1
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Ferretti A, Furlan M, Glinton KE, Fenger CD, Boschann F, Amlie-Wolf L, Zeidler S, Moretti R, Stoltenburg C, Tarquinio DC, Furia F, Parisi P, Rubboli G, Devinsky O, Mignot C, Gripp KW, Møller RS, Yang Y, Stankiewicz P, Gardella E. Epilepsy as a Novel Phenotype of BPTF-Related Disorders. Pediatr Neurol 2024; 158:17-25. [PMID: 38936258 DOI: 10.1016/j.pediatrneurol.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 05/15/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (NEDDFL) is associated to BPTF gene haploinsufficiency. Epilepsy was not included in the initial descriptions of NEDDFL, but emerging evidence indicates that epileptic seizures occur in some affected individuals. This study aims to investigate the electroclinical epilepsy features in individuals with NEDDFL. METHODS We enrolled individuals with BPTF-related seizures or interictal epileptiform discharges (IEDs) on electroencephalography (EEG). Demographic, clinical, genetic, raw EEG, and neuroimaging data as well as response to antiseizure medication were assessed. RESULTS We studied 11 individuals with a null variant in BPTF, including five previously unpublished ones. Median age at last observation was 9 years (range: 4 to 43 years). Eight individuals had epilepsy, one had a single unprovoked seizure, and two showed IEDs only. Key features included (1) early childhood epilepsy onset (median 4 years, range: 10 months to 7 years), (2) well-organized EEG background (all cases) and brief bursts of spikes and slow waves (50% of individuals), and (3) developmental delay preceding seizure onset. Spectrum of epilepsy severity varied from drug-resistant epilepsy (27%) to isolated IEDs without seizures (18%). Levetiracetam was widely used and reduced seizure frequency in 67% of the cases. CONCLUSIONS Our study provides the first characterization of BPTF-related epilepsy. Early-childhood-onset epilepsy occurs in 19% of subjects, all presenting with a well-organized EEG background associated with generalized interictal epileptiform abnormalities in half of these cases. Drug resistance is rare.
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Affiliation(s)
- Alessandro Ferretti
- Pediatrics Unit, Faculty of Medicine and Psychology, Department of Neuroscience, Mental Health and Sense Organs (NESMOS), Sapienza University of Rome, Rome, Italy; Department of Clinical Neurophysiology, Danish Epilepsy Centre, Dianalund, Denmark; Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - Margherita Furlan
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark; Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Kevin E Glinton
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Christina D Fenger
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark; Amplexa Genetics A/S, Odense, Denmark
| | - Felix Boschann
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany; Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Louise Amlie-Wolf
- Division of Medical Genetics, Nemours Children's Health, Wilmington, Delaware
| | - Shimriet Zeidler
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Raffaella Moretti
- APHP-Sorbonne Université, Département de Génétique, Hôpital Trousseau et Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Corinna Stoltenburg
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Sozialpädiatrisches Zentrum Neuropädiatrie, Berlin, Germany
| | - Daniel C Tarquinio
- Rett Syndrome Clinic, Center for Rare Neurological Diseases, Norcross, Georgia
| | - Francesca Furia
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark; Faculty of Health Sciences, Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Pasquale Parisi
- Pediatrics Unit, Faculty of Medicine and Psychology, Department of Neuroscience, Mental Health and Sense Organs (NESMOS), Sapienza University of Rome, Rome, Italy
| | - Guido Rubboli
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark; Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark; Member of ERN EpiCARE
| | - Orrin Devinsky
- NYU Langone Epilepsy Center, Department of Neurology, NYU Grossman School of Medicine, New York City, New York
| | - Cyril Mignot
- APHP-Sorbonne Université, Département de Génétique, Hôpital Trousseau et Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Karen W Gripp
- Division of Medical Genetics, Nemours Children's Health, Wilmington, Delaware
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark; Faculty of Health Sciences, Department of Regional Health Research, University of Southern Denmark, Odense, Denmark; Member of ERN EpiCARE
| | - Yaping Yang
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas; AiLife Diagnostics, Pearland, Texas
| | - Pawel Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Elena Gardella
- Department of Clinical Neurophysiology, Danish Epilepsy Centre, Dianalund, Denmark; Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark; Faculty of Health Sciences, Department of Regional Health Research, University of Southern Denmark, Odense, Denmark; Member of ERN EpiCARE.
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Iurlaro M, Masoni F, Flyamer IM, Wirbelauer C, Iskar M, Burger L, Giorgetti L, Schübeler D. Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF. Nat Genet 2024; 56:1203-1212. [PMID: 38816647 PMCID: PMC11176080 DOI: 10.1038/s41588-024-01767-x] [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: 07/07/2023] [Accepted: 04/23/2024] [Indexed: 06/01/2024]
Abstract
Catalytic activity of the imitation switch (ISWI) family of remodelers is critical for nucleosomal organization and DNA binding of certain transcription factors, including the insulator protein CTCF. Here we define the contribution of individual subcomplexes by deriving a panel of isogenic mouse stem cell lines, each lacking one of six ISWI accessory subunits. Individual deletions of subunits of either CERF, RSF, ACF, WICH or NoRC subcomplexes only moderately affect the chromatin landscape, while removal of the NURF-specific subunit BPTF leads to a strong reduction in chromatin accessibility and SNF2H ATPase localization around CTCF sites. This affects adjacent nucleosome occupancy and CTCF binding. At a group of sites with reduced chromatin accessibility, CTCF binding persists but cohesin occupancy is reduced, resulting in decreased insulation. These results suggest that CTCF binding can be separated from its function as an insulator in nuclear organization and identify a specific role for NURF in mediating SNF2H localization and chromatin opening at bound CTCF sites.
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Affiliation(s)
- Mario Iurlaro
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Disease Area Oncology, Novartis Biomedical Research, Basel, Switzerland
| | - Francesca Masoni
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Ilya M Flyamer
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Murat Iskar
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- Faculty of Science, University of Basel, Basel, Switzerland.
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3
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Ma X, Zhao LL, Yu YC, Cheng Y. Engrailed: Pathological and physiological effects of a multifunctional developmental gene. Genesis 2024; 62:e23557. [PMID: 37830136 DOI: 10.1002/dvg.23557] [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: 06/23/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023]
Abstract
Engrailed-1 (EN1) is a developmental gene that encodes En1, a highly conserved transcription factor involved in regionalization during early embryogenesis and in the later maintenance of normal neurons. After birth, EN1 still plays a role in the development and physiology of the body; for example, it exerts a protective effect on midbrain dopaminergic (mDA) neurons, and loss of EN1 causes mDA neurons in the ventral midbrain to gradually die approximately 6 weeks after birth, resulting in motor and nonmotor symptoms similar to those observed in Parkinson's disease. Notably, EN1 has been identified as a possible susceptibility gene for idiopathic Parkinson's disease in humans. EN1 is involved in the processes of wound-healing scar production and tissue and organ fibrosis. Additionally, EN1 can lead to tumorigenesis and thus provides a target for the treatment of some tumors. In this review, we summarize the effects of EN1 on embryonic organ development, describe the consequences of the deletion or overexpression of the EN1 gene, and discuss the pathways in which EN1 is involved. We hope to clarify the role of EN1 as a developmental gene and present potential therapeutic targets for diseases involving the EN1 gene.
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Affiliation(s)
- Xiang Ma
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, P.R. China
| | - Liang-Liang Zhao
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, P.R. China
| | - Yi-Chun Yu
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, P.R. China
| | - Yan Cheng
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, P.R. China
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4
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Radzisheuskaya A, Peña‐Rømer I, Lorenzini E, Koche R, Zhan Y, Shliaha PV, Cooper AJ, Fan Z, Shlyueva D, Johansen JV, Hendrickson RC, Helin K. An alternative NURF complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions. EMBO J 2023; 42:e114221. [PMID: 37987160 PMCID: PMC10711654 DOI: 10.15252/embj.2023114221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 10/19/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
Efficient treatment of acute myeloid leukemia (AML) patients remains a challenge despite recent therapeutic advances. Here, using a CRISPRi screen targeting chromatin factors, we identified the nucleosome-remodeling factor (NURF) subunit BPTF as an essential regulator of AML cell survival. We demonstrate that BPTF forms an alternative NURF chromatin remodeling complex with SMARCA5 and BAP18, which regulates the accessibility of a large set of insulator regions in leukemic cells. This ensures efficient CTCF binding and boundary formation between topologically associated domains that is essential for maintaining the leukemic transcriptional programs. We also demonstrate that the well-studied PHD2-BROMO chromatin reader domains of BPTF, while contributing to complex recruitment to chromatin, are dispensable for leukemic cell growth. Taken together, our results uncover how the alternative NURF complex contributes to leukemia and provide a rationale for its targeting in AML.
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Affiliation(s)
- Aliaksandra Radzisheuskaya
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Isabel Peña‐Rømer
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Eugenia Lorenzini
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Richard Koche
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Yingqian Zhan
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Pavel V Shliaha
- Microchemistry & Proteomics CoreMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | | | - Zheng Fan
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Daria Shlyueva
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Jens V Johansen
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
| | - Ronald C Hendrickson
- Microchemistry & Proteomics CoreMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Kristian Helin
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
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5
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Picketts D, Mirzaa G, Yan K, Relator R, Timpano S, Yalcin B, Collins S, Ziegler A, Pao E, Oyama N, Brischoux-Boucher E, Piard J, Monaghan K, Sacoto MG, Dobyns W, Park K, Fernández-Mayoralas D, Fernández-Jaén A, Jayakar P, Brusco A, Antona V, Giorgio E, Kvarnung M, Isidor B, Conrad S, Cogné B, Deb W, Stuurman KE, Sterbova K, Smal N, Weckhuysen S, Oegema R, Innes M, Latsko M, Ben-Omran T, Yeh R, Kruer M, Bakhtiari S, Papavasiliou A, Moutton S, Nambot S, Chanprasert S, Paolucci S, Miller K, Burton B, Kim K, O'Heir E, Bruwer Z, Donald K, Kleefstra T, Goldstein A, Angle B, Bontempo K, Miny P, Joset P, Demurger F, Hobson E, Pang L, Carpenter L, Li D, Bonneau D, Sadikovic B. Pathogenic variants in SMARCA1 cause an X-linked neurodevelopmental disorder modulated by NURF complex composition. RESEARCH SQUARE 2023:rs.3.rs-3317938. [PMID: 37841849 PMCID: PMC10571636 DOI: 10.21203/rs.3.rs-3317938/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Pathogenic variants in ATP-dependent chromatin remodeling proteins are a recurrent cause of neurodevelopmental disorders (NDDs). The NURF complex consists of BPTF and either the SNF2H (SMARCA5) or SNF2L (SMARCA1) ISWI-chromatin remodeling enzyme. Pathogenic variants in BPTF and SMARCA5 were previously implicated in NDDs. Here, we describe 40 individuals from 30 families with de novo or maternally inherited pathogenic variants in SMARCA1. This novel NDD was associated with mild to severe ID/DD, delayed or regressive speech development, and some recurrent facial dysmorphisms. Individuals carrying SMARCA1 loss-of-function variants exhibited a mild genome-wide DNA methylation profile and a high penetrance of macrocephaly. Genetic dissection of the NURF complex using Smarca1, Smarca5, and Bptfsingle and double mouse knockouts revealed the importance of NURF composition and dosage for proper forebrain development. Finally, we propose that genetic alterations affecting different NURF components result in a NDD with a broad clinical spectrum.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Emily Pao
- Seattle Children's Research Institute
| | | | | | | | | | | | | | - Kristen Park
- University of Colorado Denver School of Medicine
| | | | - Alberto Fernández-Jaén
- Department of Pediatrics and Neurology, Hospital Universitario Quirónsalud, School of Medicine, Universidad Europea de Madrid
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital
| | | | | | | | | | | | | | | | | | - K E Stuurman
- Department of Clinical Genetics, Erasmus University Medical Center
| | | | | | | | | | | | - Maeson Latsko
- The Steve and Cindy Rasmussen Institute for Genomic Medicine
| | | | | | | | | | | | | | - Sophie Nambot
- Centre de Génétique et Centre de référence «Anomalies du Développement et Syndromes Malformatifs», Hôpital d'Enfants, Centre Hospitalier
| | | | | | | | | | | | | | | | - Kirsten Donald
- Division of Developmental Paediatrics, Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Klipfontein Road/Private Bag, Rondebosch, 7700/7701, Cape Town, South A
| | | | | | | | | | | | | | | | | | | | | | - Dong Li
- The Children's Hospital of Philadelphia
| | - Dominique Bonneau
- Department of Biochemistry and Genetics, University Hospital of Angers, F-49000
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6
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Salvato I, Ricciardi L, Dal Col J, Nigro A, Giurato G, Memoli D, Sellitto A, Lamparelli EP, Crescenzi MA, Vitale M, Vatrella A, Nucera F, Brun P, Caicci F, Dama P, Stiff T, Castellano L, Idrees S, Johansen MD, Faiz A, Wark PA, Hansbro PM, Adcock IM, Caramori G, Stellato C. Expression of targets of the RNA-binding protein AUF-1 in human airway epithelium indicates its role in cellular senescence and inflammation. Front Immunol 2023; 14:1192028. [PMID: 37483631 PMCID: PMC10360199 DOI: 10.3389/fimmu.2023.1192028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction The RNA-binding protein AU-rich-element factor-1 (AUF-1) participates to posttranscriptional regulation of genes involved in inflammation and cellular senescence, two pathogenic mechanisms of chronic obstructive pulmonary disease (COPD). Decreased AUF-1 expression was described in bronchiolar epithelium of COPD patients versus controls and in vitro cytokine- and cigarette smoke-challenged human airway epithelial cells, prompting the identification of epithelial AUF-1-targeted transcripts and function, and investigation on the mechanism of its loss. Results RNA immunoprecipitation-sequencing (RIP-Seq) identified, in the human airway epithelial cell line BEAS-2B, 494 AUF-1-bound mRNAs enriched in their 3'-untranslated regions for a Guanine-Cytosine (GC)-rich binding motif. AUF-1 association with selected transcripts and with a synthetic GC-rich motif were validated by biotin pulldown. AUF-1-targets' steady-state levels were equally affected by partial or near-total AUF-1 loss induced by cytomix (TNFα/IL1β/IFNγ/10 nM each) and siRNA, respectively, with differential transcript decay rates. Cytomix-mediated decrease in AUF-1 levels in BEAS-2B and primary human small-airways epithelium (HSAEC) was replicated by treatment with the senescence- inducer compound etoposide and associated with readouts of cell-cycle arrest, increase in lysosomal damage and senescence-associated secretory phenotype (SASP) factors, and with AUF-1 transfer in extracellular vesicles, detected by transmission electron microscopy and immunoblotting. Extensive in-silico and genome ontology analysis found, consistent with AUF-1 functions, enriched RIP-Seq-derived AUF-1-targets in COPD-related pathways involved in inflammation, senescence, gene regulation and also in the public SASP proteome atlas; AUF-1 target signature was also significantly represented in multiple transcriptomic COPD databases generated from primary HSAEC, from lung tissue and from single-cell RNA-sequencing, displaying a predominant downregulation of expression. Discussion Loss of intracellular AUF-1 may alter posttranscriptional regulation of targets particularly relevant for protection of genomic integrity and gene regulation, thus concurring to airway epithelial inflammatory responses related to oxidative stress and accelerated aging. Exosomal-associated AUF-1 may in turn preserve bound RNA targets and sustain their function, participating to spreading of inflammation and senescence to neighbouring cells.
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Affiliation(s)
- Ilaria Salvato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Luca Ricciardi
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Jessica Dal Col
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Annunziata Nigro
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Domenico Memoli
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Assunta Sellitto
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Erwin Pavel Lamparelli
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Maria Assunta Crescenzi
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Monica Vitale
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Alessandro Vatrella
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Francesco Nucera
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Paola Brun
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Paola Dama
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Thomas Stiff
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Leandro Castellano
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sobia Idrees
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Matt D. Johansen
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Alen Faiz
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Peter A. Wark
- Immune Health, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
- Immune Health, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Ian M. Adcock
- National Heart and Lung Institute, Imperial College London and the National Institute for Health and Care Research (NIHR) Imperial Biomedical Research Centre, London, United Kingdom
| | - Gaetano Caramori
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
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7
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Bomber ML, Wang J, Liu Q, Barnett KR, Layden HM, Hodges E, Stengel KR, Hiebert SW. Human SMARCA5 is continuously required to maintain nucleosome spacing. Mol Cell 2023; 83:507-522.e6. [PMID: 36630954 PMCID: PMC9974918 DOI: 10.1016/j.molcel.2022.12.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023]
Abstract
Genetic models suggested that SMARCA5 was required for DNA-templated events including transcription, DNA replication, and DNA repair. We engineered a degron tag into the endogenous alleles of SMARCA5, a catalytic component of the imitation switch complexes in three different human cell lines to define the effects of rapid degradation of this key regulator. Degradation of SMARCA5 was associated with a rapid increase in global nucleosome repeat length, which may allow greater chromatin compaction. However, there were few changes in nascent transcription within the first 6 h of degradation. Nevertheless, we demonstrated a requirement for SMARCA5 to control nucleosome repeat length at G1/S and during the S phase. SMARCA5 co-localized with CTCF and H2A.Z, and we found a rapid loss of CTCF DNA binding and disruption of nucleosomal phasing around CTCF binding sites. This spatiotemporal analysis indicates that SMARCA5 is continuously required for maintaining nucleosomal spacing.
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Affiliation(s)
- Monica L Bomber
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kelly R Barnett
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Hillary M Layden
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Emily Hodges
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kristy R Stengel
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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8
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Sigismondo G, Arseni L, Palacio-Escat N, Hofmann TG, Seiffert M, Krijgsveld J. Multi-layered chromatin proteomics identifies cell vulnerabilities in DNA repair. Nucleic Acids Res 2023; 51:687-711. [PMID: 36629267 PMCID: PMC9881138 DOI: 10.1093/nar/gkac1264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
The DNA damage response (DDR) is essential to maintain genome stability, and its deregulation predisposes to carcinogenesis while encompassing attractive targets for cancer therapy. Chromatin governs the DDR via the concerted interplay among different layers, including DNA, histone post-translational modifications (hPTMs) and chromatin-associated proteins. Here, we employ multi-layered proteomics to characterize chromatin-mediated functional interactions of repair proteins, signatures of hPTMs and the DNA-bound proteome during DNA double-strand break (DSB) repair at high temporal resolution. Our data illuminate the dynamics of known and novel DDR-associated factors both at chromatin and at DSBs. We functionally attribute novel chromatin-associated proteins to repair by non-homologous end-joining (NHEJ), homologous recombination (HR) and DSB repair pathway choice. We reveal histone reader ATAD2, microtubule organizer TPX2 and histone methyltransferase G9A as regulators of HR and involved in poly-ADP-ribose polymerase-inhibitor sensitivity. Furthermore, we distinguish hPTMs that are globally induced by DNA damage from those specifically acquired at sites flanking DSBs (γH2AX foci-specific) and profiled their dynamics during the DDR. Integration of complementary chromatin layers implicates G9A-mediated monomethylation of H3K56 in DSBs repair via HR. Our data provide a dynamic chromatin-centered view of the DDR that can be further mined to identify novel mechanistic links and cell vulnerabilities in DSB repair.
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Affiliation(s)
- Gianluca Sigismondo
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Lavinia Arseni
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Nicolàs Palacio-Escat
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas G Hofmann
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Martina Seiffert
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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9
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Chen S, Rosin LF, Pegoraro G, Moshkovich N, Murphy PJ, Yu G, Lei EP. NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization. Nucleic Acids Res 2022; 50:7906-7924. [PMID: 35819192 PMCID: PMC9371915 DOI: 10.1093/nar/gkac600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/26/2022] [Accepted: 06/29/2022] [Indexed: 11/14/2022] Open
Abstract
Chromatin insulators are DNA-protein complexes that can prevent the spread of repressive chromatin and block communication between enhancers and promoters to regulate gene expression. In Drosophila, the gypsy chromatin insulator complex consists of three core proteins: CP190, Su(Hw), and Mod(mdg4)67.2. These factors concentrate at nuclear foci termed insulator bodies, and changes in insulator body localization have been observed in mutants defective for insulator function. Here, we identified NURF301/E(bx), a nucleosome remodeling factor, as a novel regulator of gypsy insulator body localization through a high-throughput RNAi imaging screen. NURF301 promotes gypsy-dependent insulator barrier activity and physically interacts with gypsy insulator proteins. Using ChIP-seq, we found that NURF301 co-localizes with insulator proteins genome-wide, and NURF301 promotes chromatin association of Su(Hw) and CP190 at gypsy insulator binding sites. These effects correlate with NURF301-dependent nucleosome repositioning. At the same time, CP190 and Su(Hw) both facilitate recruitment of NURF301 to chromatin. Finally, Oligopaint FISH combined with immunofluorescence revealed that NURF301 promotes 3D contact between insulator bodies and gypsy insulator DNA binding sites, and NURF301 is required for proper nuclear positioning of gypsy binding sites. Our data provide new insights into how a nucleosome remodeling factor and insulator proteins cooperatively contribute to nuclear organization.
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Affiliation(s)
- Shue Chen
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Leah F Rosin
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility (HiTIF), Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Nellie Moshkovich
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Patrick J Murphy
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Guoyun Yu
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elissa P Lei
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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10
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Zapata G, Yan K, Picketts DJ. Generation of a mouse model of the neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (NEDDFL) syndrome. Hum Mol Genet 2022; 31:3405-3421. [PMID: 35604347 DOI: 10.1093/hmg/ddac119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Heterozygous variants in BPTF cause the neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (NEDDFL) syndrome (MIM#617755) characterized by intellectual disability (ID), speech delay, and postnatal microcephaly. BPTF functions within NURF, a complex comprising SNF2L, an ISWI chromatin remodeling protein encoded by the SMARCA1 gene. Surprisingly, ablation of Smarca1 resulted in mice with enlarged brains, a direct contrast to the phenotype of NEDDFL patients. To model the NEDDFL syndrome, we generated forebrain-specific Bptf knockout (Bptf cKO) mice. Bptf cKO mice were born in normal Mendelian ratios, survived to adulthood but were smaller in size with severe cortical hypoplasia. Prolonged progenitor cell cycle length and a high incidence of cell death reduced neuronal output. Cortical lamination was also disrupted with reduced proportions of deep layer neurons, and neuronal maturation defects that impaired the acquisition of distinct cell fates (eg. Ctip2+ neurons). RNAseq and pathway analysis identified altered expression of fate-determining transcription factors, and biological pathways involved in neural development, apoptotic signaling, and amino acid biosynthesis. Dysregulated genes were enriched for Myc binding sites, a known BPTF transcriptional co-factor. We propose Bptf cKO mice as a valuable model for further study of the NEDDFL syndrome.
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Affiliation(s)
- Gerardo Zapata
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada, K1H 8L6.,Departments of Biochemistry, Microbiology, & Immunology, University of Ottawa, Ottawa, Ontario, Canada, K1H8M5
| | - Keqin Yan
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada, K1H 8L6
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada, K1H 8L6.,Departments of Biochemistry, Microbiology, & Immunology, University of Ottawa, Ottawa, Ontario, Canada, K1H8M5.,Departments of Biochemistry, Microbiology, & Immunology, Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada, K1H8M5.,Medicine, University of Ottawa, Ottawa, Ontario, Canada, K1H8M5
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11
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Muñoz Velasco R, Jiménez Sánchez P, García García A, Blanco Martinez-Illescas R, Pastor Senovilla Á, Lozano Yagüe M, Trento A, García-Martin RM, Navarro D, Sainz B, Rodríguez Peralto JL, Sánchez-Arévalo Lobo VJ. Targeting BPTF Sensitizes Pancreatic Ductal Adenocarcinoma to Chemotherapy by Repressing ABC-Transporters and Impairing Multidrug Resistance (MDR). Cancers (Basel) 2022; 14:cancers14061518. [PMID: 35326669 PMCID: PMC8946837 DOI: 10.3390/cancers14061518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/14/2022] [Indexed: 12/30/2022] Open
Abstract
Simple Summary Pancreatic ductal adenocarcinoma is a devastating disease and an extremely chemoresistant tumour. In the present manuscript, we described the role of BPTF during tumour pancreatic ductal adenocarcinoma progression and in response to gemcitabine treatment, a gold standard treatment in this tumour type. Through different genetic approaches, we reduced BPTF levels in a panel of pancreatic ductal adenocarcinoma cell lines. We validated its therapeutic effect in cell cultures and in mouse models of pancreatic cancer. A reduction in BPTF levels impaired cell proliferation and sensitized pancreatic tumour cells to gemcitabine. We demonstrated that BPTF-silencing reduced the expression of several ABC-transporters, which are involved in gemcitabine resistance, and enhanced its accumulation in the tumour cell, improving its therapeutic effect. Abstract Pancreatic ductal adenocarcinoma (PDA) is characterized by an extremely poor prognosis due to its late diagnosis and strong chemoresistance to the current treatments. Therefore, finding new therapeutic targets is an urgent need nowadays. In this study, we report the role of the chromatin remodeler BPTF (Bromodomain PHD Finger Transcription Factor) as a therapeutic target in PDA. BPTF-silencing dramatically reduced cell proliferation and migration in vitro and in vivo in human and mouse PDA cell lines. Moreover, BPTF-silencing reduces the IC50 of gemcitabine in vitro and enhanced its therapeutic effect in vivo. Mechanistically, BPTF is required for c-MYC recruitment to the promoter of ABC-transporters and its downregulation facilitates gemcitabine accumulation in tumour cells, increases DNA damage, and a generates a strong synergistic effect in vivo. We show that BPTF is a therapeutic target in pancreatic ductal adenocarcinoma due to its strong effect on proliferation and in response to gemcitabine.
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Affiliation(s)
- Raúl Muñoz Velasco
- Molecular Oncology Group, Biosanitary Research Institute, Faculty of Experimental Sciences, Francisco de Vitoria University (UFV), 28223 Madrid, Spain; (R.M.V.); (P.J.S.); (A.G.G.); (R.B.M.-I.); (Á.P.S.); (M.L.Y.)
- Pathology Department, Hospital 12 de Octubre, Av. Córdoba, s/n, 28041 Madrid, Spain; (A.T.); (R.M.G.-M.); (J.L.R.P.)
| | - Paula Jiménez Sánchez
- Molecular Oncology Group, Biosanitary Research Institute, Faculty of Experimental Sciences, Francisco de Vitoria University (UFV), 28223 Madrid, Spain; (R.M.V.); (P.J.S.); (A.G.G.); (R.B.M.-I.); (Á.P.S.); (M.L.Y.)
- Pathology Department, Hospital 12 de Octubre, Av. Córdoba, s/n, 28041 Madrid, Spain; (A.T.); (R.M.G.-M.); (J.L.R.P.)
| | - Ana García García
- Molecular Oncology Group, Biosanitary Research Institute, Faculty of Experimental Sciences, Francisco de Vitoria University (UFV), 28223 Madrid, Spain; (R.M.V.); (P.J.S.); (A.G.G.); (R.B.M.-I.); (Á.P.S.); (M.L.Y.)
- Pathology Department, Hospital 12 de Octubre, Av. Córdoba, s/n, 28041 Madrid, Spain; (A.T.); (R.M.G.-M.); (J.L.R.P.)
| | - Raquel Blanco Martinez-Illescas
- Molecular Oncology Group, Biosanitary Research Institute, Faculty of Experimental Sciences, Francisco de Vitoria University (UFV), 28223 Madrid, Spain; (R.M.V.); (P.J.S.); (A.G.G.); (R.B.M.-I.); (Á.P.S.); (M.L.Y.)
- Pathology Department, Hospital 12 de Octubre, Av. Córdoba, s/n, 28041 Madrid, Spain; (A.T.); (R.M.G.-M.); (J.L.R.P.)
| | - Ángela Pastor Senovilla
- Molecular Oncology Group, Biosanitary Research Institute, Faculty of Experimental Sciences, Francisco de Vitoria University (UFV), 28223 Madrid, Spain; (R.M.V.); (P.J.S.); (A.G.G.); (R.B.M.-I.); (Á.P.S.); (M.L.Y.)
- Pathology Department, Hospital 12 de Octubre, Av. Córdoba, s/n, 28041 Madrid, Spain; (A.T.); (R.M.G.-M.); (J.L.R.P.)
| | - Marian Lozano Yagüe
- Molecular Oncology Group, Biosanitary Research Institute, Faculty of Experimental Sciences, Francisco de Vitoria University (UFV), 28223 Madrid, Spain; (R.M.V.); (P.J.S.); (A.G.G.); (R.B.M.-I.); (Á.P.S.); (M.L.Y.)
- Pathology Department, Hospital 12 de Octubre, Av. Córdoba, s/n, 28041 Madrid, Spain; (A.T.); (R.M.G.-M.); (J.L.R.P.)
| | - Alfonsina Trento
- Pathology Department, Hospital 12 de Octubre, Av. Córdoba, s/n, 28041 Madrid, Spain; (A.T.); (R.M.G.-M.); (J.L.R.P.)
| | - Rosa María García-Martin
- Pathology Department, Hospital 12 de Octubre, Av. Córdoba, s/n, 28041 Madrid, Spain; (A.T.); (R.M.G.-M.); (J.L.R.P.)
| | - Diego Navarro
- Department of Cancer Biology, Instituto de Investigaciones Biomédicas Alberto Sols (IIBM), CSIC-UAM, 28029 Madrid, Spain; (D.N.); (B.S.J.)
- Chronic Diseases and Cancer Area 3-Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28029 Madrid, Spain
| | - Bruno Sainz
- Department of Cancer Biology, Instituto de Investigaciones Biomédicas Alberto Sols (IIBM), CSIC-UAM, 28029 Madrid, Spain; (D.N.); (B.S.J.)
- Chronic Diseases and Cancer Area 3-Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red, Área Cáncer, CIBERONC, ISCIII, 28029 Madrid, Spain
| | - José Luis Rodríguez Peralto
- Pathology Department, Hospital 12 de Octubre, Av. Córdoba, s/n, 28041 Madrid, Spain; (A.T.); (R.M.G.-M.); (J.L.R.P.)
| | - Víctor Javier Sánchez-Arévalo Lobo
- Molecular Oncology Group, Biosanitary Research Institute, Faculty of Experimental Sciences, Francisco de Vitoria University (UFV), 28223 Madrid, Spain; (R.M.V.); (P.J.S.); (A.G.G.); (R.B.M.-I.); (Á.P.S.); (M.L.Y.)
- Pathology Department, Hospital 12 de Octubre, Av. Córdoba, s/n, 28041 Madrid, Spain; (A.T.); (R.M.G.-M.); (J.L.R.P.)
- Correspondence:
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12
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Zahid H, Buchholz CR, Singh M, Ciccone MF, Chan A, Nithianantham S, Shi K, Aihara H, Fischer M, Schönbrunn E, Dos Santos CO, Landry JW, Pomerantz WCK. New Design Rules for Developing Potent Cell-Active Inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF Bromodomain Inhibition. J Med Chem 2021; 64:13902-13917. [PMID: 34515477 DOI: 10.1021/acs.jmedchem.1c01294] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The nucleosome remodeling factor (NURF) alters chromatin accessibility through interactions with its largest subunit,the bromodomain PHD finger transcription factor BPTF. BPTF is overexpressed in several cancers and is an emerging anticancer target. Targeting the BPTF bromodomain presents a potential strategy for its inhibition and the evaluation of its functional significance; however, inhibitor development for BPTF has lagged behind those of other bromodomains. Here we describe the development of pyridazinone-based BPTF inhibitors. The lead compound, BZ1, possesses a high potency (Kd = 6.3 nM) and >350-fold selectivity over BET bromodomains. We identify an acidic triad in the binding pocket to guide future designs. We show that our inhibitors sensitize 4T1 breast cancer cells to doxorubicin but not BPTF knockdown cells, suggesting a specificity to BPTF. Given the high potency and good physicochemical properties of these inhibitors, we anticipate that they will be useful starting points for chemical tool development to explore the biological roles of BPTF.
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Affiliation(s)
- Huda Zahid
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Caroline R Buchholz
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Manjulata Singh
- The Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Michael F Ciccone
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, United States
| | - Alice Chan
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Stanley Nithianantham
- Department of Chemical Biology & Therapeutics and Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Marcus Fischer
- Department of Chemical Biology & Therapeutics and Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ernst Schönbrunn
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Camila O Dos Santos
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, United States
| | - Joseph W Landry
- The Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
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13
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14
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Zahid H, Olson NM, Pomerantz WCK. Opportunity knocks for uncovering the new function of an understudied nucleosome remodeling complex member, the bromodomain PHD finger transcription factor, BPTF. Curr Opin Chem Biol 2021; 63:57-67. [PMID: 33706239 PMCID: PMC8384639 DOI: 10.1016/j.cbpa.2021.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/25/2021] [Accepted: 02/01/2021] [Indexed: 12/27/2022]
Abstract
Nucleosome remodeling provides access to genomic DNA for recruitment of the transcriptional machinery to mediate gene expression. The aberrant function of nucleosome remodeling complexes has been correlated to human cancer, making them emerging therapeutic targets. The bromodomain PHD finger transcription factor, BPTF, is the largest member of the human nucleosome remodeling factor NURF. Over the last five years, BPTF has become increasingly identified as a protumorigenic factor, prompting investigations into the molecular mechanisms associated with BPTF function. Despite a druggable bromodomain, small molecule discovery is at an early stage. Here we highlight recent investigations into the biology being discovered for BPTF, chemical biology approaches used to study its function, and small molecule inhibitors being designed as future chemical probes and therapeutics.
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Affiliation(s)
- Huda Zahid
- 207Pleasant St. SE, Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Noelle M Olson
- 207Pleasant St. SE, Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - William C K Pomerantz
- 207Pleasant St. SE, Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
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15
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Boyson SP, Gao C, Quinn K, Boyd J, Paculova H, Frietze S, Glass KC. Functional Roles of Bromodomain Proteins in Cancer. Cancers (Basel) 2021; 13:3606. [PMID: 34298819 PMCID: PMC8303718 DOI: 10.3390/cancers13143606] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/31/2022] Open
Abstract
Histone acetylation is generally associated with an open chromatin configuration that facilitates many cellular processes including gene transcription, DNA repair, and DNA replication. Aberrant levels of histone lysine acetylation are associated with the development of cancer. Bromodomains represent a family of structurally well-characterized effector domains that recognize acetylated lysines in chromatin. As part of their fundamental reader activity, bromodomain-containing proteins play versatile roles in epigenetic regulation, and additional functional modules are often present in the same protein, or through the assembly of larger enzymatic complexes. Dysregulated gene expression, chromosomal translocations, and/or mutations in bromodomain-containing proteins have been correlated with poor patient outcomes in cancer. Thus, bromodomains have emerged as a highly tractable class of epigenetic targets due to their well-defined structural domains, and the increasing ease of designing or screening for molecules that modulate the reading process. Recent developments in pharmacological agents that target specific bromodomains has helped to understand the diverse mechanisms that bromodomains play with their interaction partners in a variety of chromatin processes, and provide the promise of applying bromodomain inhibitors into the clinical field of cancer treatment. In this review, we explore the expression and protein interactome profiles of bromodomain-containing proteins and discuss them in terms of functional groups. Furthermore, we highlight our current understanding of the roles of bromodomain-containing proteins in cancer, as well as emerging strategies to specifically target bromodomains, including combination therapies using bromodomain inhibitors alongside traditional therapeutic approaches designed to re-program tumorigenesis and metastasis.
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Affiliation(s)
- Samuel P. Boyson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
| | - Cong Gao
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Kathleen Quinn
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Joseph Boyd
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Hana Paculova
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
- University of Vermont Cancer Center, Burlington, VT 05405, USA
| | - Karen C. Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- University of Vermont Cancer Center, Burlington, VT 05405, USA
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16
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Mélin L, Calosing C, Kharenko OA, Hansen HC, Gagnon A. Synthesis of NVS-BPTF-1 and evaluation of its biological activity. Bioorg Med Chem Lett 2021; 47:128208. [PMID: 34146702 DOI: 10.1016/j.bmcl.2021.128208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/09/2021] [Accepted: 06/13/2021] [Indexed: 02/06/2023]
Abstract
BPTF (bromodomain and PHD finger containing transcription factor) is a multidomain protein that plays essential roles in transcriptional regulation, T-cell homeostasis and stem cell pluripotency. As part of the chromatin remodeling complex hNURF (nucleosome remodeling factor), BPTF epigenetic reader subunits are particularly important for BPTF cellular function. Here we report the synthesis of NVS-BPTF-1, a previously reported highly potent and selective BPTF-bromodomain inhibitor. Evaluation of the impact of the inhibition of BPTF-bromodomain using NVS-BPTF-1 on selected proteins involved in the antigen processing pathway revealed that exclusively targeting BPTF-bromodomain is insufficient to observe an increase of PSMB8, PSMB9, TAP1 and TAP2 proteins.
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Affiliation(s)
- Léa Mélin
- Département de chimie, Université du Québec à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada
| | - Cyrus Calosing
- Zenith Epigenetics Ltd, Suite 300, 4820 Richard Road SW, Calgary, AB T3E 6L1, Canada
| | - Olesya A Kharenko
- Zenith Epigenetics Ltd, Suite 300, 4820 Richard Road SW, Calgary, AB T3E 6L1, Canada
| | - Henrik C Hansen
- Zenith Epigenetics Ltd, Suite 300, 4820 Richard Road SW, Calgary, AB T3E 6L1, Canada
| | - Alexandre Gagnon
- Département de chimie, Université du Québec à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada.
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17
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Dilshat R, Vu HN, Steingrímsson E. Epigenetic regulation during melanocyte development and homeostasis. Exp Dermatol 2021; 30:1033-1050. [PMID: 34003523 DOI: 10.1111/exd.14391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 04/09/2021] [Accepted: 05/09/2021] [Indexed: 12/26/2022]
Abstract
Melanocytes originate in the neural crest as precursor cells which then migrate and proliferate to reach their destination where they differentiate into pigment-producing cells. Melanocytes not only determine the colour of hair, skin and eyes but also protect against the harmful effects of UV irradiation. The establishment of the melanocyte lineage is regulated by a defined set of transcription factors and signalling pathways that direct the specific gene expression programmes underpinning melanoblast specification, survival, migration, proliferation and differentiation. In addition, epigenetic modifiers and replacement histones play key roles in regulating gene expression and its timing during the different steps of this process. Here, we discuss the evidence for the role of epigenetic regulators in melanocyte development and function and how they interact with transcription factors and signalling pathways to establish and maintain this important cell lineage.
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Affiliation(s)
- Ramile Dilshat
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
| | - Hong Nhung Vu
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
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18
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Li D, Wang Q, Gong NN, Kurolap A, Feldman HB, Boy N, Brugger M, Grand K, McWalter K, Guillen Sacoto MJ, Wakeling E, Hurst J, March ME, Bhoj EJ, Nowaczyk MJM, Gonzaga-Jauregui C, Mathew M, Dava-Wala A, Siemon A, Bartholomew D, Huang Y, Lee H, Martinez-Agosto JA, Schwaibold EMC, Brunet T, Choukair D, Pais LS, White SM, Christodoulou J, Brown D, Lindstrom K, Grebe T, Tiosano D, Kayser MS, Tan TY, Deardorff MA, Song Y, Hakonarson H. Pathogenic variants in SMARCA5, a chromatin remodeler, cause a range of syndromic neurodevelopmental features. SCIENCE ADVANCES 2021; 7:7/20/eabf2066. [PMID: 33980485 PMCID: PMC8115915 DOI: 10.1126/sciadv.abf2066] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/23/2021] [Indexed: 05/17/2023]
Abstract
Intellectual disability encompasses a wide spectrum of neurodevelopmental disorders, with many linked genetic loci. However, the underlying molecular mechanism for more than 50% of the patients remains elusive. We describe pathogenic variants in SMARCA5, encoding the ATPase motor of the ISWI chromatin remodeler, as a cause of a previously unidentified neurodevelopmental disorder, identifying 12 individuals with de novo or dominantly segregating rare heterozygous variants. Accompanying phenotypes include mild developmental delay, frequent postnatal short stature and microcephaly, and recurrent dysmorphic features. Loss of function of the SMARCA5 Drosophila ortholog Iswi led to smaller body size, reduced sensory dendrite complexity, and tiling defects in larvae. In adult flies, Iswi neural knockdown caused decreased brain size, aberrant mushroom body morphology, and abnormal locomotor function. Iswi loss of function was rescued by wild-type but not mutant SMARCA5. Our results demonstrate that SMARCA5 pathogenic variants cause a neurodevelopmental syndrome with mild facial dysmorphia.
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Affiliation(s)
- Dong Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Qin Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Naihua N Gong
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Alina Kurolap
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Hagit Baris Feldman
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nikolas Boy
- Division of Child Neurology and Metabolic Medicine, Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Technical University Munich, Munich, Germany
- Institute of Human Genetics, University Hospital LMU Munich, Goethestr. 29, Munich, Germany
| | - Katheryn Grand
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | - Emma Wakeling
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jane Hurst
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Michael E March
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elizabeth J Bhoj
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Małgorzata J M Nowaczyk
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | | | - Mariam Mathew
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Ashita Dava-Wala
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Amy Siemon
- Department of Pediatrics and Clinical Genetics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Dennis Bartholomew
- Department of Pediatrics and Clinical Genetics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Yue Huang
- Department of Human Genetics; Division of Medical Genetics, Department of Pediatrics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine; Department of Human Genetics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics; Division of Medical Genetics, Department of Pediatrics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Eva M C Schwaibold
- Department of Pathology and Laboratory Medicine; Department of Human Genetics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Theresa Brunet
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Daniela Choukair
- Division of Paediatric Endocrinology and Diabetes, Department of Paediatrics, University Hospital Heidelberg, Heidelberg, Germany
| | - Lynn S Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - John Christodoulou
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Dana Brown
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Kristin Lindstrom
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Theresa Grebe
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
- College of Medicine, University of Arizona, Phoenix, 475 N. 5th Street, Phoenix, AZ, USA
| | - Dov Tiosano
- Pediatric Endocrinology Unit, Ruth Rappaport Children's Hospital, Rambam Healthcare Campus, Haifa, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Matthew S Kayser
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Matthew A Deardorff
- Departments of Pathology and Pediatrics, Children's Hospital Los Angeles, and University of Southern California, Los Angeles, CA, USA
| | - Yuanquan Song
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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19
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Kwon SY, Jang B, Badenhorst P. The ISWI chromatin remodelling factor NURF is not required for mitotic male X chromosome organisation. MICROPUBLICATION BIOLOGY 2021; 2021:10.17912/micropub.biology.000360. [PMID: 33537560 PMCID: PMC7841436 DOI: 10.17912/micropub.biology.000360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The nucleosome remodelling factor (NURF) is an ISWI-class ATP-dependent chromatin remodeling enzyme required both for gene expression and higher order chromatin organisation. NURF binds to histone modifications that decorate the Drosophila polytene male X chromosome and is required to maintain correct organisation of this chromosome. NURF mutants exhibit distorted and decondensed polytene male X chromosomes dependent on the presence of the male-specific lethal (MSL) complex. Here we tested whether mitotic chromosomes similarly require NURF to maintain correct morphology. Surprisingly, although the MSL complex remains associated with mitotic male X chromosomes, NURF is not required to maintain morphology. While the ISWI subunit of NURF is known to remain associated with mitotic chromosomes we show that the NURF specificity subunit Nurf301/BPTF dissociates from chromatin during both Drosophila and human mitosis, further illuminating that NURF is dispensable for mitotic chromosome organisation.
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Affiliation(s)
- So Yeon Kwon
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, United Kingdom,
Correspondence to: So Yeon Kwon (); Paul Badenhorst ()
| | - Boyun Jang
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Paul Badenhorst
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, United Kingdom,
Correspondence to: So Yeon Kwon (); Paul Badenhorst ()
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20
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Liu X. A Structural Perspective on Gene Repression by Polycomb Repressive Complex 2. Subcell Biochem 2020; 96:519-562. [PMID: 33252743 DOI: 10.1007/978-3-030-58971-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Polycomb Repressive Complex 2 (PRC2) is a major repressive chromatin complex formed by the Polycomb Group (PcG) proteins. PRC2 mediates trimethylation of histone H3 lysine 27 (H3K27me3), a hallmark of gene silencing. PRC2 is a key regulator of development, impacting many fundamental biological processes, like stem cell differentiation in mammals and vernalization in plants. Misregulation of PRC2 function is linked to a variety of human cancers and developmental disorders. In correlation with its diverse roles in development, PRC2 displays a high degree of compositional complexity and plasticity. Structural biology research over the past decade has shed light on the molecular mechanisms of the assembly, catalysis, allosteric activation, autoinhibition, chemical inhibition, dimerization and chromatin targeting of various developmentally regulated PRC2 complexes. In addition to these aspects, structure-function analysis is also discussed in connection with disease data in this chapter.
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Affiliation(s)
- Xin Liu
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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21
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Magaña-Acosta M, Valadez-Graham V. Chromatin Remodelers in the 3D Nuclear Compartment. Front Genet 2020; 11:600615. [PMID: 33329746 PMCID: PMC7673392 DOI: 10.3389/fgene.2020.600615] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/07/2020] [Indexed: 12/15/2022] Open
Abstract
Chromatin remodeling complexes (CRCs) use ATP hydrolysis to maintain correct expression profiles, chromatin stability, and inherited epigenetic states. More than 20 CRCs have been described to date, which encompass four large families defined by their ATPase subunits. These complexes and their subunits are conserved from yeast to humans through evolution. Their activities depend on their catalytic subunits which through ATP hydrolysis provide the energy necessary to fulfill cellular functions such as gene transcription, DNA repair, and transposon silencing. These activities take place at the first levels of chromatin compaction, and CRCs have been recognized as essential elements of chromatin dynamics. Recent studies have demonstrated an important role for these complexes in the maintenance of higher order chromatin structure. In this review, we present an overview of the organization of the genome within the cell nucleus, the different levels of chromatin compaction, and importance of the architectural proteins, and discuss the role of CRCs and how their functions contribute to the dynamics of the 3D genome organization.
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Affiliation(s)
- Mauro Magaña-Acosta
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Viviana Valadez-Graham
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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22
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Arzate-Mejía RG, Lottenbach Z, Schindler V, Jawaid A, Mansuy IM. Long-Term Impact of Social Isolation and Molecular Underpinnings. Front Genet 2020; 11:589621. [PMID: 33193727 PMCID: PMC7649797 DOI: 10.3389/fgene.2020.589621] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/28/2020] [Indexed: 11/17/2022] Open
Abstract
Prolonged periods of social isolation can have detrimental effects on the physiology and behavior of exposed individuals in humans and animal models. This involves complex molecular mechanisms across tissues in the body which remain partly identified. This review discusses the biology of social isolation and describes the acute and lasting effects of prolonged periods of social isolation with a focus on the molecular events leading to behavioral alterations. We highlight the role of epigenetic mechanisms and non-coding RNA in the control of gene expression as a response to social isolation, and the consequences for behavior. Considering the use of strict quarantine during epidemics, like currently with COVID-19, we provide a cautionary tale on the indiscriminate implementation of such form of social isolation and its potential damaging and lasting effects in mental health.
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Affiliation(s)
- Rodrigo G Arzate-Mejía
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zurich and Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Zurich, Switzerland
| | | | | | - Ali Jawaid
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zurich and Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Zurich, Switzerland
| | - Isabelle M Mansuy
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zurich and Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Zurich, Switzerland
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23
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Alvarez-Saavedra M, Yan K, De Repentigny Y, Hashem LE, Chaudary N, Sarwar S, Yang D, Ioshikhes I, Kothary R, Hirayama T, Yagi T, Picketts DJ. Snf2h Drives Chromatin Remodeling to Prime Upper Layer Cortical Neuron Development. Front Mol Neurosci 2019; 12:243. [PMID: 31680852 PMCID: PMC6811508 DOI: 10.3389/fnmol.2019.00243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/20/2019] [Indexed: 01/23/2023] Open
Abstract
Alterations in the homeostasis of either cortical progenitor pool, namely the apically located radial glial (RG) cells or the basal intermediate progenitors (IPCs) can severely impair cortical neuron production. Such changes are reflected by microcephaly and are often associated with cognitive defects. Genes encoding epigenetic regulators are a frequent cause of intellectual disability and many have been shown to regulate progenitor cell growth, including our inactivation of the Smarca1 gene encoding Snf2l, which is one of two ISWI mammalian orthologs. Loss of the Snf2l protein resulted in dysregulation of Foxg1 and IPC proliferation leading to macrocephaly. Here we show that inactivation of the closely related Smarca5 gene encoding the Snf2h chromatin remodeler is necessary for embryonic IPC expansion and subsequent specification of callosal projection neurons. Telencephalon-specific Smarca5 cKO embryos have impaired cell cycle kinetics and increased cell death, resulting in fewer Tbr2+ and FoxG1+ IPCs by mid-neurogenesis. These deficits give rise to adult mice with a dramatic reduction in Satb2+ upper layer neurons, and partial agenesis of the corpus callosum. Mice survive into adulthood but molecularly display reduced expression of the clustered protocadherin genes that may further contribute to altered dendritic arborization and a hyperactive behavioral phenotype. Our studies provide novel insight into the developmental function of Snf2h-dependent chromatin remodeling processes during brain development.
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Affiliation(s)
- Matías Alvarez-Saavedra
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Keqin Yan
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Yves De Repentigny
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Lukas E. Hashem
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Nidhi Chaudary
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Shihab Sarwar
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Doo Yang
- Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Ilya Ioshikhes
- Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Rashmi Kothary
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Teruyoshi Hirayama
- KOKORO-Biology Group, Integrated Biology Laboratories, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, Tokushima, Japan
| | - Takeshi Yagi
- KOKORO-Biology Group, Integrated Biology Laboratories, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - David J. Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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24
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Xu W, Long L, Zhao Y, Stevens L, Felipe I, Munoz J, Ellis RE, McGrath PT. Evolution of Yin and Yang isoforms of a chromatin remodeling subunit precedes the creation of two genes. eLife 2019; 8:e48119. [PMID: 31498079 PMCID: PMC6752949 DOI: 10.7554/elife.48119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/05/2019] [Indexed: 12/13/2022] Open
Abstract
Genes can encode multiple isoforms, broadening their functions and providing a molecular substrate to evolve phenotypic diversity. Evolution of isoform function is a potential route to adapt to new environments. Here we show that de novo, beneficial alleles in the nurf-1 gene became fixed in two laboratory lineages of C. elegans after isolation from the wild in 1951, before methods of cryopreservation were developed. nurf-1 encodes an ortholog of BPTF, a large (>300 kD) multidomain subunit of the NURF chromatin remodeling complex. Using CRISPR-Cas9 genome editing and transgenic rescue, we demonstrate that in C. elegans, nurf-1 has split into two, largely non-overlapping isoforms (NURF-1.D and NURF-1.B, which we call Yin and Yang, respectively) that share only two of 26 exons. Both isoforms are essential for normal gametogenesis but have opposite effects on male/female gamete differentiation. Reproduction in hermaphrodites, which involves production of both sperm and oocytes, requires a balance of these opposing Yin and Yang isoforms. Transgenic rescue and genetic position of the fixed mutations suggest that different isoforms are modified in each laboratory strain. In a related clade of Caenorhabditis nematodes, the shared exons have duplicated, resulting in the split of the Yin and Yang isoforms into separate genes, each containing approximately 200 amino acids of duplicated sequence that has undergone accelerated protein evolution following the duplication. Associated with this duplication event is the loss of two additional nurf-1 transcripts, including the long-form transcript and a newly identified, highly expressed transcript encoded by the duplicated exons. We propose these lost transcripts are non-functional side products necessary to transcribe the Yin and Yang transcripts in the same cells. Our work demonstrates how gene sharing, through the production of multiple isoforms, can precede the creation of new, independent genes.
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Affiliation(s)
- Wen Xu
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaUnited States
| | - Lijiang Long
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaUnited States
- Interdisciplinary Graduate Program in Quantitative BiosciencesGeorgia Institute of TechnologyAtlantaUnited States
| | - Yuehui Zhao
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaUnited States
| | - Lewis Stevens
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
| | - Irene Felipe
- Epithelial Carcinogenesis GroupSpanish National Cancer Research Center-CNIOMadridSpain
| | - Javier Munoz
- Proteomics Unit-ProteoRed-ISCIIISpanish National Cancer Research Center-CNIOMadridSpain
| | - Ronald E Ellis
- Department of Molecular BiologyRowan University School of Osteopathic MedicineStratfordUnited States
| | - Patrick T McGrath
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaUnited States
- Parker H. Petit Institute of Bioengineering and BioscienceGeorgia Institute of TechnologyAtlantaUnited States
- School of PhysicsGeorgia Institute of TechnologyAtlantaUnited States
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25
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Herriges JC, Arch EM, Burgio PA, Baldwin EE, LaGrave D, Lamb AN, Toydemir RM. Delineating the Clinical Spectrum Associated With Xq25q26.2 Duplications: Report of 2 Families and Review of the Literature. J Child Neurol 2019; 34:86-93. [PMID: 30458662 DOI: 10.1177/0883073818811454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To date, 13 patients with interstitial microduplications involving Xq25q26.2 have been reported. Here, we report 6 additional patients from 2 families with duplications involving Xq25q26.2. Family I carries a 5.3-Mb duplication involving 26 genes. This duplication was identified in 3 patients and was associated with microcephaly, growth failure, developmental delay, and dysmorphic features. Family II carries an overlapping 791-kb duplication that involves 3 genes. This duplication was identified in 3 patients and was associated with learning disability and speech delay. The size and gene content of published overlapping Xq25q26.2 duplications vary, making it difficult to define a critical region or establish a genotype-phenotype correlation. However, patients with overlapping duplications have been found to share common clinical features including microcephaly, growth failure, intellectual disability, learning difficulties, and dysmorphic features. The 2 families presented here provide additional insight into the phenotypic spectrum and clinical significance of duplications in this region.
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Affiliation(s)
- John C Herriges
- 1 Department of Pathology, University of Utah, Salt Lake City, UT, USA.,2 ARUP Laboratories, Salt Lake City, UT, USA
| | - Ellen M Arch
- 3 Genetics and Developmental Medicine, Dixie Regional Medical Center, St George, UT, USA
| | - Pamela A Burgio
- 4 Pediatrics Medical Group, Renown Regional Medical Center, Reno, NV, USA
| | | | | | - Allen N Lamb
- 1 Department of Pathology, University of Utah, Salt Lake City, UT, USA.,2 ARUP Laboratories, Salt Lake City, UT, USA
| | - Reha M Toydemir
- 1 Department of Pathology, University of Utah, Salt Lake City, UT, USA.,2 ARUP Laboratories, Salt Lake City, UT, USA.,5 Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
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26
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Mungamuri SK. Targeting the epigenome as a therapeutic strategy for pancreatic tumors. THERANOSTIC APPROACH FOR PANCREATIC CANCER 2019:211-244. [DOI: 10.1016/b978-0-12-819457-7.00011-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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27
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Liu T, Han Z, Li H, Zhu Y, Sun Z, Zhu A. LncRNA DLEU1 contributes to colorectal cancer progression via activation of KPNA3. Mol Cancer 2018; 17:118. [PMID: 30098595 PMCID: PMC6087004 DOI: 10.1186/s12943-018-0873-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/02/2018] [Indexed: 01/05/2023] Open
Abstract
Background Accumulating evidences show that long noncoding RNAs (lncRNA) play essential roles in the development and progression of various malignancies. However, their functions remains poorly understood and many lncRNAs have not been defined in colorectal cancer (CRC). In this study, we investigated the role of DLEU1 in CRC. Methods Quantitative real-time PCR was used to detect the expression of DLEU1 and survival analysis was adopted to explore the association between DLEU1 expression and the prognosis of CRC patients. CRC cells were stably transfected with lentivirus approach and cell proliferation, migration, invasion and cell apoptosis, as well as tumorigenesis in nude mice were performed to assess the effects of DLEU1 in BCa. Biotin-coupled probe pull down assay, RNA immunoprecipitation and Fluorescence in situ hybridization assays were conducted to confirm the relationship between DLEU1 and SMARCA1. Results Here we revealed that DLEU1 was crucial for activation of KPNA3 by recruiting SMARCA1, an essential subunit of the NURF chromatin remodeling complex, in CRC. DLEU1 was indispensible for the deposition of SMARCA1 at the promoter of KPNA3 gene. Increased expression of DLEU1 and KPNA3 was observed in human CRC tissues. And higher expression of DLEU1 or KPNA3 in patients indicates lower survival rate and poorer prognosis. DLEU1 knockdown remarkably inhibited CRC cell proliferation, migration and invasion in vitro and in vivo while overexpressing KPNA3 in the meantime reversed it. Conclusions Our results identify DLEU1 as a key regulator by a novel DLEU1/SMARCA1/KPNA3 axis in CRC development and progression, which may provide a potential biomarker and therapeutic target for the management of CRC. Electronic supplementary material The online version of this article (10.1186/s12943-018-0873-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tianyou Liu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, #23 Youzheng Street, Harbin, 150001, Heilongjiang Province, China.
| | - Zhiyang Han
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, #23 Youzheng Street, Harbin, 150001, Heilongjiang Province, China
| | - Huanyu Li
- Department of General Surgery, Mulan Country People's Hospital, Harbin, 150001, China
| | - Yuekun Zhu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, #23 Youzheng Street, Harbin, 150001, Heilongjiang Province, China
| | - Ziquan Sun
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, #23 Youzheng Street, Harbin, 150001, Heilongjiang Province, China
| | - Anlong Zhu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, #23 Youzheng Street, Harbin, 150001, Heilongjiang Province, China
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28
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Li D, Song H, Mei H, Fang E, Wang X, Yang F, Li H, Chen Y, Huang K, Zheng L, Tong Q. Armadillo repeat containing 12 promotes neuroblastoma progression through interaction with retinoblastoma binding protein 4. Nat Commun 2018; 9:2829. [PMID: 30026490 PMCID: PMC6053364 DOI: 10.1038/s41467-018-05286-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 06/25/2018] [Indexed: 12/18/2022] Open
Abstract
Recent studies suggest the emerging roles of armadillo (ARM) family proteins in tumor progression. However, the functions and underlying mechanisms of ARM members in tumorigenesis and aggressiveness of neuroblastoma (NB) remain to be determined. Herein, we identify armadillo repeat containing 12 (ARMC12) as an ARM member associated with NB progression. ARMC12 promotes the growth and aggressiveness of NB cell lines. Mechanistically, ARMC12 physically interacts with retinoblastoma binding protein 4 (RBBP4) to facilitate the formation and activity of polycomb repressive complex 2, resulting in transcriptional repression of tumor suppressive genes. Blocking the interaction between ARMC12 and RBBP4 by cell-penetrating inhibitory peptide activates the downstream gene expression and suppresses the tumorigenesis and aggressiveness of NB cells. Both ARMC12 and RBBP4 are upregulated in NB tissues, and are associated with unfavorable outcome of patients. These findings suggest the crucial roles of ARMC12 in tumor progression and a potential therapeutic approach for NB. Armadillo (ARM) family proteins can act as oncogenes or tumor suppressors. Here, the authors show that a new ARM protein (ARMC12) is upregulated in neuroblastoma, binds the PRC2 component RBBP4, and inhibits transcription of tumor suppressive genes.
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Affiliation(s)
- Dan Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, P.R. China
| | - Huajie Song
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, P.R. China
| | - Hong Mei
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, P.R. China
| | - Erhu Fang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, P.R. China
| | - Xiaojing Wang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, P.R. China
| | - Feng Yang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, P.R. China
| | - Huanhuan Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, P.R. China
| | - Yajun Chen
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, P.R. China
| | - Kai Huang
- Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, P.R. China
| | - Liduan Zheng
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, P.R. China. .,Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, P.R. China.
| | - Qiangsong Tong
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, P.R. China. .,Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, P.R. China.
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29
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Abstract
Gene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. The degree to which the arrangement of motif sites within regulatory elements determines their function remains unclear. Here, we show that the positional distribution of TF motif sites within nucleosome-depleted regions of DNA fall into six distinct classes. These patterns are highly consistent across cell types and bring together factors that have similar functional and binding properties. Furthermore, the position of motif sites appears to be related to their known functions. Our results suggest that TFs play distinct roles in forming a functional enhancer, facilitated by their position within a regulatory sequence. Gene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. TF binding occurs in nucleosome-depleted regions of DNA (NDRs), which generally encompass regions with lengths similar to those protected by nucleosomes. However, less is known about where within these regions specific TFs tend to be found. Here, we characterize the positional bias of inferred binding sites for 103 TFs within ∼500,000 NDRs across 47 cell types. We find that distinct classes of TFs display different binding preferences: Some tend to have binding sites toward the edges, some toward the center, and some at other positions within the NDR. These patterns are highly consistent across cell types, suggesting that they may reflect TF-specific intrinsic structural or functional characteristics. In particular, TF classes with binding sites at NDR edges are enriched for those known to interact with histones and chromatin remodelers, whereas TFs with central enrichment interact with other TFs and cofactors such as p300. Our results suggest distinct regiospecific binding patterns and functions of TF classes within enhancers.
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30
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Sokpor G, Castro-Hernandez R, Rosenbusch J, Staiger JF, Tuoc T. ATP-Dependent Chromatin Remodeling During Cortical Neurogenesis. Front Neurosci 2018; 12:226. [PMID: 29686607 PMCID: PMC5900035 DOI: 10.3389/fnins.2018.00226] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/22/2018] [Indexed: 12/20/2022] Open
Abstract
The generation of individual neurons (neurogenesis) during cortical development occurs in discrete steps that are subtly regulated and orchestrated to ensure normal histogenesis and function of the cortex. Notably, various gene expression programs are known to critically drive many facets of neurogenesis with a high level of specificity during brain development. Typically, precise regulation of gene expression patterns ensures that key events like proliferation and differentiation of neural progenitors, specification of neuronal subtypes, as well as migration and maturation of neurons in the developing cortex occur properly. ATP-dependent chromatin remodeling complexes regulate gene expression through utilization of energy from ATP hydrolysis to reorganize chromatin structure. These chromatin remodeling complexes are characteristically multimeric, with some capable of adopting functionally distinct conformations via subunit reconstitution to perform specific roles in major aspects of cortical neurogenesis. In this review, we highlight the functions of such chromatin remodelers during cortical development. We also bring together various proposed mechanisms by which ATP-dependent chromatin remodelers function individually or in concert, to specifically modulate vital steps in cortical neurogenesis.
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Affiliation(s)
- Godwin Sokpor
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Ricardo Castro-Hernandez
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Joachim Rosenbusch
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Jochen F Staiger
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
| | - Tran Tuoc
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
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31
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Goodwin LR, Picketts DJ. The role of ISWI chromatin remodeling complexes in brain development and neurodevelopmental disorders. Mol Cell Neurosci 2017; 87:55-64. [PMID: 29249292 DOI: 10.1016/j.mcn.2017.10.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/04/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022] Open
Abstract
The mammalian ISWI (Imitation Switch) genes SMARCA1 and SMARCA5 encode the ATP-dependent chromatin remodeling proteins SNF2L and SNF2H. The ISWI proteins interact with BAZ (bromodomain adjacent to PHD zinc finger) domain containing proteins to generate eight distinct remodeling complexes. ISWI complex-mediated nucleosome positioning within genes and gene regulatory elements is proving important for the transition from a committed progenitor state to a differentiated cell state. Genetic studies have implicated the involvement of many ATP-dependent chromatin remodeling proteins in neurodevelopmental disorders (NDDs), including SMARCA1. Here we review the characterization of mice inactivated for ISWI and their interacting proteins, as it pertains to brain development and disease. A better understanding of chromatin dynamics during neural development is a prerequisite to understanding disease pathologies and the development of therapeutics for these complex disorders.
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Affiliation(s)
- Laura R Goodwin
- Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Department of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada.
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32
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Hoffmeister H, Fuchs A, Erdel F, Pinz S, Gröbner-Ferreira R, Bruckmann A, Deutzmann R, Schwartz U, Maldonado R, Huber C, Dendorfer AS, Rippe K, Längst G. CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality. Nucleic Acids Res 2017; 45:10534-10554. [PMID: 28977666 PMCID: PMC5737555 DOI: 10.1093/nar/gkx711] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/08/2017] [Indexed: 12/22/2022] Open
Abstract
CHD3 and CHD4 (Chromodomain Helicase DNA binding protein), two highly similar representatives of the Mi-2 subfamily of SF2 helicases, are coexpressed in many cell lines and tissues and have been reported to act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). Besides CHD proteins, NuRD contains several repressors like HDAC1/2, MTA2/3 and MBD2/3, arguing for a role as a transcriptional repressor. However, the subunit composition varies among cell- and tissue types and physiological conditions. In particular, it is unclear if CHD3 and CHD4 coexist in the same NuRD complex or whether they form distinct NuRD complexes with specific functions. We mapped the CHD composition of NuRD complexes in mammalian cells and discovered that they are isoform-specific, containing either the monomeric CHD3 or CHD4 ATPase. Both types of complexes exhibit similar intranuclear mobility, interact with HP1 and rapidly accumulate at UV-induced DNA repair sites. But, CHD3 and CHD4 exhibit distinct nuclear localization patterns in unperturbed cells, revealing a subset of specific target genes. Furthermore, CHD3 and CHD4 differ in their nucleosome remodeling and positioning behaviour in vitro. The proteins form distinct CHD3- and CHD4-NuRD complexes that do not only repress, but can just as well activate gene transcription of overlapping and specific target genes.
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Affiliation(s)
- Helen Hoffmeister
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Andreas Fuchs
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Fabian Erdel
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Sophia Pinz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Regina Gröbner-Ferreira
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Rainer Deutzmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Uwe Schwartz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Rodrigo Maldonado
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Claudia Huber
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Anne-Sarah Dendorfer
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Karsten Rippe
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Gernot Längst
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
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33
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Haploinsufficiency of the Chromatin Remodeler BPTF Causes Syndromic Developmental and Speech Delay, Postnatal Microcephaly, and Dysmorphic Features. Am J Hum Genet 2017; 101:503-515. [PMID: 28942966 DOI: 10.1016/j.ajhg.2017.08.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/10/2017] [Indexed: 12/13/2022] Open
Abstract
Bromodomain PHD finger transcription factor (BPTF) is the largest subunit of nucleosome remodeling factor (NURF), a member of the ISWI chromatin-remodeling complex. However, the clinical consequences of disruption of this complex remain largely uncharacterized. BPTF is required for anterior-posterior axis formation of the mouse embryo and was shown to promote posterior neuroectodermal fate by enhancing Smad2-activated wnt8 expression in zebrafish. Here, we report eight loss-of-function and two missense variants (eight de novo and two of unknown origin) in BPTF on 17q24.2. The BPTF variants were found in unrelated individuals aged between 2.1 and 13 years, who manifest variable degrees of developmental delay/intellectual disability (10/10), speech delay (10/10), postnatal microcephaly (7/9), and dysmorphic features (9/10). Using CRISPR-Cas9 genome editing of bptf in zebrafish to induce a loss of gene function, we observed a significant reduction in head size of F0 mutants compared to control larvae. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) and phospho-histone H3 (PH3) staining to assess apoptosis and cell proliferation, respectively, showed a significant increase in cell death in F0 mutants compared to controls. Additionally, we observed a substantial increase of the ceratohyal angle of the craniofacial skeleton in bptf F0 mutants, indicating abnormal craniofacial patterning. Taken together, our data demonstrate the pathogenic role of BPTF haploinsufficiency in syndromic neurodevelopmental anomalies and extend the clinical spectrum of human disorders caused by ablation of chromatin remodeling complexes.
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34
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Khoshnood B, Dacklin I, Grabbe C. A proteomics approach to identify targets of the ubiquitin-like molecule Urm1 in Drosophila melanogaster. PLoS One 2017; 12:e0185611. [PMID: 28953965 PMCID: PMC5617222 DOI: 10.1371/journal.pone.0185611] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/15/2017] [Indexed: 12/14/2022] Open
Abstract
By covalently conjugating to target proteins, ubiquitin-like modifiers (UBLs) act as important regulators of target protein localization and activity, thereby playing a critical role in the orchestration of cellular biology. The most ancient and one of the least studied UBLs is Urm1, a dual-function protein that in parallel to performing similar functions as its prokaryotic ancestors in tRNA modification, also has adopted the capacity to conjugate to cellular proteins analogous to ubiquitin and other UBL modifiers. In order to increase the understanding of Urm1 and its role in multicellular organisms, we have used affinity purification followed by mass spectrometry to identify putative targets of Urm1 conjugation (urmylation) at three developmental stages of the Drosophila melanogaster lifecycle. Altogether we have recovered 79 Urm1-interacting proteins in Drosophila, which include the already established Urm1 binding partners Prx5 and Uba4, together with 77 candidate urmylation targets that are completely novel in the fly. Among these, the majority was exclusively identified during either embryogenesis, larval stages or in adult flies. We further present biochemical evidence that four of these proteins are covalently conjugated by Urm1, whereas the fifth verified Urm1-binding protein appears to interact with Urm1 via non-covalent means. Besides recapitulating the previously established roles of Urm1 in tRNA modification and during oxidative stress, functional clustering of the newly identified Urm1-associated proteins further positions Urm1 in protein networks that control other types of cellular stress, such as immunological threats and DNA damage. In addition, the functional characteristics of several of the candidate targets strongly match the phenotypes displayed by Urm1n123 null animals, including embryonic lethality, reduced fertility and shortened lifespan. In conclusion, this identification of candidate targets of urmylation significantly increases the knowledge of Urm1 and presents an excellent starting point for unravelling the role of Urm1 in the context of a complex living organism.
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Affiliation(s)
| | - Ingrid Dacklin
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Caroline Grabbe
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- * E-mail:
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35
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Hota SK, Bruneau BG. ATP-dependent chromatin remodeling during mammalian development. Development 2017; 143:2882-97. [PMID: 27531948 DOI: 10.1242/dev.128892] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Precise gene expression ensures proper stem and progenitor cell differentiation, lineage commitment and organogenesis during mammalian development. ATP-dependent chromatin-remodeling complexes utilize the energy from ATP hydrolysis to reorganize chromatin and, hence, regulate gene expression. These complexes contain diverse subunits that together provide a multitude of functions, from early embryogenesis through cell differentiation and development into various adult tissues. Here, we review the functions of chromatin remodelers and their different subunits during mammalian development. We discuss the mechanisms by which chromatin remodelers function and highlight their specificities during mammalian cell differentiation and organogenesis.
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Affiliation(s)
- Swetansu K Hota
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA Department of Pediatrics, University of California, San Francisco, CA 94143, USA Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
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36
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Oppikofer M, Bai T, Gan Y, Haley B, Liu P, Sandoval W, Ciferri C, Cochran AG. Expansion of the ISWI chromatin remodeler family with new active complexes. EMBO Rep 2017; 18:1697-1706. [PMID: 28801535 DOI: 10.15252/embr.201744011] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 02/01/2023] Open
Abstract
ISWI chromatin remodelers mobilize nucleosomes to control DNA accessibility. Complexes isolated to date pair one of six regulatory subunits with one of two highly similar ATPases. However, we find that each endogenously expressed ATPase co-purifies with every regulatory subunit, substantially increasing the diversity of ISWI complexes, and we additionally identify BAZ2B as a novel, seventh regulatory subunit. Through reconstitution of catalytically active human ISWI complexes, we demonstrate that the new interactions described here are stable and direct. Finally, we profile the nucleosome remodeling functions of the now expanded family of ISWI chromatin remodelers. By revealing the combinatorial nature of ISWI complexes, we provide a basis for better understanding ISWI function in normal settings and disease.
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Affiliation(s)
- Mariano Oppikofer
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Tianyi Bai
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Yutian Gan
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Peter Liu
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Wendy Sandoval
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Claudio Ciferri
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Andrea G Cochran
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA
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37
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Mayes K, Elsayed Z, Alhazmi A, Waters M, Alkhatib SG, Roberts M, Song C, Peterson K, Chan V, Ailaney N, Malapati P, Blevins T, Lisnić B, Dumur CI, Landry JW. BPTF inhibits NK cell activity and the abundance of natural cytotoxicity receptor co-ligands. Oncotarget 2017; 8:64344-64357. [PMID: 28969075 PMCID: PMC5610007 DOI: 10.18632/oncotarget.17834] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/26/2017] [Indexed: 11/25/2022] Open
Abstract
Using syngeneic BALB/c mouse breast cancer models, we show that the chromatin remodeling subunit bromodomain PHD finger transcription factor (BPTF) suppresses natural killer (NK) cell antitumor activity in the tumor microenvironment (TME). In culture, BPTF suppresses direct natural cytotoxicity receptor (NCR) mediated NK cell cytolytic activity to mouse and human cancer cell lines, demonstrating conserved functions. Blocking mouse NCR1 in vivo rescues BPTF KD tumor weights, demonstrating its importance for the control of tumor growth. We discovered that BPTF occupies heparanase (Hpse) regulatory elements, activating its expression. Increased heparanase activity results in reduced cell surface abundance of the NCR co-ligands: heparan sulfate proteoglycans (HSPGs). Using gain and loss of function approaches we show that elevated heparanase levels suppress NK cell cytolytic activity to tumor cells in culture. These results suggest that BPTF activates heparanase expression, which in turn reduces cell surface HSPGs and NCR co-ligands, inhibiting NK cell activity. Furthermore, gene expression data from human breast cancer tumors shows that elevated BPTF expression correlates with reduced antitumor immune cell signatures, supporting conserved roles for BPTF in suppressing antitumor immunity. Conditional BPTF depletion in established mouse breast tumors enhances antitumor immunity, suggesting that inhibiting BPTF could provide a novel immunotherapy.
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Affiliation(s)
- Kimberly Mayes
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Zeinab Elsayed
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Aiman Alhazmi
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Michael Waters
- The Department of Biochemistry, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Suehyb G Alkhatib
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Mark Roberts
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Carolyn Song
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Kristen Peterson
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Vivian Chan
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Nikhil Ailaney
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Pumoli Malapati
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Tana Blevins
- The Department of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Berislav Lisnić
- The Center for Proteomics and Department for Histology and Embryology, University of Rijeka, Faculty of Medicine, 51000 Rijeka, Croatia
| | - Catherine I Dumur
- The Department of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Joseph W Landry
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
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38
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The Cac2 subunit is essential for productive histone binding and nucleosome assembly in CAF-1. Sci Rep 2017; 7:46274. [PMID: 28418026 PMCID: PMC5394680 DOI: 10.1038/srep46274] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/13/2017] [Indexed: 11/08/2022] Open
Abstract
Nucleosome assembly following DNA replication controls epigenome maintenance and genome integrity. Chromatin assembly factor 1 (CAF-1) is the histone chaperone responsible for histone (H3-H4)2 deposition following DNA synthesis. Structural and functional details for this chaperone complex and its interaction with histones are slowly emerging. Using hydrogen-deuterium exchange coupled to mass spectrometry, combined with in vitro and in vivo mutagenesis studies, we identified the regions involved in the direct interaction between the yeast CAF-1 subunits, and mapped the CAF-1 domains responsible for H3-H4 binding. The large subunit, Cac1 organizes the assembly of CAF-1. Strikingly, H3-H4 binding is mediated by a composite interface, shaped by Cac1-bound Cac2 and the Cac1 acidic region. Cac2 is indispensable for productive histone binding, while deletion of Cac3 has only moderate effects on H3-H4 binding and nucleosome assembly. These results define direct structural roles for yeast CAF-1 subunits and uncover a previously unknown critical function of the middle subunit in CAF-1.
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39
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Shao G, Wang Y, Guan S, Burlingame AL, Lu F, Knox R, Ferriero DM, Jiang X. Proteomic Analysis of Mouse Cortex Postsynaptic Density following Neonatal Brain Hypoxia-Ischemia. Dev Neurosci 2017; 39:66-81. [PMID: 28315865 PMCID: PMC5519436 DOI: 10.1159/000456030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/11/2017] [Indexed: 02/02/2023] Open
Abstract
Proteomics of the synapses and postsynaptic densities (PSDs) have provided a deep understanding of protein composition and signal networks in the adult brain, which underlie neuronal plasticity and neurodegenerative or psychiatric disorders. However, there is a paucity of knowledge about the architecture and organization of PSDs in the immature brain, and how it is modified by brain injury in an early developing stage. Mass spectrometry (MS)-based proteomic analysis was performed on PSDs prepared from cortices of postnatal day 9 naïve mice or pups which had suffered hypoxic-ischemic (HI) brain injury. 512 proteins of different functional groups were identified from PSDs collected 1 h after HI injury, among which 60 have not been reported previously. Seven newly identified proteins involved in neural development were highlighted. HI injury increased the yield of PSDs at early time points upon reperfusion, and multiple proteins were recruited into PSDs following the insult. Quantitative analysis was performed using spectral counting, and proteins whose relative expression was more than 50% up- or downregulated compared to the sham animals 1 h after HI insult were reported. Validation with Western blotting demonstrated changes in expression and phosphorylation of the N-methyl-D-aspartate receptor, activation of a series of postsynaptic protein kinases and dysregulation of scaffold and adaptor proteins in response to neonatal HI insult. This work, along with other recent studies of synaptic protein profiling in the immature brain, builds a foundation for future investigation on the molecular mechanisms underlying developing plasticity. Furthermore, it provides insights into the biochemical changes of PSDs following early brain hypoxia-ischemia, which is helpful for understanding not only the injury mechanisms, but also the process of repair or replenishment of neuronal circuits during recovery from brain damage.
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Affiliation(s)
- Guo Shao
- Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, China
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40
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Mayes K, Alkhatib SG, Peterson K, Alhazmi A, Song C, Chan V, Blevins T, Roberts M, Dumur CI, Wang XY, Landry JW. BPTF Depletion Enhances T-cell-Mediated Antitumor Immunity. Cancer Res 2016; 76:6183-6192. [PMID: 27651309 DOI: 10.1158/0008-5472.can-15-3125] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 08/24/2016] [Indexed: 12/12/2022]
Abstract
Genetic studies in fruit flies have implicated the chromatin remodeling complex nucleosome remodeling factor (NURF) in immunity, but it has yet to be studied in mammals. Here we show that its targeting in mice enhances antitumor immunity in two syngeneic models of cancer. NURF was disabled by silencing of bromodomain PHD-finger containing transcription factor (BPTF), the largest and essential subunit of NURF. We found that both CD8+ and CD4+ T cells were necessary for enhanced antitumor activity, with elevated numbers of activated CD8+ T cells observed in BPTF-deficient tumors. Enhanced cytolytic activity was observed for CD8+ T cells cocultured with BPTF-silenced cells. Similar effects were not produced with T-cell receptor transgenic CD8+ T cells, implicating the involvement of novel antigens. Accordingly, enhanced activity was observed for individual CD8+ T-cell clones from mice bearing BPTF-silenced tumors. Mechanistic investigations revealed that NURF directly regulated the expression of genes encoding immunoproteasome subunits Psmb8 and Psmb9 and the antigen transporter genes Tap1 and Tap2 The PSMB8 inhibitor ONX-0914 reversed the effects of BPTF ablation, consistent with a critical role for the immunoproteasome in improving tumor immunogenicity. Thus, NURF normally suppresses tumor antigenicity and its depletion improves antigen processing, CD8 T-cell cytotoxicity, and antitumor immunity, identifying NURF as a candidate therapeutic target to enhance antitumor immunity. Cancer Res; 76(21); 6183-92. ©2016 AACR.
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Affiliation(s)
- Kimberly Mayes
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Suehyb G Alkhatib
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Kristen Peterson
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Aiman Alhazmi
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Carolyn Song
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Vivian Chan
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Tana Blevins
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Mark Roberts
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Catherine I Dumur
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Xiang-Yang Wang
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Joseph W Landry
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia.
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Kwon SY, Grisan V, Jang B, Herbert J, Badenhorst P. Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators. PLoS Genet 2016; 12:e1005969. [PMID: 27046080 PMCID: PMC4821604 DOI: 10.1371/journal.pgen.1005969] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/10/2016] [Indexed: 12/20/2022] Open
Abstract
NURF is a conserved higher eukaryotic ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF is able to alter chromatin dynamics to control transcription and genome organization. Previous biochemical and genetic analysis of the specificity-subunit of Drosophila NURF (Nurf301/Enhancer of Bithorax (E(bx)) has defined NURF as a critical regulator of homeotic, heat-shock and steroid-responsive gene transcription. It has been speculated that NURF controls pathway specific transcription by co-operating with sequence-specific transcription factors to remodel chromatin at dedicated enhancers. However, conclusive in vivo demonstration of this is lacking and precise regulatory elements targeted by NURF are poorly defined. To address this, we have generated a comprehensive map of in vivo NURF activity, using MNase-sequencing to determine at base pair resolution NURF target nucleosomes, and ChIP-sequencing to define sites of NURF recruitment. Our data show that, besides anticipated roles at enhancers, NURF interacts physically and functionally with the TRF2/DREF basal transcription factor to organize nucleosomes downstream of active promoters. Moreover, we detect NURF remodeling and recruitment at distal insulator sites, where NURF functionally interacts with and co-localizes with DREF and insulator proteins including CP190 to establish nucleosome-depleted domains. This insulator function of NURF is most apparent at subclasses of insulators that mark the boundaries of chromatin domains, where multiple insulator proteins co-associate. By visualizing the complete repertoire of in vivo NURF chromatin targets, our data provide new insights into how chromatin remodeling can control genome organization and regulatory interactions.
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Affiliation(s)
- So Yeon Kwon
- Institute of Biomedical Research, University of Birmingham, Edgbaston, United Kingdom
| | - Valentina Grisan
- Institute of Biomedical Research, University of Birmingham, Edgbaston, United Kingdom
| | - Boyun Jang
- Institute of Biomedical Research, University of Birmingham, Edgbaston, United Kingdom
| | - John Herbert
- Institute of Biomedical Research, University of Birmingham, Edgbaston, United Kingdom
| | - Paul Badenhorst
- Institute of Biomedical Research, University of Birmingham, Edgbaston, United Kingdom
- * E-mail:
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42
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Zhu Y, Chen Z, Zhang K, Wang M, Medovoy D, Whitaker JW, Ding B, Li N, Zheng L, Wang W. Constructing 3D interaction maps from 1D epigenomes. Nat Commun 2016; 7:10812. [PMID: 26960733 PMCID: PMC4792925 DOI: 10.1038/ncomms10812] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/24/2016] [Indexed: 12/28/2022] Open
Abstract
The human genome is tightly packaged into chromatin whose functional output depends on both one-dimensional (1D) local chromatin states and three-dimensional (3D) genome organization. Currently, chromatin modifications and 3D genome organization are measured by distinct assays. An emerging question is whether it is possible to deduce 3D interactions by integrative analysis of 1D epigenomic data and associate 3D contacts to functionality of the interacting loci. Here we present EpiTensor, an algorithm to identify 3D spatial associations within topologically associating domains (TADs) from 1D maps of histone modifications, chromatin accessibility and RNA-seq. We demonstrate that active promoter–promoter, promoter–enhancer and enhancer–enhancer associations identified by EpiTensor are highly concordant with those detected by Hi-C, ChIA-PET and eQTL analyses at 200 bp resolution. Moreover, EpiTensor has identified a set of interaction hotspots, characterized by higher chromatin and transcriptional activity as well as enriched TF and ncRNA binding across diverse cell types, which may be critical for stabilizing the local 3D interactions. The human genome is highly organized, with one-dimensional chromatin states packaged into higher level three-dimensional architecture. Here, the authors present EpiTensor that can identify 3D spatial associations from 1D epigenetic information.
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Affiliation(s)
- Yun Zhu
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - Zhao Chen
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - Kai Zhang
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - Mengchi Wang
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - David Medovoy
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - John W Whitaker
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - Bo Ding
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - Nan Li
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - Lina Zheng
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA.,Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093-0359, USA
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43
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Wiechens N, Singh V, Gkikopoulos T, Schofield P, Rocha S, Owen-Hughes T. The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors. PLoS Genet 2016; 12:e1005940. [PMID: 27019336 PMCID: PMC4809547 DOI: 10.1371/journal.pgen.1005940] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 02/25/2016] [Indexed: 12/22/2022] Open
Abstract
Within the genomes of metazoans, nucleosomes are highly organised adjacent to the binding sites for a subset of transcription factors. Here we have sought to investigate which chromatin remodelling enzymes are responsible for this. We find that the ATP-dependent chromatin remodelling enzyme SNF2H plays a major role organising arrays of nucleosomes adjacent to the binding sites for the architectural transcription factor CTCF sites and acts to promote CTCF binding. At many other factor binding sites SNF2H and the related enzyme SNF2L contribute to nucleosome organisation. The action of SNF2H at CTCF sites is functionally important as depletion of CTCF or SNF2H affects transcription of a common group of genes. This suggests that chromatin remodelling ATPase's most closely related to the Drosophila ISWI protein contribute to the function of many human gene regulatory elements.
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Affiliation(s)
- Nicola Wiechens
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Vijender Singh
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Triantaffyllos Gkikopoulos
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Pieta Schofield
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Sonia Rocha
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
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Mariani L, Lussi YC, Vandamme J, Riveiro A, Salcini AE. The H3K4me3/2 histone demethylase RBR-2 controls axon guidance by repressing the actin-remodeling gene wsp-1. Development 2016; 143:851-63. [PMID: 26811384 DOI: 10.1242/dev.132985] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/16/2016] [Indexed: 12/25/2022]
Abstract
The dynamic regulation of histone modifications is important for modulating transcriptional programs during development. Aberrant H3K4 methylation is associated with neurological disorders, but how the levels and the recognition of this modification affect specific neuronal processes is unclear. Here, we show that RBR-2, the sole homolog of the KDM5 family of H3K4me3/2 demethylases in Caenorhabditis elegans, ensures correct axon guidance by controlling the expression of the actin regulator wsp-1. Loss of rbr-2 results in increased levels of H3K4me3 at the transcriptional start site of wsp-1, with concomitant higher wsp-1 expression responsible for defective axon guidance. In agreement, overexpression of WSP-1 mimics rbr-2 loss, and its depletion restores normal axon guidance in rbr-2 mutants. NURF-1, an H3K4me3-binding protein and member of the chromatin-remodeling complex NURF, is required for promoting aberrant wsp-1 transcription in rbr-2 mutants and its ablation restores wild-type expression of wsp-1 and axon guidance. Thus, our results establish a precise role for epigenetic regulation in neuronal development by demonstrating a functional link between RBR-2 activity, H3K4me3 levels, the NURF complex and the expression of WSP-1.
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Affiliation(s)
- Luca Mariani
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Yvonne C Lussi
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Julien Vandamme
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alba Riveiro
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anna Elisabetta Salcini
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
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45
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Epigenomic regulation of oncogenesis by chromatin remodeling. Oncogene 2016; 35:4423-36. [PMID: 26804164 DOI: 10.1038/onc.2015.513] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/27/2015] [Accepted: 12/07/2015] [Indexed: 02/08/2023]
Abstract
Disruption of the intricate gene expression program represents one of major driving factors for the development, progression and maintenance of human cancer, and is often associated with acquired therapeutic resistance. At the molecular level, cancerous phenotypes are the outcome of cellular functions of critical genes, regulatory interactions of histones and chromatin remodeling complexes in response to dynamic and persistent upstream signals. A large body of genetic and biochemical evidence suggests that the chromatin remodelers integrate the extracellular and cytoplasmic signals to control gene activity. Consequently, widespread dysregulation of chromatin remodelers and the resulting inappropriate expression of regulatory genes, together, lead to oncogenesis. We summarize the recent developments and current state of the dysregulation of the chromatin remodeling components as the driving mechanism underlying the growth and progression of human tumors. Because chromatin remodelers, modifying enzymes and protein-protein interactions participate in interpreting the epigenetic code, selective chromatin remodelers and bromodomains have emerged as new frontiers for pharmacological intervention to develop future anti-cancer strategies to be used either as single-agent or in combination therapies with chemotherapeutics or radiotherapy.
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46
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Koludrovic D, Laurette P, Strub T, Keime C, Le Coz M, Coassolo S, Mengus G, Larue L, Davidson I. Chromatin-Remodelling Complex NURF Is Essential for Differentiation of Adult Melanocyte Stem Cells. PLoS Genet 2015; 11:e1005555. [PMID: 26440048 PMCID: PMC4595011 DOI: 10.1371/journal.pgen.1005555] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 09/07/2015] [Indexed: 12/23/2022] Open
Abstract
MIcrophthalmia-associated Transcription Factor (MITF) regulates melanocyte and melanoma physiology. We show that MITF associates the NURF chromatin-remodelling factor in melanoma cells. ShRNA-mediated silencing of the NURF subunit BPTF revealed its essential role in several melanoma cell lines and in untransformed melanocytes in vitro. Comparative RNA-seq shows that MITF and BPTF co-regulate overlapping gene expression programs in cell lines in vitro. Somatic and specific inactivation of Bptf in developing murine melanoblasts in vivo shows that Bptf regulates their proliferation, migration and morphology. Once born, Bptf-mutant mice display premature greying where the second post-natal coat is white. This second coat is normally pigmented by differentiated melanocytes derived from the adult melanocyte stem cell (MSC) population that is stimulated to proliferate and differentiate at anagen. An MSC population is established and maintained throughout the life of the Bptf-mutant mice, but these MSCs are abnormal and at anagen, give rise to reduced numbers of transient amplifying cells (TACs) that do not express melanocyte markers and fail to differentiate into mature melanin producing melanocytes. MSCs display a transcriptionally repressed chromatin state and Bptf is essential for reactivation of the melanocyte gene expression program at anagen, the subsequent normal proliferation of TACs and their differentiation into mature melanocytes. The melanocytes pigmenting the coat of adult mice derive from the melanocyte stem cell population residing in the permanent bulge area of the hair follicle. At each angen phase, melanocyte stem cells are stimulated to generate proliferative transient amplifying cells that migrate to the bulb of the follicle where they differentiate into mature melanin producing melanocytes, a processes involving MIcrophthalmia-associated Transcription Factor (MITF) the master regulator of the melanocyte lineage. We show that MITF associates with the NURF chromatin-remodelling factor in melanoma cells. NURF acts downstream of MITF in melanocytes and melanoma cells co-regulating gene expression in vitro. In vivo, mice lacking the NURF subunit Bptf in the melanocyte lineage show premature greying as they are unable to generate mature melanocytes from the adult stem cell population. We find that the melanocyte stem cells from these animals are abnormal and that once they are stimulated at anagen, Bptf is required to ensure the expression of melanocyte markers and their differentiation into mature adult melanocytes. Chromatin remodelling by NURF therefore appears to be essential for the transition of the transcriptionally quiescent stem cell to the differentiated state.
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Affiliation(s)
- Dana Koludrovic
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
- Beaston Institute for Cancer Research, Glasgow, United Kingdom
| | - Patrick Laurette
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
| | - Thomas Strub
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Céline Keime
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
| | - Madeleine Le Coz
- Institut Curie CNRS UMR3347, INSERM U1021, Bat 110, Orsay, France
| | - Sebastien Coassolo
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
| | - Gabrielle Mengus
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
| | - Lionel Larue
- Institut Curie CNRS UMR3347, INSERM U1021, Bat 110, Orsay, France
- Equipes labélisées Ligue Contre le Cancer, Orsay and Strasbourg, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
- Equipes labélisées Ligue Contre le Cancer, Orsay and Strasbourg, France
- * E-mail:
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47
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Abstract
Regulation of chromatin structure is an essential component of the DNA damage response (DDR), which effectively preserves the integrity of DNA by a network of multiple DNA repair and associated signaling pathways. Within the DDR, chromatin is modified and remodeled to facilitate efficient DNA access, to control the activity of repair proteins and to mediate signaling. The mammalian ISWI family has recently emerged as one of the major ATP-dependent chromatin remodeling complex families that function in the DDR, as it is implicated in at least 3 major DNA repair pathways: homologous recombination, non-homologous end-joining and nucleotide excision repair. In this review, we discuss the various manners through which different ISWI complexes regulate DNA repair and how they are targeted to chromatin containing damaged DNA.
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Key Words
- ACF1
- ACF1, ATP-utilizing Chromatin assembly and remodeling Factor 1
- ATP-dependent chromatin remodeling
- BER, Base Excision Repair
- DDR, DNA Damage Response
- DNA damage response
- DSB, Double Strand Break
- GG-NER, Global Genome Nucleotide Excision Repair
- HR, Homologous Recombination
- Homologous Recombination
- ISWI
- ISWI, Imitation SWItch
- MRN, MRE11/Rad50/NBS1
- NER, Nucleotide Excision Repair
- NHEJ, Non-Homologous End Joining
- Non-Homologous End-Joining
- Nucleotide Excision Repair
- PAR, Poly(ADP-Ribose)
- RNApolII, RNA Polymerase II
- RSF1, Remodeling and Spacing Factor 1
- SMARCA, SWI-SNF-related Matrix-associated Actin-dependent Regulator of Chromatin A
- SMARCA5/SNF2H
- TC-NER, Transcription-Coupled Nucleotide Excision Repair
- WSTF
- WSTF, Williams Syndrome Transcription Factor
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Affiliation(s)
- Özge Z Aydin
- a Department of Genetics ; Cancer Genomics Netherlands; Erasmus MC ; Rotterdam , The Netherlands
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48
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The Chromatin Remodeling Protein Bptf Promotes Posterior Neuroectodermal Fate by Enhancing Smad2-Activated wnt8a Expression. J Neurosci 2015; 35:8493-506. [PMID: 26041917 DOI: 10.1523/jneurosci.0377-15.2015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
During vertebrate embryogenesis, the neuroectoderm is induced from dorsal ectoderm and then partitioned into anterior and posterior neuroectodermal domains by posteriorizing signals, such as Wnt and fibroblast growth factor. However, little is known about epigenetic regulation of posteriorizing gene expression. Here, we report a requirement of the chromatin remodeling protein Bptf for neuroectodermal posteriorization in zebrafish embryos. Knockdown of bptf leads to an expansion of the anterior neuroectoderm at the expense of the posterior ectoderm. Bptf functionally and physically interacts with p-Smad2, which is activated by non-Nodal TGF-β signaling, to promote the expression of wnt8a, a critical gene for neural posteriorization. Bptf and Smad2 directly bind to and activate the wnt8a promoter through recruiting NURF remodeling complex. When bptf function or TGF-β signal transduction is inhibited, the nucleosome density on the wnt8a promoter is increased. We propose that Bptf and TGF-β/Smad2 mediate nucleosome remodeling to regulate wnt8a expression and hence neural posteriorization.
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49
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Mayes K, Qiu Z, Alhazmi A, Landry JW. ATP-dependent chromatin remodeling complexes as novel targets for cancer therapy. Adv Cancer Res 2015; 121:183-233. [PMID: 24889532 DOI: 10.1016/b978-0-12-800249-0.00005-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The progression to advanced stage cancer requires changes in many characteristics of a cell. These changes are usually initiated through spontaneous mutation. As a result of these mutations, gene expression is almost invariably altered allowing the cell to acquire tumor-promoting characteristics. These abnormal gene expression patterns are in part enabled by the posttranslational modification and remodeling of nucleosomes in chromatin. These chromatin modifications are established by a functionally diverse family of enzymes including histone and DNA-modifying complexes, histone deposition pathways, and chromatin remodeling complexes. Because the modifications these enzymes deposit are essential for maintaining tumor-promoting gene expression, they have recently attracted much interest as novel therapeutic targets. One class of enzyme that has not generated much interest is the chromatin remodeling complexes. In this review, we will present evidence from the literature that these enzymes have both causal and enabling roles in the transition to advanced stage cancers; as such, they should be seriously considered as high-value therapeutic targets. Previously published strategies for discovering small molecule regulators to these complexes are described. We close with thoughts on future research, the field should perform to further develop this potentially novel class of therapeutic target.
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Affiliation(s)
- Kimberly Mayes
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Zhijun Qiu
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Aiman Alhazmi
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Joseph W Landry
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA.
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50
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Kenzior A, Folk WR. Arabidopsis thaliana MSI4/FVE associates with members of a novel family of plant specific PWWP/RRM domain proteins. PLANT MOLECULAR BIOLOGY 2015; 87:329-339. [PMID: 25600937 DOI: 10.1007/s11103-014-0280-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 12/30/2014] [Indexed: 06/04/2023]
Abstract
AtMSI4/FVE/ACG1, one of five Arabidopsis thaliana genes encoding MSI1-like proteins, helps determine plant growth and development (including control of flowering), as well as responses to certain biotic and abiotic stresses. We reasoned that the product of this gene, AtMSI4, acts through protein partners, which we have co-immunopurified with AtMSI4 from A. thaliana suspension culture cells and identified by liquid chromatography-mass spectrometry (LC-MS). Many of the proteins associated with AtMSI4 have distinct RNA recognition motif (RRM) domains, which we determined to be responsible for association with AtMSI4; and most of the associated RRM domain proteins also contain PWWP domains that are specific to plants. We propose these novel ATMSI4-associated proteins help form nucleoprotein complexes that determine pleiotropic functional properties of AtMSI4/FVE/ACG1 involving plant development and responses to stress.
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Affiliation(s)
- Alexander Kenzior
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO, 65211, USA,
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