 11:23. [PMID: 37367477 DOI: 10.3390/jdb11020023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/10/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
Parkinson's disease (PD) is the most serious movement disorder, but the actual cause of this disease is still unknown. Induced pluripotent stem cell-derived neural cultures from PD patients carry the potential for experimental modeling of underlying molecular events. We analyzed the RNA-seq data of iPSC-derived neural precursor cells (NPCs) and terminally differentiated neurons (TDNs) from healthy donors (HD) and PD patients with mutations in PARK2 published previously. The high level of transcription of HOX family protein-coding genes and lncRNA transcribed from the HOX clusters was revealed in the neural cultures from PD patients, while in HD NPCs and TDNs, the majority of these genes were not expressed or slightly transcribed. The results of this analysis were generally confirmed by qPCR. The HOX paralogs in the 3' clusters were activated more strongly than the genes of the 5' cluster. The abnormal activation of the HOX gene program upon neuronal differentiation in the cells of PD patients raises the possibility that the abnormal expression of these key regulators of neuronal development impacts PD pathology. Further research is needed to investigate this hypothesis.
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Affiliation(s)
- Viya B Fedoseyeva
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
| | - Ekaterina V Novosadova
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
| | - Valentina V Nenasheva
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
| | - Lyudmila V Novosadova
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
| | - Igor A Grivennikov
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
| | - Vyacheslav Z Tarantul
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
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11
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Imagawa E, Seyama R, Aoi H, Uchiyama Y, Marcarini BG, Furquim I, Honjo RS, Bertola DR, Kim CA, Matsumoto N. Imagawa-Matsumoto syndrome: SUZ12-related overgrowth disorder. Clin Genet 2023; 103:383-391. [PMID: 36645289 DOI: 10.1111/cge.14296] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/17/2023]
Abstract
The SUZ12 gene encodes a subunit of polycomb repressive complex 2 (PRC2) that is essential for development by silencing the expression of multiple genes. Germline heterozygous variants in SUZ12 have been found in Imagawa-Matsumoto syndrome (IMMAS) characterized by overgrowth and multiple dysmorphic features. Similarly, both EZH2 and EED also encode a subunit of PRC2 each and their pathogenic variants cause Weaver syndrome and Cohen-Gibson syndrome, respectively. Clinical manifestations of these syndromes significantly overlap, although their different prevalence rates have recently been noted: generalized overgrowth, intellectual disability, scoliosis, and excessive loose skin appear to be less prevalent in IMMAS than in the other two syndromes. We could not determine any apparent genotype-phenotype correlation in IMMAS. The phenotype of neurofibromatosis type 1 arising from NF1 deletion was also shown to be modified by the deletion of SUZ12, 560 kb away. This review deepens our understanding of the clinical and genetic characteristics of IMMAS together with other overgrowth syndromes related to PRC2. We also report on a novel IMMAS patient carrying a splicing variant (c.1023+1G>C) in SUZ12. This patient had a milder phenotype than other previously reported IMMAS cases, with no macrocephaly or overgrowth phenotypes, highlighting the clinical variation in IMMAS.
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Affiliation(s)
- Eri Imagawa
- Department of Pediatrics, The Jikei University School of Medicine, Tokyo, Japan
| | - Rie Seyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Hiromi Aoi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Bruno Guimaraes Marcarini
- Genetics Unit, Instituto da Crianca, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Isabel Furquim
- Genetics Unit, Instituto da Crianca, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Rachel Sayuri Honjo
- Genetics Unit, Instituto da Crianca, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Debora Romeo Bertola
- Genetics Unit, Instituto da Crianca, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Chong Ae Kim
- Genetics Unit, Instituto da Crianca, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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12
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Ajuyah P, Mayoh C, Lau LMS, Barahona P, Wong M, Chambers H, Valdes-Mora F, Senapati A, Gifford AJ, D'Arcy C, Hansford JR, Manoharan N, Nicholls W, Williams MM, Wood PJ, Cowley MJ, Tyrrell V, Haber M, Ekert PG, Ziegler DS, Khuong-Quang DA. Histone H3-wild type diffuse midline gliomas with H3K27me3 loss are a distinct entity with exclusive EGFR or ACVR1 mutation and differential methylation of homeobox genes. Sci Rep 2023; 13:3775. [PMID: 36882456 PMCID: PMC9992705 DOI: 10.1038/s41598-023-30395-4] [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: 09/13/2022] [Accepted: 02/22/2023] [Indexed: 03/09/2023] Open
Abstract
Diffuse midline gliomas (DMG) harbouring H3K27M mutation are paediatric tumours with a dismal outcome. Recently, a new subtype of midline gliomas has been described with similar features to DMG, including loss of H3K27 trimethylation, but lacking the canonical H3K27M mutation (H3-WT). Here, we report a cohort of five H3-WT tumours profiled by whole-genome sequencing, RNA sequencing and DNA methylation profiling and combine their analysis with previously published cases. We show that these tumours have recurrent and mutually exclusive mutations in either ACVR1 or EGFR and are characterised by high expression of EZHIP associated to its promoter hypomethylation. Affected patients share a similar poor prognosis as patients with H3K27M DMG. Global molecular analysis of H3-WT and H3K27M DMG reveal distinct transcriptome and methylome profiles including differential methylation of homeobox genes involved in development and cellular differentiation. Patients have distinct clinical features, with a trend demonstrating ACVR1 mutations occurring in H3-WT tumours at an older age. This in-depth exploration of H3-WT tumours further characterises this novel DMG, H3K27-altered sub-group, characterised by a specific immunohistochemistry profile with H3K27me3 loss, wild-type H3K27M and positive EZHIP. It also gives new insights into the possible mechanism and pathway regulation in these tumours, potentially opening new therapeutic avenues for these tumours which have no known effective treatment. This study has been retrospectively registered on clinicaltrial.gov on 8 November 2017 under the registration number NCT03336931 ( https://clinicaltrials.gov/ct2/show/NCT03336931 ).
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Affiliation(s)
- Pamela Ajuyah
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia
| | - Chelsea Mayoh
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Loretta M S Lau
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia.,Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia
| | - Paulette Barahona
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia
| | - Marie Wong
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Hazel Chambers
- Department of Anatomical Pathology, Royal Children's Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Fatima Valdes-Mora
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Akanksha Senapati
- Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia
| | - Andrew J Gifford
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,Anatomical Pathology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Colleen D'Arcy
- Department of Anatomical Pathology, Royal Children's Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Jordan R Hansford
- Children's Cancer Centre, Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.,Michael Rice Cancer Centre, Women's and Children's Hospital, Adelaide, SA, Australia.,South Australia Health and Medical Research Institute, Adelaide, SA, Australia.,South Australia Immunogenomics Cancer Institute, Adelaide, SA, Australia.,University of Adelaide, Adelaide, SA, Australia
| | - Neevika Manoharan
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia
| | - Wayne Nicholls
- Oncology Service, Children's Health Queensland Hospital & Health Service, Brisbane, QLD, Australia
| | - Molly M Williams
- Children's Cancer Centre, Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Paul J Wood
- Department of Paediatrics, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Mark J Cowley
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Vanessa Tyrrell
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Michelle Haber
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Paul G Ekert
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia.,Cancer Immunology Program, Peter MacCallum Cancer Centre, Parkville, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - David S Ziegler
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia. .,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia. .,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia. .,Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia.
| | - Dong-Anh Khuong-Quang
- Children's Cancer Centre, Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia. .,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.
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13
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Richer S, Tian Y, Schoenfelder S, Hurst L, Murrell A, Pisignano G. Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters. Genome Biol 2023; 24:40. [PMID: 36869353 PMCID: PMC9983196 DOI: 10.1186/s13059-023-02876-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND There is widespread interest in the three-dimensional chromatin conformation of the genome and its impact on gene expression. However, these studies frequently do not consider parent-of-origin differences, such as genomic imprinting, which result in monoallelic expression. In addition, genome-wide allele-specific chromatin conformation associations have not been extensively explored. There are few accessible bioinformatic workflows for investigating allelic conformation differences and these require pre-phased haplotypes which are not widely available. RESULTS We developed a bioinformatic pipeline, "HiCFlow," that performs haplotype assembly and visualization of parental chromatin architecture. We benchmarked the pipeline using prototype haplotype phased Hi-C data from GM12878 cells at three disease-associated imprinted gene clusters. Using Region Capture Hi-C and Hi-C data from human cell lines (1-7HB2, IMR-90, and H1-hESCs), we can robustly identify the known stable allele-specific interactions at the IGF2-H19 locus. Other imprinted loci (DLK1 and SNRPN) are more variable and there is no "canonical imprinted 3D structure," but we could detect allele-specific differences in A/B compartmentalization. Genome-wide, when topologically associating domains (TADs) are unbiasedly ranked according to their allele-specific contact frequencies, a set of allele-specific TADs could be defined. These occur in genomic regions of high sequence variation. In addition to imprinted genes, allele-specific TADs are also enriched for allele-specific expressed genes. We find loci that have not previously been identified as allele-specific expressed genes such as the bitter taste receptors (TAS2Rs). CONCLUSIONS This study highlights the widespread differences in chromatin conformation between heterozygous loci and provides a new framework for understanding allele-specific expressed genes.
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Affiliation(s)
- Stephen Richer
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Yuan Tian
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- UCL Cancer Institute, University College London, Paul O'Gorman Building, London, UK
| | | | - Laurence Hurst
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Adele Murrell
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - Giuseppina Pisignano
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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14
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Xie L, Ding N, Sheng S, Zhang H, Yin H, Gao L, Zhang H, Ma S, Yang A, Li G, Jiao Y, Shi Q, Jiang Y, Zhang H. Cooperation between NSPc1 and DNA methylation represses HOXA11 expression and promotes apoptosis of trophoblast cells during preeclampsia. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1-13. [PMID: 36815373 PMCID: PMC10157525 DOI: 10.3724/abbs.2023012] [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: 05/16/2022] [Accepted: 07/03/2022] [Indexed: 02/05/2023] Open
Abstract
Accumulating evidence has shown that the apoptosis of trophoblast cells plays an important role in the pathogenesis of preeclampsia, and an intricate interplay between DNA methylation and polycomb group (PcG) protein-mediated gene silencing has been highlighted recently. Here, we provide evidence that the expression of nervous system polycomb 1 (NSPc1), a BMI1 homologous polycomb protein, is significantly elevated in trophoblast cells during preeclampsia, which accelerates trophoblast cell apoptosis. Since NSPc1 acts predominantly as a transcriptional inactivator that specifically represses HOXA11 expression in trophoblast cells during preeclampsia, we further show that NSPc1 is required for DNMT3a recruitment and maintenance of the DNA methylation in the HOXA11 promoter in trophoblast cells during preeclampsia. In addition, we find that the interplay of DNMT3a and NSPc1 represses the expression of HOXA11 and promotes trophoblast cell apoptosis. Taken together, these results indicate that the cooperation between NSPc1 and DNMT3a reduces HOXA11 expression in preeclampsia pathophysiology, which provides novel therapeutic approaches for targeted inhibition of trophoblast cell apoptosis during preeclampsia pathogenesis.
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Affiliation(s)
- Lin Xie
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
- School of Basic Medical SciencesNingxia Medical UniversityYinchuan750004China
| | - Ning Ding
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
- School of Basic Medical SciencesNingxia Medical UniversityYinchuan750004China
| | - Siqi Sheng
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
- School of Basic Medical SciencesNingxia Medical UniversityYinchuan750004China
| | - Honghong Zhang
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
- School of Basic Medical SciencesNingxia Medical UniversityYinchuan750004China
| | - He Yin
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
- Department of Clinical MedicineNingxia Medical UniversityYinchuan750004China
| | - Lina Gao
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
- Department of Clinical MedicineNingxia Medical UniversityYinchuan750004China
| | - Hui Zhang
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
- School of Basic Medical SciencesNingxia Medical UniversityYinchuan750004China
| | - Shengchao Ma
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
- School of Basic Medical SciencesNingxia Medical UniversityYinchuan750004China
| | - Anning Yang
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
- School of Basic Medical SciencesNingxia Medical UniversityYinchuan750004China
| | - Guizhong Li
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
- School of Basic Medical SciencesNingxia Medical UniversityYinchuan750004China
| | - Yun Jiao
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
- Department of Infectious DiseasesGeneral Hospital of Ningxia Medical UniversityYinchuan750004China
| | - Qing Shi
- Department of GynecologyGeneral Hospital of Ningxia Medical UniversityYinchuan750004China
| | - Yideng Jiang
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
- School of Basic Medical SciencesNingxia Medical UniversityYinchuan750004China
| | - Huiping Zhang
- Department of Medical GeneticsMaternal and Child Health of Hunan ProvinceChangsha410008China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
- General Hospital of Ningxia Medical UniversityYinchuan750004China
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15
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Fu MP, Merrill SM, Sharma M, Gibson WT, Turvey SE, Kobor MS. Rare diseases of epigenetic origin: Challenges and opportunities. Front Genet 2023; 14:1113086. [PMID: 36814905 PMCID: PMC9939656 DOI: 10.3389/fgene.2023.1113086] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
Rare diseases (RDs), more than 80% of which have a genetic origin, collectively affect approximately 350 million people worldwide. Progress in next-generation sequencing technology has both greatly accelerated the pace of discovery of novel RDs and provided more accurate means for their diagnosis. RDs that are driven by altered epigenetic regulation with an underlying genetic basis are referred to as rare diseases of epigenetic origin (RDEOs). These diseases pose unique challenges in research, as they often show complex genetic and clinical heterogeneity arising from unknown gene-disease mechanisms. Furthermore, multiple other factors, including cell type and developmental time point, can confound attempts to deconvolute the pathophysiology of these disorders. These challenges are further exacerbated by factors that contribute to epigenetic variability and the difficulty of collecting sufficient participant numbers in human studies. However, new molecular and bioinformatics techniques will provide insight into how these disorders manifest over time. This review highlights recent studies addressing these challenges with innovative solutions. Further research will elucidate the mechanisms of action underlying unique RDEOs and facilitate the discovery of treatments and diagnostic biomarkers for screening, thereby improving health trajectories and clinical outcomes of affected patients.
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Affiliation(s)
- Maggie P. Fu
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Sarah M. Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Mehul Sharma
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - William T. Gibson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Stuart E. Turvey
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada,*Correspondence: Michael S. Kobor,
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16
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Abstract
Hox genes encode evolutionarily conserved transcription factors that are essential for the proper development of bilaterian organisms. Hox genes are unique because they are spatially and temporally regulated during development in a manner that is dictated by their tightly linked genomic organization. Although their genetic function during embryonic development has been interrogated, less is known about how these transcription factors regulate downstream genes to direct morphogenetic events. Moreover, the continued expression and function of Hox genes at postnatal and adult stages highlights crucial roles for these genes throughout the life of an organism. Here, we provide an overview of Hox genes, highlighting their evolutionary history, their unique genomic organization and how this impacts the regulation of their expression, what is known about their protein structure, and their deployment in development and beyond.
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Affiliation(s)
- Katharine A. Hubert
- Program in Genetics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Deneen M. Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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17
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Feng W, Destain H, Smith JJ, Kratsios P. Maintenance of neurotransmitter identity by Hox proteins through a homeostatic mechanism. Nat Commun 2022; 13:6097. [PMID: 36243871 PMCID: PMC9569373 DOI: 10.1038/s41467-022-33781-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Hox transcription factors play fundamental roles during early patterning, but they are also expressed continuously, from embryonic stages through adulthood, in the nervous system. However, the functional significance of their sustained expression remains unclear. In C. elegans motor neurons (MNs), we find that LIN-39 (Scr/Dfd/Hox4-5) is continuously required during post-embryonic life to maintain neurotransmitter identity, a core element of neuronal function. LIN-39 acts directly to co-regulate genes that define cholinergic identity (e.g., unc-17/VAChT, cho-1/ChT). We further show that LIN-39, MAB-5 (Antp/Hox6-8) and the transcription factor UNC-3 (Collier/Ebf) operate in a positive feedforward loop to ensure continuous and robust expression of cholinergic identity genes. Finally, we identify a two-component design principle for homeostatic control of Hox gene expression in adult MNs: Hox transcriptional autoregulation is counterbalanced by negative UNC-3 feedback. These findings uncover a noncanonical role for Hox proteins during post-embryonic life, critically broadening their functional repertoire from early patterning to the control of neurotransmitter identity.
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Affiliation(s)
- Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- University of Chicago Neuroscience Institute, Chicago, IL, USA
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL, USA
| | - Honorine Destain
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- University of Chicago Neuroscience Institute, Chicago, IL, USA
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL, USA
| | - Jayson J Smith
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- University of Chicago Neuroscience Institute, Chicago, IL, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, USA.
- University of Chicago Neuroscience Institute, Chicago, IL, USA.
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL, USA.
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18
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Sawai A, Pfennig S, Bulajić M, Miller A, Khodadadi-Jamayran A, Mazzoni EO, Dasen JS. PRC1 sustains the integrity of neural fate in the absence of PRC2 function. eLife 2022; 11:e72769. [PMID: 34994686 PMCID: PMC8765755 DOI: 10.7554/elife.72769] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/06/2022] [Indexed: 12/13/2022] Open
Abstract
Polycomb repressive complexes (PRCs) 1 and 2 maintain stable cellular memories of early fate decisions by establishing heritable patterns of gene repression. PRCs repress transcription through histone modifications and chromatin compaction, but their roles in neuronal subtype diversification are poorly defined. We found that PRC1 is essential for the specification of segmentally restricted spinal motor neuron (MN) subtypes, while PRC2 activity is dispensable to maintain MN positional identities during terminal differentiation. Mutation of the core PRC1 component Ring1 in mice leads to increased chromatin accessibility and ectopic expression of a broad variety of fates determinants, including Hox transcription factors, while neuronal class-specific features are maintained. Loss of MN subtype identities in Ring1 mutants is due to the suppression of Hox-dependent specification programs by derepressed Hox13 paralogs (Hoxa13, Hoxb13, Hoxc13, Hoxd13). These results indicate that PRC1 can function in the absence of de novo PRC2-dependent histone methylation to maintain chromatin topology and postmitotic neuronal fate.
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Affiliation(s)
- Ayana Sawai
- Neuroscience Institute, Department of Neuroscience and Physiology, NYU School of MedicineNew YorkUnited States
| | - Sarah Pfennig
- Neuroscience Institute, Department of Neuroscience and Physiology, NYU School of MedicineNew YorkUnited States
| | - Milica Bulajić
- Department of Biology, New York UniversityNew YorkUnited States
| | - Alexander Miller
- Neuroscience Institute, Department of Neuroscience and Physiology, NYU School of MedicineNew YorkUnited States
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories, Office of Science and Research, NYU School of MedcineNew YorkUnited States
| | | | - Jeremy S Dasen
- Neuroscience Institute, Department of Neuroscience and Physiology, NYU School of MedicineNew YorkUnited States
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Cai C, Peng X, Zhang Y. Downregulation of cell division cycle-associated protein 7 (CDCA7) suppresses cell proliferation, arrests cell cycle of ovarian cancer, and restrains angiogenesis by modulating enhancer of zeste homolog 2 (EZH2) expression. Bioengineered 2021; 12:7007-7019. [PMID: 34551671 PMCID: PMC8806772 DOI: 10.1080/21655979.2021.1965441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The purpose of the current study was to investigate the biological function of cell division cycle-associated protein 7 (CDCA7) on ovarian cancer (OC) progression and analyze the molecular mechanism of CDCA7 on OC cellular processes and angiogenesis. CDCA7 expression in OC tissues and adjacent normal tissues was obtained from Gene Expression Profiling Interactive Analysis (GEPIA) and in various cancer cell lines was obtained from Cancer Cell Line Encyclopedia (CCLE). Moreover, CDCA7 expression in adjacent normal tissues and tumor tissues of OC patients as well as in normal ovarian epithelial cells (NOEC) and ovarian cancer cells (OVCAR3, SKOV3, CAOV-3, A2780) was further confirmed via Western blot assay and Reverse transcription-quantitative polymerase chain reaction (RT-qPCR). In addition, Immunohistochemistry (IHC) was also applied for determination of CDCA7 expression in tissues of OC patients. Then, SKOV3 cells were introduced with shRNA-CDCA7 for functional experiments. GeneMANIA database analysis and coimmunoprecipitation (Co-IP) assay verified the interaction between CDCA7 and enhancer of zeste homolog 2 (EZH2) to probe the potential mechanism. CDCA7 expression was elevated in tumor tissues of OC patients and OC cell lines. CDCA7 silencing restrained the proliferative, migrative and invasive capacities and arrested cell cycle of OC cells. In addition, CDCA7 knockdown induced a weaker in vitro angiogenesis of HUVECs. Mechanistically, CDCA7 interacted with EZH2. Downregulation of CDCA7 arrested angiogenesis by suppressing EZH2 expression. To sum up, the current study revealed the impact and potential mechanism of CDCA7 on OC cellular processes, developing a promising molecular target for OC therapies.
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Affiliation(s)
- Chunyan Cai
- Department Of Gynaecology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, China
| | - Xing Peng
- Department Of Gynaecology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, China
| | - Yumei Zhang
- Department Of Gynaecology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, China
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20
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Vodnala M, Choi EB, Fong YW. Low complexity domains, condensates, and stem cell pluripotency. World J Stem Cells 2021; 13:416-438. [PMID: 34136073 PMCID: PMC8176841 DOI: 10.4252/wjsc.v13.i5.416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Biological reactions require self-assembly of factors in the complex cellular milieu. Recent evidence indicates that intrinsically disordered, low-complexity sequence domains (LCDs) found in regulatory factors mediate diverse cellular processes from gene expression to DNA repair to signal transduction, by enriching specific biomolecules in membraneless compartments or hubs that may undergo liquid-liquid phase separation (LLPS). In this review, we discuss how embryonic stem cells take advantage of LCD-driven interactions to promote cell-specific transcription, DNA damage response, and DNA repair. We propose that LCD-mediated interactions play key roles in stem cell maintenance and safeguarding genome integrity.
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Affiliation(s)
- Munender Vodnala
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Eun-Bee Choi
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Yick W Fong
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
- Harvard Stem Cell Institute, Cambridge, MA 02138, United States.
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