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Zhang X, Duan S, Apostolou PE, Wu X, Watanabe J, Gallitto M, Barron T, Taylor KR, Woo PJ, Hua X, Zhou H, Wei HJ, McQuillan N, Kang KD, Friedman GK, Canoll PD, Chang K, Wu CC, Hashizume R, Vakoc CR, Monje M, McKhann GM, Gogos JA, Zhang Z. CHD2 Regulates Neuron-Glioma Interactions in Pediatric Glioma. Cancer Discov 2024; 14:1732-1754. [PMID: 38767413 PMCID: PMC11456263 DOI: 10.1158/2159-8290.cd-23-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/05/2024] [Accepted: 05/16/2024] [Indexed: 05/22/2024]
Abstract
High-grade gliomas (HGG) are deadly diseases for both adult and pediatric patients. Recently, it has been shown that neuronal activity promotes the progression of multiple subgroups of HGG. However, epigenetic mechanisms that govern this process remain elusive. Here we report that the chromatin remodeler chromodomain helicase DNA-binding protein 2 (CHD2) regulates neuron-glioma interactions in diffuse midline glioma (DMG) characterized by onco-histone H3.1K27M. Depletion of CHD2 in H3.1K27M DMG cells compromises cell viability and neuron-to-glioma synaptic connections in vitro, neuron-induced proliferation of H3.1K27M DMG cells in vitro and in vivo, activity-dependent calcium transients in vivo, and extends the survival of H3.1K27M DMG-bearing mice. Mechanistically, CHD2 coordinates with the transcription factor FOSL1 to control the expression of axon-guidance and synaptic genes in H3.1K27M DMG cells. Together, our study reveals a mechanism whereby CHD2 controls the intrinsic gene program of the H3.1K27M DMG subtype, which in turn regulates the tumor growth-promoting interactions of glioma cells with neurons. Significance: Neurons drive the proliferation and invasion of glioma cells. Here we show that chromatin remodeler chromodomain helicase DNA-binding protein 2 controls the epigenome and expression of axon-guidance and synaptic genes, thereby promoting neuron-induced proliferation of H3.1K27M diffuse midline glioma and the pathogenesis of this deadly disease.
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Affiliation(s)
- Xu Zhang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- These authors contributed equally
| | - Shoufu Duan
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- These authors contributed equally
| | - Panagiota E. Apostolou
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Xiaoping Wu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jun Watanabe
- Department of Pediatrics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Matthew Gallitto
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tara Barron
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Kathryn R. Taylor
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Pamelyn J. Woo
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Xu Hua
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hui Zhou
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hong-Jian Wei
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nicholas McQuillan
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kyung-Don Kang
- Department of Pediatrics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Division of Pediatrics, Neuro-Oncology Section, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gregory K. Friedman
- Department of Pediatrics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Division of Pediatrics, Neuro-Oncology Section, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peter D. Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kenneth Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Cheng-Chia Wu
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rintaro Hashizume
- Department of Pediatrics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | | | - Michelle Monje
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, CA 94305, USA
| | - Guy M. McKhann
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Joseph A. Gogos
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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2
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LaFlamme CW, Rastin C, Sengupta S, Pennington HE, Russ-Hall SJ, Schneider AL, Bonkowski ES, Almanza Fuerte EP, Allan TJ, Zalusky MPG, Goffena J, Gibson SB, Nyaga DM, Lieffering N, Hebbar M, Walker EV, Darnell D, Olsen SR, Kolekar P, Djekidel MN, Rosikiewicz W, McConkey H, Kerkhof J, Levy MA, Relator R, Lev D, Lerman-Sagie T, Park KL, Alders M, Cappuccio G, Chatron N, Demain L, Genevieve D, Lesca G, Roscioli T, Sanlaville D, Tedder ML, Gupta S, Jones EA, Weisz-Hubshman M, Ketkar S, Dai H, Worley KC, Rosenfeld JA, Chao HT, Neale G, Carvill GL, Wang Z, Berkovic SF, Sadleir LG, Miller DE, Scheffer IE, Sadikovic B, Mefford HC. Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement. Nat Commun 2024; 15:6524. [PMID: 39107278 PMCID: PMC11303402 DOI: 10.1038/s41467-024-50159-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 06/28/2024] [Indexed: 08/09/2024] Open
Abstract
Sequence-based genetic testing identifies causative variants in ~ 50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. We interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 582 individuals with genetically unsolved DEEs. We identify rare differentially methylated regions (DMRs) and explanatory episignatures to uncover causative and candidate genetic etiologies in 12 individuals. Using long-read sequencing, we identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and four copy number variants. We also identify pathogenic variants associated with episignatures. Finally, we refine the CHD2 episignature using an 850 K methylation array and bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate variants as 2% (12/582) for unsolved DEE cases.
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Affiliation(s)
- Christy W LaFlamme
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Cassandra Rastin
- Department of Pathology & Laboratory Medicine, Western University, London, ON, N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Soham Sengupta
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Helen E Pennington
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Mathematics & Statistics, Rhodes College, Memphis, TN, 38112, USA
| | - Sophie J Russ-Hall
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Amy L Schneider
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Emily S Bonkowski
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Edith P Almanza Fuerte
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Talia J Allan
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Miranda Perez-Galey Zalusky
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
| | - Joy Goffena
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
| | - Sophia B Gibson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Denis M Nyaga
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Nico Lieffering
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Malavika Hebbar
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
| | - Emily V Walker
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Daniel Darnell
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Scott R Olsen
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Pandurang Kolekar
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mohamed Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Dorit Lev
- Institute of Medical Genetics, Wolfson Medical Center, Holon, 58100, Israel
| | - Tally Lerman-Sagie
- Fetal Neurology Clinic, Pediatric Neurology Unit, Wolfson Medical Center, Holon, 58100, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Kristen L Park
- Departments of Pediatrics and Neurology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Marielle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Gerarda Cappuccio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Nicolas Chatron
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM, U1315, Lyon, France
| | - Leigh Demain
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - David Genevieve
- Montpellier University, Inserm Unit 1183, Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndrome, Clinical Genetic Department, CHU Montpellier, Montpellier, France
| | - Gaetan Lesca
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM, U1315, Lyon, France
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, NSW, Australia
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Damien Sanlaville
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM, U1315, Lyon, France
| | | | - Sachin Gupta
- TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Elizabeth A Jones
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Monika Weisz-Hubshman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Genetic Department, Houston, TX, 77030, USA
| | - Shamika Ketkar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kim C Worley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX, 77030, USA
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC, Australia
- Florey Institute and Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Bekim Sadikovic
- Department of Pathology & Laboratory Medicine, Western University, London, ON, N5A 3K7, Canada.
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada.
| | - Heather C Mefford
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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Ogbe SE, Wang J, Shi Y, Wang Y, Xu Z, Abankwa JK, Dal Pozzo L, Zhao S, Zhou H, Peng Y, Chu X, Wang X, Bian Y. Insights into the epitranscriptomic role of N 6-methyladenosine on aging skeletal muscle. Biomed Pharmacother 2024; 177:117041. [PMID: 38964182 DOI: 10.1016/j.biopha.2024.117041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
The modification of RNA through the N6-methyladenosine (m6A) has emerged as a growing area of research due to its regulatory role in gene expression and various biological processes regulating the expression of genes. m6A RNA methylation is a post-transcriptional modification that is dynamic and reversible and found in mRNA, tRNA, rRNA, and other non-coding RNA of most eukaryotic cells. It is executed by special proteins known as "writers," which initiate methylation; "erasers," which remove methylation; and "readers," which recognize it and regulate the expression of the gene. Modification by m6A regulates gene expression by affecting the splicing, translation, stability, and localization of mRNA. Aging causes molecular and cellular damage, which forms the basis of most age-related diseases. The decline in skeletal muscle mass and functionality because of aging leads to metabolic disorders and morbidities. The inability of aged muscles to regenerate and repair after injury poses a great challenge to the geriatric populace. This review seeks to explore the m6A epigenetic regulation in the myogenesis and regeneration processes in skeletal muscle as well as the progress made on the m6A epigenetic regulation of aging skeletal muscles.
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Affiliation(s)
- Susan Enechojo Ogbe
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Department of Physiology, Federal University, Wukari, Taraba 670101, Nigeria
| | - JiDa Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - YueXuan Shi
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Ying Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zhe Xu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Joseph Kofi Abankwa
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Lisa Dal Pozzo
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - ShuWu Zhao
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - HuiFang Zhou
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - YanFei Peng
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - XiaoQian Chu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - XiangLing Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - YuHong Bian
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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Saito Y, Harada A, Ushijima M, Tanaka K, Higuchi R, Baba A, Murakami D, Nutt SL, Nakagawa T, Ohkawa Y, Baba Y. Plasma cell differentiation is regulated by the expression of histone variant H3.3. Nat Commun 2024; 15:5004. [PMID: 38902223 PMCID: PMC11190180 DOI: 10.1038/s41467-024-49375-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: 05/13/2023] [Accepted: 06/04/2024] [Indexed: 06/22/2024] Open
Abstract
The differentiation of B cells into plasma cells is associated with substantial transcriptional and epigenetic remodeling. H3.3 histone variant marks active chromatin via replication-independent nucleosome assembly. However, its role in plasma cell development remains elusive. Herein, we show that during plasma cell differentiation, H3.3 is downregulated, and the deposition of H3.3 and chromatin accessibility are dynamically changed. Blockade of H3.3 downregulation by enforced H3.3 expression impairs plasma cell differentiation in an H3.3-specific sequence-dependent manner. Mechanistically, enforced H3.3 expression inhibits the upregulation of plasma cell-associated genes such as Irf4, Prdm1, and Xbp1 and maintains the expression of B cell-associated genes, Pax5, Bach2, and Bcl6. Concomitantly, sustained H3.3 expression prevents the structure of chromatin accessibility characteristic for plasma cells. Our findings suggest that appropriate H3.3 expression and deposition control plasma cell differentiation.
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Affiliation(s)
- Yuichi Saito
- Division of Immunology and Genome Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Miho Ushijima
- Division of Immunology and Genome Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kaori Tanaka
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Ryota Higuchi
- Division of Immunology and Genome Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Akemi Baba
- Division of Immunology and Genome Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Daisuke Murakami
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3050, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Takashi Nakagawa
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
| | - Yoshihiro Baba
- Division of Immunology and Genome Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
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5
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Choi J, Kim T, Cho EJ. HIRA vs. DAXX: the two axes shaping the histone H3.3 landscape. Exp Mol Med 2024; 56:251-263. [PMID: 38297159 PMCID: PMC10907377 DOI: 10.1038/s12276-023-01145-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 02/02/2024] Open
Abstract
H3.3, the most common replacement variant for histone H3, has emerged as an important player in chromatin dynamics for controlling gene expression and genome integrity. While replicative variants H3.1 and H3.2 are primarily incorporated into nucleosomes during DNA synthesis, H3.3 is under the control of H3.3-specific histone chaperones for spatiotemporal incorporation throughout the cell cycle. Over the years, there has been progress in understanding the mechanisms by which H3.3 affects domain structure and function. Furthermore, H3.3 distribution and relative abundance profoundly impact cellular identity and plasticity during normal development and pathogenesis. Recurrent mutations in H3.3 and its chaperones have been identified in neoplastic transformation and developmental disorders, providing new insights into chromatin biology and disease. Here, we review recent findings emphasizing how two distinct histone chaperones, HIRA and DAXX, take part in the spatial and temporal distribution of H3.3 in different chromatin domains and ultimately achieve dynamic control of chromatin organization and function. Elucidating the H3.3 deposition pathways from the available histone pool will open new avenues for understanding the mechanisms by which H3.3 epigenetically regulates gene expression and its impact on cellular integrity and pathogenesis.
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Affiliation(s)
- Jinmi Choi
- Sungkyunkwan University School of Pharmacy, Seoburo 2066, Jangan-gu Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Taewan Kim
- Sungkyunkwan University School of Pharmacy, Seoburo 2066, Jangan-gu Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Eun-Jung Cho
- Sungkyunkwan University School of Pharmacy, Seoburo 2066, Jangan-gu Suwon, Gyeonggi-do, 16419, Republic of Korea.
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Voon HPJ, Hii L, Garvie A, Udugama M, Krug B, Russo C, Chüeh AC, Daly RJ, Morey A, Bell TDM, Turner SJ, Rosenbluh J, Daniel P, Firestein R, Mann JR, Collas P, Jabado N, Wong LH. Pediatric glioma histone H3.3 K27M/G34R mutations drive abnormalities in PML nuclear bodies. Genome Biol 2023; 24:284. [PMID: 38066546 PMCID: PMC10704828 DOI: 10.1186/s13059-023-03122-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Point mutations in histone variant H3.3 (H3.3K27M, H3.3G34R) and the H3.3-specific ATRX/DAXX chaperone complex are frequent events in pediatric gliomas. These H3.3 point mutations affect many chromatin modifications but the exact oncogenic mechanisms are currently unclear. Histone H3.3 is known to localize to nuclear compartments known as promyelocytic leukemia (PML) nuclear bodies, which are frequently mutated and confirmed as oncogenic drivers in acute promyelocytic leukemia. RESULTS We find that the pediatric glioma-associated H3.3 point mutations disrupt the formation of PML nuclear bodies and this prevents differentiation down glial lineages. Similar to leukemias driven by PML mutations, H3.3-mutated glioma cells are sensitive to drugs that target PML bodies. We also find that point mutations in IDH1/2-which are common events in adult gliomas and myeloid leukemias-also disrupt the formation of PML bodies. CONCLUSIONS We identify PML as a contributor to oncogenesis in a subset of gliomas and show that targeting PML bodies is effective in treating these H3.3-mutated pediatric gliomas.
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Affiliation(s)
- Hsiao P J Voon
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Linda Hii
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Andrew Garvie
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Maheshi Udugama
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Brian Krug
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Caterina Russo
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Anderly C Chüeh
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Roger J Daly
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Alison Morey
- Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Toby D M Bell
- School of Chemistry, Monash University, Clayton, VIC, Australia
| | - Stephen J Turner
- Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Joseph Rosenbluh
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Paul Daniel
- Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Ron Firestein
- Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Jeffrey R Mann
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424, Oslo, Norway
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Department of Paediatrics, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Lee H Wong
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.
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7
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Muhammad T, Pastore SF, Good K, Ausió J, Vincent JB. Chromatin gatekeeper and modifier CHD proteins in development, and in autism and other neurological disorders. Psychiatr Genet 2023; 33:213-232. [PMID: 37851134 DOI: 10.1097/ypg.0000000000000353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Chromatin, a protein-DNA complex, is a dynamic structure that stores genetic information within the nucleus and responds to molecular/cellular changes in its structure, providing conditional access to the genetic machinery. ATP-dependent chromatin modifiers regulate access of transcription factors and RNA polymerases to DNA by either "opening" or "closing" the structure of chromatin, and its aberrant regulation leads to a variety of neurodevelopmental disorders. The chromodomain helicase DNA-binding (CHD) proteins are ATP-dependent chromatin modifiers involved in the organization of chromatin structure, act as gatekeepers of genomic access, and deposit histone variants required for gene regulation. In this review, we first discuss the structural and functional domains of the CHD proteins, and their binding sites, and phosphorylation, acetylation, and methylation sites. The conservation of important amino acids in SWItch/sucrose non-fermenting (SWI/SNF) domains, and their protein and mRNA tissue expression profiles are discussed. Next, we convey the important binding partners of CHD proteins, their protein complexes and activities, and their involvements in epigenetic regulation. We also show the ChIP-seq binding dynamics for CHD1, CHD2, CHD4, and CHD7 proteins at promoter regions of histone genes, as well as several genes that are critical for neurodevelopment. The role of CHD proteins in development is also discussed. Finally, this review provides information about CHD protein mutations reported in autism and neurodevelopmental disorders, and their pathogenicity. Overall, this review provides information on the progress of research into CHD proteins, their structural and functional domains, epigenetics, and their role in stem cell, development, and neurological disorders.
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Affiliation(s)
- Tahir Muhammad
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Stephen F Pastore
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Katrina Good
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
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8
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LaFlamme CW, Rastin C, Sengupta S, Pennington HE, Russ-Hall SJ, Schneider AL, Bonkowski ES, Almanza Fuerte EP, Galey M, Goffena J, Gibson SB, Allan TJ, Nyaga DM, Lieffering N, Hebbar M, Walker EV, Darnell D, Olsen SR, Kolekar P, Djekidel N, Rosikiewicz W, McConkey H, Kerkhof J, Levy MA, Relator R, Lev D, Lerman-Sagie T, Park KL, Alders M, Cappuccio G, Chatron N, Demain L, Genevieve D, Lesca G, Roscioli T, Sanlaville D, Tedder ML, Hubshman MW, Ketkar S, Dai H, Worley KC, Rosenfeld JA, Chao HT, Neale G, Carvill GL, Wang Z, Berkovic SF, Sadleir LG, Miller DE, Scheffer IE, Sadikovic B, Mefford HC. Diagnostic Utility of Genome-wide DNA Methylation Analysis in Genetically Unsolved Developmental and Epileptic Encephalopathies and Refinement of a CHD2 Episignature. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.11.23296741. [PMID: 37873138 PMCID: PMC10592992 DOI: 10.1101/2023.10.11.23296741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Sequence-based genetic testing currently identifies causative genetic variants in ∼50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. Rare epigenetic variations ("epivariants") can drive disease by modulating gene expression at single loci, whereas genome-wide DNA methylation changes can result in distinct "episignature" biomarkers for monogenic disorders in a growing number of rare diseases. Here, we interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 516 individuals with genetically unsolved DEEs who had previously undergone extensive genetic testing. We identified rare differentially methylated regions (DMRs) and explanatory episignatures to discover causative and candidate genetic etiologies in 10 individuals. We then used long-read sequencing to identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and two copy number variants. We also identify pathogenic sequence variants associated with episignatures; some had been missed by previous exome sequencing. Although most DEE genes lack known episignatures, the increase in diagnostic yield for DNA methylation analysis in DEEs is comparable to the added yield of genome sequencing. Finally, we refine an episignature for CHD2 using an 850K methylation array which was further refined at higher CpG resolution using bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate genetic causes as ∼2% (10/516) for unsolved DEE cases.
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9
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Zhang X, Che Y, Mao L, Li D, Deng J, Guo Y, Zhao Q, Zhang X, Wang L, Gao X, Chen Y, Zhang T. H3.3B controls aortic dissection progression by regulating vascular smooth muscle cells phenotypic transition and vascular inflammation. Genomics 2023; 115:110685. [PMID: 37454936 DOI: 10.1016/j.ygeno.2023.110685] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/13/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Aortic dissection is a devastating cardiovascular disease with a high lethality. Histone variants maintain the genomic integrity and play important roles in development and diseases. However, the role of histone variants in aortic dissection has not been well identified. In the present study, H3f3b knockdown reduced the synthetic genes expression of VSMCs, while overexpressing H3f3b exacerbated the cellular immune response of VSMCs induced by inflammatory cytokines. Combined RNA-seq and ChIP-seq analyses revealed that histone variant H3.3B directly bound to the genes related to extracellular matrix, VSMC synthetic phenotype, cytokine responses and TGFβ signaling pathway, and regulated their expressions. In addition, VSMC-specific H3f3b knockin aggravated aortic dissection development in mice, while H3f3b knockout significantly reduced the incidence of aortic dissection. In term of mechanisms, H3.3B regulated Spp1 and Ccl2 genes, inducing the apoptosis of VSMCs and recruiting macrophages. This study demonstrated the vital roles of H3.3B in phenotypic transition of VSMCs, loss of media VSMCs, and vascular inflammation in aortic dissection.
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Affiliation(s)
- Xuelin Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Yang Che
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Lin Mao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Dandan Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Jianqing Deng
- Vascular Surgery Department, The First Medical Center of PLA General Hospital, Beijing 100853, China
| | - Yilong Guo
- Vascular Surgery Department, The First Medical Center of PLA General Hospital, Beijing 100853, China
| | - Quanyi Zhao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China; Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen 518057, China
| | - Xingzhong Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Li Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China; Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen 518057, China; Key Laboratory of Application of Pluripotent Stem Cells in Heart Regeneration,Chinese Academy of Medical Sciences, Beijing 100037, China.
| | - Xiang Gao
- Department of Vascular Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
| | - Yinan Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China; Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen 518057, China.
| | - Tao Zhang
- Vascular Surgery Department, Peking University People's Hospital, Beijing 100044, China.
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10
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Korff C, Atkinson E, Adaway M, Klunk A, Wek RC, Vashishth D, Wallace JM, Anderson-Baucum EK, Evans-Molina C, Robling AG, Bidwell JP. NMP4, an Arbiter of Bone Cell Secretory Capacity and Regulator of Skeletal Response to PTH Therapy. Calcif Tissue Int 2023; 113:110-125. [PMID: 37147466 PMCID: PMC10330242 DOI: 10.1007/s00223-023-01088-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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/21/2023] [Indexed: 05/07/2023]
Abstract
The skeleton is a secretory organ, and the goal of some osteoporosis therapies is to maximize bone matrix output. Nmp4 encodes a novel transcription factor that regulates bone cell secretion as part of its functional repertoire. Loss of Nmp4 enhances bone response to osteoanabolic therapy, in part, by increasing the production and delivery of bone matrix. Nmp4 shares traits with scaling factors, which are transcription factors that influence the expression of hundreds of genes to govern proteome allocation for establishing secretory cell infrastructure and capacity. Nmp4 is expressed in all tissues and while global loss of this gene leads to no overt baseline phenotype, deletion of Nmp4 has broad tissue effects in mice challenged with certain stressors. In addition to an enhanced response to osteoporosis therapies, Nmp4-deficient mice are less sensitive to high fat diet-induced weight gain and insulin resistance, exhibit a reduced disease severity in response to influenza A virus (IAV) infection, and resist the development of some forms of rheumatoid arthritis. In this review, we present the current understanding of the mechanisms underlying Nmp4 regulation of the skeletal response to osteoanabolics, and we discuss how this unique gene contributes to the diverse phenotypes among different tissues and stresses. An emerging theme is that Nmp4 is important for the infrastructure and capacity of secretory cells that are critical for health and disease.
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Affiliation(s)
- Crystal Korff
- Department of Medical and Molecular Genetics, Indiana University School of Medicine (IUSM), Indianapolis, IN, 46202, USA
| | - Emily Atkinson
- Department of Anatomy, Cell Biology & Physiology, IUSM, Indianapolis, IN, 46202, USA
| | - Michele Adaway
- Department of Anatomy, Cell Biology & Physiology, IUSM, Indianapolis, IN, 46202, USA
| | - Angela Klunk
- Department of Anatomy, Cell Biology & Physiology, IUSM, Indianapolis, IN, 46202, USA
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, IUSM, Indianapolis, IN, USA
| | - Deepak Vashishth
- Center for Biotechnology & Interdisciplinary Studies and Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Joseph M Wallace
- Department of Biomedical Engineering, Indiana University-Purdue University at Indianapolis, Indianapolis, IN, 46202, USA
- Indiana Center for Musculoskeletal Health, IUSM, Indianapolis, IN, USA
| | - Emily K Anderson-Baucum
- Department of Pediatrics and the Herman B Wells Center for Pediatric Research, IUSM, Indianapolis, IN, USA
| | - Carmella Evans-Molina
- Department of Pediatrics and the Herman B Wells Center for Pediatric Research, IUSM, Indianapolis, IN, USA
- Center for Diabetes and Metabolic Disease and the Wells Center for Pediatric Research, IUSM, Indianapolis, IN, USA
- Richard L. Roudebush VA Medical Center, Indianapolis, IN, 46202, USA
- Department of Medicine, IUSM, Indianapolis, IN, USA
| | - Alexander G Robling
- Department of Anatomy, Cell Biology & Physiology, IUSM, Indianapolis, IN, 46202, USA
- Indiana Center for Musculoskeletal Health, IUSM, Indianapolis, IN, USA
- Richard L. Roudebush VA Medical Center, Indianapolis, IN, 46202, USA
| | - Joseph P Bidwell
- Department of Anatomy, Cell Biology & Physiology, IUSM, Indianapolis, IN, 46202, USA.
- Indiana Center for Musculoskeletal Health, IUSM, Indianapolis, IN, USA.
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11
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Kleijwegt C, Bressac F, Seurre C, Bouchereau W, Cohen C, Texier P, Simonet T, Schaeffer L, Lomonte P, Corpet A. Interplay between PML NBs and HIRA for H3.3 dynamics following type I interferon stimulus. eLife 2023; 12:e80156. [PMID: 37227756 PMCID: PMC10212570 DOI: 10.7554/elife.80156] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 04/25/2023] [Indexed: 05/26/2023] Open
Abstract
Promyelocytic leukemia Nuclear Bodies (PML NBs) are nuclear membrane-less organelles physically associated with chromatin underscoring their crucial role in genome function. The H3.3 histone chaperone complex HIRA accumulates in PML NBs upon senescence, viral infection or IFN-I treatment in primary cells. Yet, the molecular mechanisms of this partitioning and its function in regulating histone dynamics have remained elusive. By using specific approaches, we identify intermolecular SUMO-SIM interactions as an essential mechanism for HIRA recruitment in PML NBs. Hence, we describe a role of PML NBs as nuclear depot centers to regulate HIRA distribution in the nucleus, dependent both on SP100 and DAXX/H3.3 levels. Upon IFN-I stimulation, PML is required for interferon-stimulated genes (ISGs) transcription and PML NBs become juxtaposed to ISGs loci at late time points of IFN-I treatment. HIRA and PML are necessary for the prolonged H3.3 deposition at the transcriptional end sites of ISGs, well beyond the peak of transcription. Though, HIRA accumulation in PML NBs is dispensable for H3.3 deposition on ISGs. We thus uncover a dual function for PML/PML NBs, as buffering centers modulating the nuclear distribution of HIRA, and as chromosomal hubs regulating ISGs transcription and thus HIRA-mediated H3.3 deposition at ISGs upon inflammatory response.
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Affiliation(s)
- Constance Kleijwegt
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Florent Bressac
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Coline Seurre
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Wilhelm Bouchereau
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Camille Cohen
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Pascale Texier
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Thomas Simonet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), team Nerve-Muscle interactionsLyonFrance
| | - Laurent Schaeffer
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), team Nerve-Muscle interactionsLyonFrance
| | - Patrick Lomonte
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Armelle Corpet
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
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12
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Beacon TH, Davie JR. Chicken Erythrocyte: Epigenomic Regulation of Gene Activity. Int J Mol Sci 2023; 24:ijms24098287. [PMID: 37175991 PMCID: PMC10179511 DOI: 10.3390/ijms24098287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
The chicken genome is one-third the size of the human genome and has a similarity of sixty percent when it comes to gene content. Harboring similar genome sequences, chickens' gene arrangement is closer to the human genomic organization than it is to rodents. Chickens have been used as model organisms to study evolution, epigenome, and diseases. The chicken nucleated erythrocyte's physiological function is to carry oxygen to the tissues and remove carbon dioxide. The erythrocyte also supports the innate immune response in protecting the chicken from pathogens. Among the highly studied aspects in the field of epigenetics are modifications of DNA, histones, and their variants. In understanding the organization of transcriptionally active chromatin, studies on the chicken nucleated erythrocyte have been important. Through the application of a variety of epigenomic approaches, we and others have determined the chromatin structure of expressed/poised genes involved in the physiological functions of the erythrocyte. As the chicken erythrocyte has a nucleus and is readily isolated from the animal, the chicken erythrocyte epigenome has been studied as a biomarker of an animal's long-term exposure to stress. In this review, epigenomic features that allow erythroid gene expression in a highly repressive chromatin background are presented.
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Affiliation(s)
- Tasnim H Beacon
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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13
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Battistelli C, Garbo S, Maione R. MyoD-Induced Trans-Differentiation: A Paradigm for Dissecting the Molecular Mechanisms of Cell Commitment, Differentiation and Reprogramming. Cells 2022; 11:3435. [PMID: 36359831 PMCID: PMC9654159 DOI: 10.3390/cells11213435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 10/23/2022] [Accepted: 10/28/2022] [Indexed: 10/20/2023] Open
Abstract
The discovery of the skeletal muscle-specific transcription factor MyoD represents a milestone in the field of transcriptional regulation during differentiation and cell-fate reprogramming. MyoD was the first tissue-specific factor found capable of converting non-muscle somatic cells into skeletal muscle cells. A unique feature of MyoD, with respect to other lineage-specific factors able to drive trans-differentiation processes, is its ability to dramatically change the cell fate even when expressed alone. The present review will outline the molecular strategies by which MyoD reprograms the transcriptional regulation of the cell of origin during the myogenic conversion, focusing on the activation and coordination of a complex network of co-factors and epigenetic mechanisms. Some molecular roadblocks, found to restrain MyoD-dependent trans-differentiation, and the possible ways for overcoming these barriers, will also be discussed. Indeed, they are of critical importance not only to expand our knowledge of basic muscle biology but also to improve the generation skeletal muscle cells for translational research.
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Affiliation(s)
| | | | - Rossella Maione
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy
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14
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Lewis EMA, Chapman G, Kaushik K, Determan J, Antony I, Meganathan K, Narasimhan M, Gontarz P, Zhang B, Kroll KL. Regulation of human cortical interneuron development by the chromatin remodeling protein CHD2. Sci Rep 2022; 12:15636. [PMID: 36115870 PMCID: PMC9482661 DOI: 10.1038/s41598-022-19654-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Mutations in the chromodomain helicase DNA binding protein 2 (CHD2) gene are associated with neurodevelopmental disorders. However, mechanisms by which CHD2 regulates human brain development remain largely uncharacterized. Here, we used a human embryonic stem cell model of cortical interneuron (hcIN) development to elucidate its roles in this process. We identified genome-wide CHD2 binding profiles during hcIN differentiation, defining direct CHD2 targets related to neurogenesis in hcIN progenitors and to neuronal function in hcINs. CHD2 bound sites were frequently coenriched with histone H3 lysine 27 acetylation (H3K27ac) and associated with high gene expression, indicating roles for CHD2 in promoting gene expression during hcIN development. Binding sites for different classes of transcription factors were enriched at CHD2 bound regions during differentiation, suggesting transcription factors that may cooperatively regulate stage-specific gene expression with CHD2. We also demonstrated that CHD2 haploinsufficiency altered CHD2 and H3K27ac coenrichment on chromatin and expression of associated genes, decreasing acetylation and expression of cell cycle genes while increasing acetylation and expression of neuronal genes, to cause precocious differentiation. Together, these data describe CHD2 direct targets and mechanisms by which CHD2 prevents precocious hcIN differentiation, which are likely to be disrupted by pathogenic CHD2 mutation to cause neurodevelopmental disorders.
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Affiliation(s)
- E M A Lewis
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - G Chapman
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - K Kaushik
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - J Determan
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - I Antony
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - K Meganathan
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - M Narasimhan
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - P Gontarz
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - B Zhang
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - K L Kroll
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
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15
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Vicente-García C, Hernández-Camacho JD, Carvajal JJ. Regulation of myogenic gene expression. Exp Cell Res 2022; 419:113299. [DOI: 10.1016/j.yexcr.2022.113299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/22/2022]
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16
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Hada M, Miura H, Tanigawa A, Matoba S, Inoue K, Ogonuki N, Hirose M, Watanabe N, Nakato R, Fujiki K, Hasegawa A, Sakashita A, Okae H, Miura K, Shikata D, Arima T, Shirahige K, Hiratani I, Ogura A. Highly rigid H3.1/H3.2-H3K9me3 domains set a barrier for cell fate reprogramming in trophoblast stem cells. Genes Dev 2022; 36:84-102. [PMID: 34992147 PMCID: PMC8763053 DOI: 10.1101/gad.348782.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/21/2021] [Indexed: 01/22/2023]
Abstract
Here, Hada et al. comprehensively analyzed epigenomic features of mouse trophoblast stem cells (TSCs). They used genome-wide, high-throughput analyses to show that the TSC genome contains large-scale (>1-Mb) rigid heterochromatin architectures that have a high degree of histone H3.1/3.2–H3K9me3 accumulation, termed TSC-defined highly heterochromatinized domains (THDs), and are uniquely developed in placental lineage cells that serve to protect them from fate reprogramming to stably maintain placental function. The placenta is a highly evolved, specialized organ in mammals. It differs from other organs in that it functions only for fetal maintenance during gestation. Therefore, there must be intrinsic mechanisms that guarantee its unique functions. To address this question, we comprehensively analyzed epigenomic features of mouse trophoblast stem cells (TSCs). Our genome-wide, high-throughput analyses revealed that the TSC genome contains large-scale (>1-Mb) rigid heterochromatin architectures with a high degree of histone H3.1/3.2–H3K9me3 accumulation, which we termed TSC-defined highly heterochromatinized domains (THDs). Importantly, depletion of THDs by knockdown of CAF1, an H3.1/3.2 chaperone, resulted in down-regulation of TSC markers, such as Cdx2 and Elf5, and up-regulation of the pluripotent marker Oct3/4, indicating that THDs maintain the trophoblastic nature of TSCs. Furthermore, our nuclear transfer technique revealed that THDs are highly resistant to genomic reprogramming. However, when H3K9me3 was removed, the TSC genome was fully reprogrammed, giving rise to the first TSC cloned offspring. Interestingly, THD-like domains are also present in mouse and human placental cells in vivo, but not in other cell types. Thus, THDs are genomic architectures uniquely developed in placental lineage cells, which serve to protect them from fate reprogramming to stably maintain placental function.
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Affiliation(s)
- Masashi Hada
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan.,Institute of Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology, Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Akie Tanigawa
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology, Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Shogo Matoba
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan.,Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Kimiko Inoue
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan.,Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Narumi Ogonuki
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Michiko Hirose
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Naomi Watanabe
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Ryuichiro Nakato
- Institute of Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Katsunori Fujiki
- Institute of Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Ayumi Hasegawa
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Akihiko Sakashita
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai 980-8575, Japan
| | - Kento Miura
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan.,Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | - Daiki Shikata
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai 980-8575, Japan
| | - Katsuhiko Shirahige
- Institute of Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology, Center for Biosystems Dynamics Research, Kobe 650-0047, Japan.,RIKEN Cluster for Pioneering Research, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan.,Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan.,RIKEN Cluster for Pioneering Research, Hirosawa, Wako, Saitama 351-0198, Japan
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17
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Mbadhi MN, Tang JM, Zhang JX. Histone Lysine Methylation and Long Non-Coding RNA: The New Target Players in Skeletal Muscle Cell Regeneration. Front Cell Dev Biol 2021; 9:759237. [PMID: 34926450 PMCID: PMC8678087 DOI: 10.3389/fcell.2021.759237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
Satellite stem cell availability and high regenerative capacity have made them an ideal therapeutic approach for muscular dystrophies and neuromuscular diseases. Adult satellite stem cells remain in a quiescent state and become activated upon muscular injury. A series of molecular mechanisms succeed under the control of epigenetic regulation and various myogenic regulatory transcription factors myogenic regulatory factors, leading to their differentiation into skeletal muscles. The regulation of MRFs via various epigenetic factors, including DNA methylation, histone modification, and non-coding RNA, determine the fate of myogenesis. Furthermore, the development of histone deacetylation inhibitors (HDACi) has shown promising benefits in their use in clinical trials of muscular diseases. However, the complete application of using satellite stem cells in the clinic is still not achieved. While therapeutic advancements in the use of HDACi in clinical trials have emerged, histone methylation modulations and the long non-coding RNA (lncRNA) are still under study. A comprehensive understanding of these other significant epigenetic modulations is still incomplete. This review aims to discuss some of the current studies on these two significant epigenetic modulations, histone methylation and lncRNA, as potential epigenetic targets in skeletal muscle regeneration. Understanding the mechanisms that initiate myoblast differentiation from its proliferative state to generate new muscle fibres will provide valuable information to advance the field of regenerative medicine and stem cell transplant.
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Affiliation(s)
- Magdaleena Naemi Mbadhi
- Hubei Key Laboratory of Embryonic Stem Cell Research, Department of Physiology, Faculty of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Jun-Ming Tang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Department of Physiology, Faculty of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Jing-Xuan Zhang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Department of Physiology, Faculty of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
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18
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Esteves de Lima J, Relaix F. Epigenetic Regulation of Myogenesis: Focus on the Histone Variants. Int J Mol Sci 2021; 22:ijms222312727. [PMID: 34884532 PMCID: PMC8657657 DOI: 10.3390/ijms222312727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 01/04/2023] Open
Abstract
Skeletal muscle development and regeneration rely on the successive activation of specific transcription factors that engage cellular fate, promote commitment, and drive differentiation. Emerging evidence demonstrates that epigenetic regulation of gene expression is crucial for the maintenance of the cell differentiation status upon division and, therefore, to preserve a specific cellular identity. This depends in part on the regulation of chromatin structure and its level of condensation. Chromatin architecture undergoes remodeling through changes in nucleosome composition, such as alterations in histone post-translational modifications or exchange in the type of histone variants. The mechanisms that link histone post-translational modifications and transcriptional regulation have been extensively evaluated in the context of cell fate and differentiation, whereas histone variants have attracted less attention in the field. In this review, we discuss the studies that have provided insights into the role of histone variants in the regulation of myogenic gene expression, myoblast differentiation, and maintenance of muscle cell identity.
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19
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Abstract
Chromatin is highly dynamic, undergoing continuous global changes in its structure and type of histone and DNA modifications governed by processes such as transcription, repair, replication, and recombination. Members of the chromodomain helicase DNA-binding (CHD) family of enzymes are ATP-dependent chromatin remodelers that are intimately involved in the regulation of chromatin dynamics, altering nucleosomal structure and DNA accessibility. Genetic studies in yeast, fruit flies, zebrafish, and mice underscore essential roles of CHD enzymes in regulating cellular fate and identity, as well as proper embryonic development. With the advent of next-generation sequencing, evidence is emerging that these enzymes are subjected to frequent DNA copy number alterations or mutations and show aberrant expression in malignancies and other human diseases. As such, they might prove to be valuable biomarkers or targets for therapeutic intervention.
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Affiliation(s)
- Andrej Alendar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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20
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Liu C, Kang N, Guo Y, Gong P. Advances in Chromodomain Helicase DNA-Binding (CHD) Proteins Regulating Stem Cell Differentiation and Human Diseases. Front Cell Dev Biol 2021; 9:710203. [PMID: 34616726 PMCID: PMC8488160 DOI: 10.3389/fcell.2021.710203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/29/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Regulation of gene expression is critical for stem cell differentiation, tissue development, and human health maintenance. Recently, epigenetic modifications of histone and chromatin remodeling have been verified as key controllers of gene expression and human diseases. Objective: In this study, we review the role of chromodomain helicase DNA-binding (CHD) proteins in stem cell differentiation, cell fate decision, and several known human developmental disorders and cancers. Conclusion: CHD proteins play a crucial role in stem cell differentiation and human diseases.
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Affiliation(s)
- Caojie Liu
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Ning Kang
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Yuchen Guo
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Ping Gong
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
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21
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Esteves de Lima J, Relaix F. Master regulators of skeletal muscle lineage development and pluripotent stem cells differentiation. CELL REGENERATION 2021; 10:31. [PMID: 34595600 PMCID: PMC8484369 DOI: 10.1186/s13619-021-00093-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/24/2021] [Indexed: 12/16/2022]
Abstract
In vertebrates, the skeletal muscles of the body and their associated stem cells originate from muscle progenitor cells, during development. The specification of the muscles of the trunk, head and limbs, relies on the activity of distinct genetic hierarchies. The major regulators of trunk and limb muscle specification are the paired-homeobox transcription factors PAX3 and PAX7. Distinct gene regulatory networks drive the formation of the different muscles of the head. Despite the redeployment of diverse upstream regulators of muscle progenitor differentiation, the commitment towards the myogenic fate requires the expression of the early myogenic regulatory factors MYF5, MRF4, MYOD and the late differentiation marker MYOG. The expression of these genes is activated by muscle progenitors throughout development, in several waves of myogenic differentiation, constituting the embryonic, fetal and postnatal phases of muscle growth. In order to achieve myogenic cell commitment while maintaining an undifferentiated pool of muscle progenitors, several signaling pathways regulate the switch between proliferation and differentiation of myoblasts. The identification of the gene regulatory networks operating during myogenesis is crucial for the development of in vitro protocols to differentiate pluripotent stem cells into myoblasts required for regenerative medicine.
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Affiliation(s)
| | - Frédéric Relaix
- Univ Paris Est Creteil, INSERM, EnvA, EFS, AP-HP, IMRB, 94010, Creteil, France.
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22
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Sharma T, Robinson DCL, Witwicka H, Dilworth FJ, Imbalzano AN. The Bromodomains of the mammalian SWI/SNF (mSWI/SNF) ATPases Brahma (BRM) and Brahma Related Gene 1 (BRG1) promote chromatin interaction and are critical for skeletal muscle differentiation. Nucleic Acids Res 2021; 49:8060-8077. [PMID: 34289068 PMCID: PMC8373147 DOI: 10.1093/nar/gkab617] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/17/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Skeletal muscle regeneration is mediated by myoblasts that undergo epigenomic changes to establish the gene expression program of differentiated myofibers. mSWI/SNF chromatin remodeling enzymes coordinate with lineage-determining transcription factors to establish the epigenome of differentiated myofibers. Bromodomains bind to acetylated lysines on histone N-terminal tails and other proteins. The mutually exclusive ATPases of mSWI/SNF complexes, BRG1 and BRM, contain bromodomains with undefined functional importance in skeletal muscle differentiation. Pharmacological inhibition of mSWI/SNF bromodomain function using the small molecule PFI-3 reduced differentiation in cell culture and in vivo through decreased myogenic gene expression, while increasing cell cycle-related gene expression and the number of cells remaining in the cell cycle. Comparative gene expression analysis with data from myoblasts depleted of BRG1 or BRM showed that bromodomain function was required for a subset of BRG1- and BRM-dependent gene expression. Reduced binding of BRG1 and BRM after PFI-3 treatment showed that the bromodomain is required for stable chromatin binding at target gene promoters to alter gene expression. Our findings demonstrate that mSWI/SNF ATPase bromodomains permit stable binding of the mSWI/SNF ATPases to promoters required for cell cycle exit and establishment of muscle-specific gene expression.
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Affiliation(s)
- Tapan Sharma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Daniel C L Robinson
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hanna Witwicka
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - F Jeffrey Dilworth
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Anthony N Imbalzano
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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23
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Esteves de Lima J, Bou Akar R, Machado L, Li Y, Drayton-Libotte B, Dilworth FJ, Relaix F. HIRA stabilizes skeletal muscle lineage identity. Nat Commun 2021; 12:3450. [PMID: 34103504 PMCID: PMC8187366 DOI: 10.1038/s41467-021-23775-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/17/2021] [Indexed: 12/26/2022] Open
Abstract
The epigenetic mechanisms coordinating the maintenance of adult cellular lineages and the inhibition of alternative cell fates remain poorly understood. Here we show that targeted ablation of the histone chaperone HIRA in myogenic cells leads to extensive transcriptional modifications, consistent with a role in maintaining skeletal muscle cellular identity. We demonstrate that conditional ablation of HIRA in muscle stem cells of adult mice compromises their capacity to regenerate and self-renew, leading to tissue repair failure. Chromatin analysis of Hira-deficient cells show a significant reduction of histone variant H3.3 deposition and H3K27ac modification at regulatory regions of muscle genes. Additionally, we find that genes from alternative lineages are ectopically expressed in Hira-mutant cells via MLL1/MLL2-mediated increase of H3K4me3 mark at silent promoter regions. Therefore, we conclude that HIRA sustains the chromatin landscape governing muscle cell lineage identity via incorporation of H3.3 at muscle gene regulatory regions, while preventing the expression of alternative lineage genes. The epigenetic mechanisms coordinating the maintenance of adult cellular lineages remain poorly understood. Here the authors demonstrate that HIRA, a H3.3 histone chaperone, establishes the chromatin landscape required for skeletal muscle cell identity.
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Affiliation(s)
| | - Reem Bou Akar
- Univ Paris Est Creteil, INSERM, EnvA, EFS, AP-HP, IMRB, F-94010, Creteil, France
| | - Léo Machado
- Univ Paris Est Creteil, INSERM, EnvA, EFS, AP-HP, IMRB, F-94010, Creteil, France
| | - Yuefeng Li
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | | | - F Jeffrey Dilworth
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Frédéric Relaix
- Univ Paris Est Creteil, INSERM, EnvA, EFS, AP-HP, IMRB, F-94010, Creteil, France.
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24
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Clapier CR. Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer. Int J Mol Sci 2021; 22:5578. [PMID: 34070411 PMCID: PMC8197500 DOI: 10.3390/ijms22115578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/13/2023] Open
Abstract
The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions-in particular, the regulation of gene expression-and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.
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Affiliation(s)
- Cedric R Clapier
- Department of Oncological Sciences & Howard Hughes Medical Institute, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
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25
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Lee HR, Yang SJ, Choi HK, Kim JA, Oh IH. The Chromatin Remodeling Complex CHD1 Regulates the Primitive State of Mesenchymal Stromal Cells to Control Their Stem Cell Supporting Activity. Stem Cells Dev 2021; 30:363-373. [PMID: 33593142 DOI: 10.1089/scd.2020.0166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The primitive state (stemness) of mesenchymal stromal cells (MSCs) is responsible for supporting the function of tissue-specific stem cells to regenerate damaged tissues. However, molecular mechanisms regulating the stemness of MSCs remain unknown. In this study, we found that the primitive state of MSCs is hierarchically regulated by the expression levels of the chromatin remodeling complex, CHD1, with CHD1 expression levels higher in the undifferentiated state, and decreasing upon MSC differentiation. Consistently, CHD1 expression levels decrease during progressive loss of clonogenic progenitors (CFU-F) induced by passage cultures. Moreover, knockdown (KD) of CHD1 decreased CFU-F frequency, whereas CHD1 overexpression increased it. In addition, the expression of stem cell-specific genes was down- or upregulated upon KD or overexpression of CHD1, respectively, accompanied by associated changes in chromatin condensation. Importantly, altering CHD1 expression levels affected the ability of MSCs to support the self-renewing expansion of hematopoietic stem cells (HSCs). Furthermore, CHD1 levels were significantly decreased in MSCs from acute myeloid leukemia or aplastic anemia patients, where CFU-F and HSC-supporting activities are lost. Altogether, these findings show that chromatin remodeling by CHD1 is a molecular parameter that influences the primitive state of MSCs and their stem cell-supporting activity, which controls tissue regeneration.
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Affiliation(s)
- Hae-Ri Lee
- Catholic High-Performance Cell Therapy Center, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung-Jip Yang
- Catholic High-Performance Cell Therapy Center, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyun-Kyung Choi
- Catholic High-Performance Cell Therapy Center, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jin-A Kim
- Catholic High-Performance Cell Therapy Center, The Catholic University of Korea, Seoul, Republic of Korea
| | - Il-Hoan Oh
- Catholic High-Performance Cell Therapy Center, The Catholic University of Korea, Seoul, Republic of Korea
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26
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Elgaabari A, Miyawaki-Kuwakado A, Tomimatsu K, Wu Q, Tokunaga K, Izumi W, Suzuki T, Tatsumi R, Nakamura M. Epigenetic effects induced by the ectopic expression of Pax7 in 3T3-L1. J Biochem 2021; 170:107-117. [PMID: 33729538 DOI: 10.1093/jb/mvab030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/07/2021] [Indexed: 11/14/2022] Open
Abstract
Although skeletal muscle cells and adipocytes are derived from the same mesoderm, they do not transdifferentiate in vivo and are strictly distinct at the level of gene expression. To elucidate some of the regulatory mechanisms underlying this strict distinction, Pax7, a myogenic factor, was ectopically expressed in 3T3-L1 adipose progenitor cells to perturb their adipocyte differentiation potential. Transcriptome analysis showed that ectopic expression of Pax7 repressed the expression of some adipocyte genes and induced expression of some skeletal muscle cell genes. We next profiled the epigenomic state altered by Pax7 expression using H3K27ac, an activating histone mark, and H3K27me3, a repressive histone mark, as indicators. Our results show that ectopic expression of Pax7 did not result in the formation of H3K27ac at loci of skeletal muscle-related genes, but instead resulted in the formation of H3K27me3 at adipocyte-related gene loci. These findings suggest that the primary function of ectopic Pax7 expression is the formation of H3K27me3, and muscle gene expression results from secondary regulation.
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Affiliation(s)
- Alaa Elgaabari
- Alaa Elgaabari, Atsuko Miyawaki-Kuwakado, Kosuke Tomimatsu, Qianmei Wu, Kosuke Tokunaga, Wakana Izumi, Takahiro Suzuki, Ryuichi Tatsumi, Mako Nakamura.,Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Atsuko Miyawaki-Kuwakado
- Department of Bioresource Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Kosuke Tomimatsu
- Department of Bioresource Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Qianmei Wu
- Department of Bioresource Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Kosuke Tokunaga
- Alaa Elgaabari, Atsuko Miyawaki-Kuwakado, Kosuke Tomimatsu, Qianmei Wu, Kosuke Tokunaga, Wakana Izumi, Takahiro Suzuki, Ryuichi Tatsumi, Mako Nakamura
| | - Wakana Izumi
- Alaa Elgaabari, Atsuko Miyawaki-Kuwakado, Kosuke Tomimatsu, Qianmei Wu, Kosuke Tokunaga, Wakana Izumi, Takahiro Suzuki, Ryuichi Tatsumi, Mako Nakamura
| | - Takahiro Suzuki
- Alaa Elgaabari, Atsuko Miyawaki-Kuwakado, Kosuke Tomimatsu, Qianmei Wu, Kosuke Tokunaga, Wakana Izumi, Takahiro Suzuki, Ryuichi Tatsumi, Mako Nakamura
| | - Ryuichi Tatsumi
- Alaa Elgaabari, Atsuko Miyawaki-Kuwakado, Kosuke Tomimatsu, Qianmei Wu, Kosuke Tokunaga, Wakana Izumi, Takahiro Suzuki, Ryuichi Tatsumi, Mako Nakamura
| | - Mako Nakamura
- Alaa Elgaabari, Atsuko Miyawaki-Kuwakado, Kosuke Tomimatsu, Qianmei Wu, Kosuke Tokunaga, Wakana Izumi, Takahiro Suzuki, Ryuichi Tatsumi, Mako Nakamura
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27
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Wu Q, Fujii T, Harada A, Tomimatsu K, Miyawaki-Kuwakado A, Fujita M, Maehara K, Ohkawa Y. Genome-wide analysis of chromatin structure changes upon MyoD binding in proliferative myoblasts during the cell cycle. J Biochem 2021; 169:653-661. [PMID: 33479729 DOI: 10.1093/jb/mvab001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/24/2020] [Indexed: 11/13/2022] Open
Abstract
MyoD, a myogenic differentiation protein, has been studied for its critical role in skeletal muscle differentiation. MyoD-expressing myoblasts have a potency to be differentiated with proliferation of ectopic cells. However, little is known about the effect on chromatin structure of MyoD binding in proliferative myoblasts. In this study, we evaluated the chromatin structure around MyoD-bound genome regions during the cell cycle by chromatin immunoprecipitation sequencing. Genome-wide analysis of histone modifications was performed in proliferative mouse C2C12 myoblasts during three phases (G1, S, G2/M) of the cell cycle. We found that MyoD-bound genome regions had elevated levels of active histone modifications, such as H3K4me1/2/3, and H3K27ac, compared with MyoD-unbound genome regions during the cell cycle. We also demonstrated that the elevated H3K4me2/3 modification level was maintained during the cell cycle, whereas the H3K27ac and H3K4me1 modification levels decreased to the same level as MyoD-unbound genome regions during the later phases. Immunoblot analysis revealed that MyoD abundance was high in the G1 phase then decreased in the S and G2/M phases. Our results suggest that MyoD binding formed selective epigenetic memories with H3K4me2/3 during the cell cycle in addition to myogenic gene induction via active chromatin formation coupled with transcription.
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Affiliation(s)
- Qianmei Wu
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Takeru Fujii
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan.,Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Kosuke Tomimatsu
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Atsuko Miyawaki-Kuwakado
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
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28
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Wilson MM, Henshall DC, Byrne SM, Brennan GP. CHD2-Related CNS Pathologies. Int J Mol Sci 2021; 22:E588. [PMID: 33435571 PMCID: PMC7827033 DOI: 10.3390/ijms22020588] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 02/08/2023] Open
Abstract
Epileptic encephalopathies (EE) are severe epilepsy syndromes characterized by multiple seizure types, developmental delay and even regression. This class of disorders are increasingly being identified as resulting from de novo genetic mutations including many identified mutations in the family of chromodomain helicase DNA binding (CHD) proteins. In particular, several de novo pathogenic mutations have been identified in the gene encoding chromodomain helicase DNA binding protein 2 (CHD2), a member of the sucrose nonfermenting (SNF-2) protein family of epigenetic regulators. These mutations in the CHD2 gene are causative of early onset epileptic encephalopathy, abnormal brain function, and intellectual disability. Our understanding of the mechanisms by which modification or loss of CHD2 cause this condition remains poorly understood. Here, we review what is known and still to be elucidated as regards the structure and function of CHD2 and how its dysregulation leads to a highly variable range of phenotypic presentations.
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Affiliation(s)
- Marc-Michel Wilson
- Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences, Dublin 02, Ireland; (M.-M.W.); (D.C.H.)
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
| | - David C. Henshall
- Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences, Dublin 02, Ireland; (M.-M.W.); (D.C.H.)
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
| | - Susan M. Byrne
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
- Department of Paediatrics, RCSI, University of Medicine and Health Sciences, Dublin 02, Ireland
- Department of Paediatric Neurology, Our Ladies Children’s Hospital Crumlin, Dublin 12, Ireland
| | - Gary P. Brennan
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 04, Ireland
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29
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Conboy K, Henshall DC, Brennan GP. Epigenetic principles underlying epileptogenesis and epilepsy syndromes. Neurobiol Dis 2020; 148:105179. [PMID: 33181318 DOI: 10.1016/j.nbd.2020.105179] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/21/2022] Open
Abstract
Epilepsy is a network disorder driven by fundamental changes in the function of the cells which compose these networks. Driving this aberrant cellular function are large scale changes in gene expression and gene expression regulation. Recent studies have revealed rapid and persistent changes in epigenetic control of gene expression as a critical regulator of the epileptic transcriptome. Epigenetic-mediated gene output regulates many aspects of cellular physiology including neuronal structure, neurotransmitter assembly and abundance, protein abundance of ion channels and other critical neuronal processes. Thus, understanding the contribution of epigenetic-mediated gene regulation could illuminate novel regulatory mechanisms which may form the basis of novel therapeutic approaches to treat epilepsy. In this review we discuss the effects of epileptogenic brain insults on epigenetic regulation of gene expression, recent efforts to target epigenetic processes to block epileptogenesis and the prospects of an epigenetic-based therapy for epilepsy, and finally we discuss technological advancements which have facilitated the interrogation of the epigenome.
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Affiliation(s)
- Karen Conboy
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland; FutureNeuro, the SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - David C Henshall
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland; FutureNeuro, the SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
| | - Gary P Brennan
- FutureNeuro, the SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin, Ireland; School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
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30
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Poly(ADP-ribose) Polymerase 1 (PARP1) restrains MyoD-dependent gene expression during muscle differentiation. Sci Rep 2020; 10:15086. [PMID: 32934320 PMCID: PMC7493885 DOI: 10.1038/s41598-020-72155-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 08/21/2020] [Indexed: 12/13/2022] Open
Abstract
The myogenic factor MyoD regulates skeletal muscle differentiation by interacting with a variety of chromatin-modifying complexes. Although MyoD can induce and maintain chromatin accessibility at its target genes, its binding and trans-activation ability can be limited by some types of not fully characterized epigenetic constraints. In this work we analysed the role of PARP1 in regulating MyoD-dependent gene expression. PARP1 is a chromatin-associated enzyme, playing a well recognized role in DNA repair and that is implicated in transcriptional regulation. PARP1 affects gene expression through multiple mechanisms, often involving the Poly(ADP-ribosyl)ation of chromatin proteins. In line with PARP1 down-regulation during differentiation, we observed that PARP1 depletion boosts the up-regulation of MyoD targets, such as p57, myogenin, Mef2C and p21, while its re-expression reverts this effect. We also found that PARP1 interacts with some MyoD-binding regions and that its presence, independently of the enzymatic activity, interferes with MyoD recruitment and gene induction. We finally suggest a relationship between the binding of PARP1 and the loss of the activating histone modification H3K4me3 at MyoD-binding regions. This work highlights not only a novel player in the epigenetic control of myogenesis, but also a repressive and catalytic-independent mechanisms by which PARP1 regulates transcription.
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31
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Abstract
Histone variants regulate chromatin accessibility and gene transcription. Given their distinct properties and functions, histone varint substitutions allow for profound alteration of nucleosomal architecture and local chromatin landscape. Skeletal myogenesis driven by the key transcription factor MyoD is characterized by precise temporal regulation of myogenic genes. Timed substitution of variants within the nucleosomes provides a powerful means to ensure sequential expression of myogenic genes. Indeed, growing evidence has shown H3.3, H2A.Z, macroH2A, and H1b to be critical for skeletal myogenesis. However, the relative importance of various histone variants and their associated chaperones in myogenesis is not fully appreciated. In this review, we summarize the role that histone variants play in altering chromatin landscape to ensure proper muscle differentiation. The temporal regulation and cross talk between histones variants and their chaperones in conjunction with other forms of epigenetic regulation could be critical to understanding myogenesis and their involvement in myopathies.
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Affiliation(s)
- Nandini Karthik
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
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32
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Gawel K, Langlois M, Martins T, van der Ent W, Tiraboschi E, Jacmin M, Crawford AD, Esguerra CV. Seizing the moment: Zebrafish epilepsy models. Neurosci Biobehav Rev 2020; 116:1-20. [PMID: 32544542 DOI: 10.1016/j.neubiorev.2020.06.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/20/2020] [Accepted: 06/05/2020] [Indexed: 12/14/2022]
Abstract
Zebrafish are now widely accepted as a valuable animal model for a number of different central nervous system (CNS) diseases. They are suitable both for elucidating the origin of these disorders and the sequence of events culminating in their onset, and for use as a high-throughput in vivo drug screening platform. The availability of powerful and effective techniques for genome manipulation allows the rapid modelling of different genetic epilepsies and of conditions with seizures as a core symptom. With this review, we seek to summarize the current knowledge about existing epilepsy/seizures models in zebrafish (both pharmacological and genetic) and compare them with equivalent rodent and human studies. New findings obtained from the zebrafish models are highlighted. We believe that this comprehensive review will highlight the value of zebrafish as a model for investigating different aspects of epilepsy and will help researchers to use these models to their full extent.
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Affiliation(s)
- Kinga Gawel
- Chemical Neuroscience Group, Centre for Molecular Medicine Norway (NCMM), University of Oslo, Gaustadalléen 21, Forskningsparken, 0349, Oslo, Norway; Department of Experimental and Clinical Pharmacology, Medical University of Lublin, Jaczewskiego St. 8b, 20-090, Lublin, Poland
| | | | - Teresa Martins
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belval, Luxembourg
| | - Wietske van der Ent
- Chemical Neuroscience Group, Centre for Molecular Medicine Norway (NCMM), University of Oslo, Gaustadalléen 21, Forskningsparken, 0349, Oslo, Norway
| | - Ettore Tiraboschi
- Chemical Neuroscience Group, Centre for Molecular Medicine Norway (NCMM), University of Oslo, Gaustadalléen 21, Forskningsparken, 0349, Oslo, Norway; Neurophysics Group, Center for Mind/Brain Sciences, University of Trento, Piazza Manifattura 1, Building 14, 38068, Rovereto, TN, Italy
| | - Maxime Jacmin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belval, Luxembourg
| | - Alexander D Crawford
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belval, Luxembourg; Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - Camila V Esguerra
- Chemical Neuroscience Group, Centre for Molecular Medicine Norway (NCMM), University of Oslo, Gaustadalléen 21, Forskningsparken, 0349, Oslo, Norway.
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33
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Molenaar TM, Pagès-Gallego M, Meyn V, van Leeuwen F. Application of Recombination -Induced Tag Exchange (RITE) to study histone dynamics in human cells. Epigenetics 2020; 15:901-913. [PMID: 32228348 PMCID: PMC7518693 DOI: 10.1080/15592294.2020.1741777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In eukaryotes, nucleosomes form a barrier to DNA templated reactions and must be dynamically disrupted to provide access to the genome. During nucleosome (re)assembly, histones can be replaced by new histones, erasing post-translational modifications. Measuring histone turnover in mammalian cells has mostly relied on inducible overexpression of histones, which may influence and distort natural histone deposition rates. We have previously used recombination-induced tag exchange (RITE) to study histone dynamics in budding yeast. RITE is a method to follow protein turnover by genetic switching of epitope tags using Cre recombinase and does not rely on inducible overexpression. Here, we applied RITE to study the dynamics of the replication-independent histone variant H3.3 in human cells. Epitope tag-switching could be readily detected upon induction of Cre-recombinase, enabling the monitoring old and new H3.3 in the same pool of cells. However, the rate of tag-switching was lower than in yeast cells. Analysis of histone H3.3 incorporation by chromatin immunoprecipitation did not recapitulate previously reported aspects of H3.3 dynamics such as high turnover rates in active promoters and enhancers. We hypothesize that asynchronous Cre-mediated DNA recombination in the cell population leads to a low time resolution of the H3.3-RITE system in human cells. We conclude that RITE enables the detection of old and new proteins in human cells and that the time-scale of tag-switching prevents the capture of high turnover events in a population of cells. Instead, RITE might be more suited for tracking long-lived histone proteins in human cells.
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Affiliation(s)
- Thom M Molenaar
- Division of Gene Regulation, Netherlands Cancer Institute , Amsterdam, The Netherlands
| | - Marc Pagès-Gallego
- Division of Gene Regulation, Netherlands Cancer Institute , Amsterdam, The Netherlands
| | - Vanessa Meyn
- Division of Gene Regulation, Netherlands Cancer Institute , Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute , Amsterdam, The Netherlands.,Department of Medical Biology, Amsterdam UMC, Location AMC, University of Amsterdam , Amsterdam, The Netherlands
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34
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Shahin Varnoosfaderani F, Palau A, Dong W, Persson J, Durand-Dubief M, Svensson JP, Lennartsson A. A regulatory role for CHD2 in myelopoiesis. Epigenetics 2020; 15:702-714. [PMID: 31900031 PMCID: PMC7574388 DOI: 10.1080/15592294.2019.1710913] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The transcriptional program that dictates haematopoietic cell fate and differentiation requires an epigenetic regulatory and memory function, provided by a network of epigenetic factors that regulate DNA methylation, post-translational histone modifications and chromatin structure. Disturbed epigenetic regulation causes perturbations in the blood cell differentiation program that results in various types of haematopoietic disorders. Thus, accurate epigenetic regulation is essential for functional haematopoiesis. In this study, we used a CRISPR-Cas9 screening approach to identify new epigenetic regulators in myeloid differentiation. We designed a Chromatin-UMI CRISPR guide library targeting 1092 epigenetic regulators. Phorbol 12-myristate 13-acetate (PMA) treatment of the chronic myeloid leukaemia cell line K-562 was used as a megakaryocytic myeloid differentiation model. Both previously described developmental epigenetic regulators and novel factors were identified in our screen. In this study, we validated and characterized a role for the chromatin remodeller CHD2 in myeloid proliferation and megakaryocytic differentiation.
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Affiliation(s)
| | - Anna Palau
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet , Stockholm, Sweden
| | - Wenbo Dong
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet , Stockholm, Sweden
| | - Jenna Persson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm, Sweden.,High Throughput Genome Engineering, Science for Life Laboratory , Stockholm, Sweden
| | - Mickaël Durand-Dubief
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet , Stockholm, Sweden
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet , Stockholm, Sweden
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet , Stockholm, Sweden
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35
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Hong L, Gu T, He Y, Zhou C, Hu Q, Wang X, Zheng E, Huang S, Xu Z, Yang J, Yang H, Li Z, Liu D, Cai G, Wu Z. Genome-Wide Analysis of Circular RNAs Mediated ceRNA Regulation in Porcine Embryonic Muscle Development. Front Cell Dev Biol 2019; 7:289. [PMID: 31803743 PMCID: PMC6877547 DOI: 10.3389/fcell.2019.00289] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/05/2019] [Indexed: 12/19/2022] Open
Abstract
Many circular RNAs (circRNAs) have been discovered in various tissues and cell types in pig. However, the temporal expression pattern of circRNAs during porcine embryonic muscle development remains unclear. Here, we present a panorama view of circRNA expression in embryonic muscle development at 33-, 65-, and 90-days post-coitus (dpc) from Duroc pigs. An unbiased analysis reveals that more than 5,000 circRNAs specifically express in embryonic muscle development. The amount and complexity of circRNA expression is most pronounced in skeletal muscle at day 33 of gestation. Our circRNAs annotation analyses show that “hot-spot” genes produce multiple circRNA isoforms and RNA binding protein (RBPs) may regulate the biogenesis of circRNAs. Furthermore, we observed that host genes of differentially expressed circRNA across porcine muscle development are enriched in skeletal muscle function. A competing endogenous RNA (ceRNA) network analysis of circRNAs reveals that circRNAs regulate muscle gene expression by functioning as miRNA sponges. Finally, our experimental validation demonstrated that circTUT7 regulate the expression of HMG20B in a ceRNA mechanism. Our analyses show that circRNAs are dynamically expressed and interacting with muscle genes through ceRNA manner, suggesting their critical functions in embryonic skeletal muscle development.
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Affiliation(s)
- Linjun Hong
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Ting Gu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yanjuan He
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Chen Zhou
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qun Hu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xingwang Wang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Enqin Zheng
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Sixiu Huang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zheng Xu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jie Yang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Huaqiang Yang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zicong Li
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Dewu Liu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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36
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Rom A, Melamed L, Gil N, Goldrich MJ, Kadir R, Golan M, Biton I, Perry RBT, Ulitsky I. Regulation of CHD2 expression by the Chaserr long noncoding RNA gene is essential for viability. Nat Commun 2019; 10:5092. [PMID: 31704914 PMCID: PMC6841665 DOI: 10.1038/s41467-019-13075-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022] Open
Abstract
Chromodomain helicase DNA binding protein 2 (Chd2) is a chromatin remodeller implicated in neurological disease. Here we show that Chaserr, a highly conserved long noncoding RNA transcribed from a region near the transcription start site of Chd2 and on the same strand, acts in concert with the CHD2 protein to maintain proper Chd2 expression levels. Loss of Chaserr in mice leads to early postnatal lethality in homozygous mice, and severe growth retardation in heterozygotes. Mechanistically, loss of Chaserr leads to substantially increased Chd2 mRNA and protein levels, which in turn lead to transcriptional interference by inhibiting promoters found downstream of highly expressed genes. We further show that Chaserr production represses Chd2 expression solely in cis, and that the phenotypic consequences of Chaserr loss are rescued when Chd2 is perturbed as well. Targeting Chaserr is thus a potential strategy for increasing CHD2 levels in haploinsufficient individuals.
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Affiliation(s)
- Aviv Rom
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Liliya Melamed
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Gil
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | | | - Rotem Kadir
- National Institute for Biotechnology in the Negev and Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Matan Golan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Inbal Biton
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Ben-Tov Perry
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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37
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Calcineurin Broadly Regulates the Initiation of Skeletal Muscle-Specific Gene Expression by Binding Target Promoters and Facilitating the Interaction of the SWI/SNF Chromatin Remodeling Enzyme. Mol Cell Biol 2019; 39:MCB.00063-19. [PMID: 31308130 PMCID: PMC6751634 DOI: 10.1128/mcb.00063-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 07/08/2019] [Indexed: 12/22/2022] Open
Abstract
Calcineurin (Cn) is a calcium-activated serine/threonine protein phosphatase that is broadly implicated in diverse cellular processes, including the regulation of gene expression. During skeletal muscle differentiation, Cn activates the nuclear factor of activated T-cell (NFAT) transcription factor but also promotes differentiation by counteracting the negative influences of protein kinase C beta (PKCβ) via dephosphorylation and activation of Brg1, an enzymatic subunit of the mammalian SWI/SNF ATP-dependent chromatin remodeling enzyme. Here we identified four major temporal patterns of Cn-dependent gene expression in differentiating myoblasts and determined that Cn is broadly required for the activation of the myogenic gene expression program. Mechanistically, Cn promotes gene expression through direct binding to myogenic promoter sequences and facilitating the binding of Brg1, other SWI/SNF subunit proteins, and MyoD, a critical lineage determinant for skeletal muscle differentiation. We conclude that the Cn phosphatase directly impacts the expression of myogenic genes by promoting ATP-dependent chromatin remodeling and formation of transcription-competent promoters.
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38
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Zhang X, Cai S, Chen L, Yuan R, Nie Y, Ding S, Fang Y, Zhu Q, Chen K, Wei H, Chen Y, Mo D. Integrated miRNA-mRNA transcriptomic analysis reveals epigenetic-mediated embryonic muscle growth differences between Wuzhishan and Landrace pigs1. J Anim Sci 2019; 97:1967-1978. [PMID: 31222274 DOI: 10.1093/jas/skz091] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/08/2019] [Indexed: 02/07/2023] Open
Abstract
Pig is one of the major dietary protein sources for human consumption, from which muscle is the largest protein origin. However, molecular mechanisms concerning early porcine embryonic muscle development distinctions between pig breeds are still unclear. In this study, an integrated analysis of transcriptome and miRNAome was conducted using longissimus dorsi muscle of 4 early embryonic stages around the primary myofiber formation time (18-, 21-, 28-, and 35-d post coitus) from 2 pig breeds (Landrace [LR] and Wuzhishan [WZS]) differing in meat mass. The global miRNA/mRNA expression profile showed that WZS prepared for myogenic developmental processes earlier than LR. After identifying and analyzing the interaction network of top 100 up-/down-regulated miRNA and their target genes, we were able to find 3 gene clusters: chromatin modification-related (Chd2, H3f3a, Chd6, and Mll1), myogenesis-related (Pax3, Pbx1, Mef2a, and Znf423), and myosin component-related (Mylk, Myo5a, Mylk4, Myh9, and Mylk2) gene clusters. These genes may involve in miRNA-gene myogenic regulatory network that plays vital role in regulating distinct early porcine embryonic myogenic processes between LR and WZS. In summary, our study reveals an epigenetic-mediated myogenic regulatory axial that will help us to decipher molecular mechanisms concerning early porcine embryonic muscle development distinctions between pig breeds.
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Affiliation(s)
- Xumeng Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Shenzhen Kingsino Technology Co., Ltd., Shenzhen, Guangdong, China
| | - Shufang Cai
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Luxi Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Renqiang Yuan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yaping Nie
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Suying Ding
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Ying Fang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Qi Zhu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Keren Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Hong Wei
- Shenzhen Kingsino Technology Co., Ltd., Shenzhen, Guangdong, China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
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39
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Il’ina IA, Konev AY. The role of aTp-dependent chromatin remodeling factors in chromatin assembly in vivo. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chromatin assembly is a fundamental process essential for chromosome duplication subsequent to DNA replication. In addition, histone removal and incorporation take place constantly throughout the cell cycle in the course of DNA-utilizing processes, such as transcription, damage repair or recombination. In vitro studies have revealed that nucleosome assembly relies on the combined action of core histone chaperones and ATP-utilizing molecular motor proteins such as ACF or CHD1. Despite extensive biochemical characterization of ATP-dependent chromatin assembly and remodeling factors, it has remained unclear to what extent nucleosome assembly is an ATP-dependent process in vivo. Our original and published data about the functions of ATP-dependent chromatin assembly and remodeling factors clearly demonstrated that these proteins are important for nucleosome assembly and histone exchange in vivo. During male pronucleus reorganization after fertilization CHD1 has a critical role in the genomescale, replication-independent nucleosome assembly involving the histone variant H3.3. Thus, the molecular motor proteins, such as CHD1, function not only in the remodeling of existing nucleosomes but also in de novo nucleosome assembly from DNA and histones in vivo. ATP-dependent chromatin assembly and remodeling factors have been implicated in the process of histone exchange during transcription and DNA repair, in the maintenance of centromeric chromatin and in the loading and remodeling of nucleosomes behind a replication fork. Thus, chromatin remodeling factors are involved in the processes of both replication-dependent and replication-independent chromatin assembly. The role of these proteins is especially prominent in the processes of large-scale chromatin reorganization; for example, during male pronucleus formation or in DNA repair. Together, ATP-dependent chromatin assembly factors, histone chaperones and chromatin modifying enzymes form a “chromatin integrity network” to ensure proper maintenance and propagation of chromatin landscape.
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Affiliation(s)
- Iu. A. Il’ina
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”
| | - A. Yu. Konev
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”
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40
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Park J, Lee H, Han N, Kwak S, Lee HT, Kim JH, Kang K, Youn BH, Yang JH, Jeong HJ, Kang JS, Kim SY, Han JW, Youn HD, Cho EJ. Long non-coding RNA ChRO1 facilitates ATRX/DAXX-dependent H3.3 deposition for transcription-associated heterochromatin reorganization. Nucleic Acids Res 2018; 46:11759-11775. [PMID: 30335163 PMCID: PMC6294499 DOI: 10.1093/nar/gky923] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 09/20/2018] [Accepted: 10/05/2018] [Indexed: 12/23/2022] Open
Abstract
Constitutive heterochromatin undergoes a dynamic clustering and spatial reorganization during myogenic differentiation. However the detailed mechanisms and its role in cell differentiation remain largely elusive. Here, we report the identification of a muscle-specific long non-coding RNA, ChRO1, involved in constitutive heterochromatin reorganization. ChRO1 is induced during terminal differentiation of myoblasts, and is specifically localized to the chromocenters in myotubes. ChRO1 is required for efficient cell differentiation, with global impacts on gene expression. It influences DNA methylation and chromatin compaction at peri/centromeric regions. Inhibition of ChRO1 leads to defects in the spatial fusion of chromocenters, and mislocalization of H4K20 trimethylation, Suv420H2, HP1, MeCP2 and cohesin. In particular, ChRO1 specifically associates with ATRX/DAXX/H3.3 complex at chromocenters to promote H3.3 incorporation and transcriptional induction of satellite repeats, which is essential for chromocenter clustering. Thus, our results unveil a mechanism involving a lncRNA that plays a role in large-scale heterochromatin reorganization and cell differentiation.
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MESH Headings
- Animals
- CRISPR-Cas Systems
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Differentiation
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Co-Repressor Proteins
- Female
- Gene Editing
- Gene Expression Regulation, Developmental
- HEK293 Cells
- Heterochromatin/chemistry
- Heterochromatin/metabolism
- Histone-Lysine N-Methyltransferase/genetics
- Histone-Lysine N-Methyltransferase/metabolism
- Histones/genetics
- Histones/metabolism
- Humans
- Intracellular Signaling Peptides and Proteins/genetics
- Intracellular Signaling Peptides and Proteins/metabolism
- Male
- Methyl-CpG-Binding Protein 2/genetics
- Methyl-CpG-Binding Protein 2/metabolism
- Mice
- Mice, Inbred C57BL
- Molecular Chaperones
- Muscle Development/genetics
- Muscle, Skeletal/cytology
- Muscle, Skeletal/growth & development
- Muscle, Skeletal/metabolism
- NIH 3T3 Cells
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- RNA, Long Noncoding/antagonists & inhibitors
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Transcription, Genetic
- X-linked Nuclear Protein/genetics
- X-linked Nuclear Protein/metabolism
- Cohesins
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Affiliation(s)
- Jinyoung Park
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Hongmin Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Sojung Kwak
- Department of Biomedical Sciences,National Creative Research Center for Epigenome Reprogramming Network, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Han-Teo Lee
- Department of Molecular Medicine & Biopharmaceutical Sciences, Graduate School of Convergence Science and technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Jae-Hwan Kim
- Department of Biomedical Sciences,National Creative Research Center for Epigenome Reprogramming Network, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Keonjin Kang
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Byoung Ha Youn
- Medical Genome Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Jae-Hyun Yang
- Department of Genetics, Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA
| | - Hyeon-Ju Jeong
- College of Medicine, Sungkyunkwan University, Suwon, Gyeonggi-do 440-746, Republic of Korea
| | - Jong-Sun Kang
- College of Medicine, Sungkyunkwan University, Suwon, Gyeonggi-do 440-746, Republic of Korea
| | - Seon-Young Kim
- Medical Genome Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Jeung-Whan Han
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Hong-Duk Youn
- Department of Biomedical Sciences,National Creative Research Center for Epigenome Reprogramming Network, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Department of Molecular Medicine & Biopharmaceutical Sciences, Graduate School of Convergence Science and technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Eun-Jung Cho
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
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41
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Kim YJ, Khoshkhoo S, Frankowski JC, Zhu B, Abbasi S, Lee S, Wu YE, Hunt RF. Chd2 Is Necessary for Neural Circuit Development and Long-Term Memory. Neuron 2018; 100:1180-1193.e6. [PMID: 30344048 PMCID: PMC6479120 DOI: 10.1016/j.neuron.2018.09.049] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 07/31/2018] [Accepted: 09/26/2018] [Indexed: 12/18/2022]
Abstract
Considerable evidence suggests loss-of-function mutations in the chromatin remodeler CHD2 contribute to a broad spectrum of human neurodevelopmental disorders. However, it is unknown how CHD2 mutations lead to impaired brain function. Here we report mice with heterozygous mutations in Chd2 exhibit deficits in neuron proliferation and a shift in neuronal excitability that included divergent changes in excitatory and inhibitory synaptic function. Further in vivo experiments show that Chd2+/- mice displayed aberrant cortical rhythmogenesis and severe deficits in long-term memory, consistent with phenotypes observed in humans. We identified broad, age-dependent transcriptional changes in Chd2+/- mice, including alterations in neurogenesis, synaptic transmission, and disease-related genes. Deficits in interneuron density and memory caused by Chd2+/- were reproduced by Chd2 mutation restricted to a subset of inhibitory neurons and corrected by interneuron transplantation. Our results provide initial insight into how Chd2 haploinsufficiency leads to aberrant cortical network function and impaired memory.
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Affiliation(s)
- Young J Kim
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA 92697, USA.
| | - Sattar Khoshkhoo
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurology, Brigham and Women's Hospital and Massachusetts General Hospital, Harvard University, Boston, MA 02115, USA
| | - Jan C Frankowski
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA 92697, USA
| | - Bingyao Zhu
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA 92697, USA
| | - Saad Abbasi
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA 92697, USA
| | - Sunyoung Lee
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA 92697, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ye Emily Wu
- Department of Biological Chemistry and Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Robert F Hunt
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA 92697, USA.
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42
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Kasah S, Oddy C, Basson MA. Autism-linked CHD gene expression patterns during development predict multi-organ disease phenotypes. J Anat 2018; 233:755-769. [PMID: 30277262 DOI: 10.1111/joa.12889] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2018] [Indexed: 12/24/2022] Open
Abstract
Recent large-scale exome sequencing studies have identified mutations in several members of the CHD (Chromodomain Helicase DNA-binding protein) gene family in neurodevelopmental disorders. Mutations in the CHD2 gene have been linked to developmental delay, intellectual disability, autism and seizures, CHD8 mutations to autism and intellectual disability, whereas haploinsufficiency of CHD7 is associated with executive dysfunction and intellectual disability. In addition to these neurodevelopmental features, a wide range of other developmental defects are associated with mutants of these genes, especially with regards to CHD7 haploinsufficiency, which is the primary cause of CHARGE syndrome. Whilst the developmental expression of CHD7 has been reported previously, limited information on the expression of CHD2 and CHD8 during development is available. Here, we compare the expression patterns of all three genes during mouse development directly. We find high, widespread expression of these genes at early stages of development that gradually becomes restricted during later developmental stages. Chd2 and Chd8 are widely expressed in the developing central nervous system (CNS) at all stages of development, with moderate expression remaining in the neocortex, hippocampus, olfactory bulb and cerebellum of the postnatal brain. Similarly, Chd7 expression is seen throughout the CNS during late embryogenesis and early postnatal development, with strong enrichment in the cerebellum, but displays low expression in the cortex and neurogenic niches in early life. In addition to expression in the brain, novel sites of Chd2 and Chd8 expression are reported. These findings suggest additional roles for these genes in organogenesis and predict that mutation of these genes may predispose individuals to a range of other, non-neurological developmental defects.
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Affiliation(s)
- Sahrunizam Kasah
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - Christopher Oddy
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - M Albert Basson
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK.,MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
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43
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Masuzawa R, Konno R, Ohsawa I, Watanabe A, Kawano F. Muscle type-specific RNA polymerase II recruitment during PGC-1α gene transcription after acute exercise in adult rats. J Appl Physiol (1985) 2018; 125:1238-1245. [PMID: 30113273 DOI: 10.1152/japplphysiol.00202.2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Epigenetic regulation of gene expression differs between fast- and slow-twitch skeletal muscles in adult rats, although the precise mechanisms are still unknown. The present study investigates the differences in responses of RNA polymerase II (Pol II) and histone acetylation during transcriptional activation in the plantaris and soleus muscles of adult rats after acute treadmill running. We targeted the peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) gene to analyze epigenomic changes by chromatin immunoprecipitation. The mRNA expression of the PGC-1α-b isoform was significantly up-regulated in both plantaris and soleus muscles 2 h after acute running, although the magnitude of the up-regulation was more pronounced in the plantaris muscle. The sequences of proximal exons of the PGC-1α locus were expressed more in the plantaris muscle after acute running. Accumulation of Pol II was noted near the alternative exon 1 in both plantaris and soleus muscles in association with the enhanced distribution of acetylated histone 3. Accumulation of Pol II was also observed at the transcription start site, exon 2, and exon 3 in the plantaris muscle, but not the soleus muscle. It was noted that in the soleus muscle, acetylation of histone 3 at lysine 27 was enhanced throughout the PGC-1α locus in response to transcriptional activation, suggesting that elongating Pol II was capable of traveling through to the end of the locus. These results indicate that the mobility of Pol II during PGC-1αtranscription differed between fast- and slow-twitch skeletal muscles, affecting the strength of the transcriptional activity.
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Affiliation(s)
- Ryo Masuzawa
- Graduate School of Health Sciences, Matsumoto University
| | - Ryotaro Konno
- Department of Sports and Health Science, Faculty of Human Health Science, Matsumoto University
| | - Ikumi Ohsawa
- Department of Sports and Health Science, Faculty of Human Health and Science, Matsumoto University
| | | | - Fuminori Kawano
- Graduate School of Health Sciences, Matsumoto University, Japan
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44
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Ohsawa I, Konno R, Masuzawa R, Kawano F. Amount of daily exercise is an essential stimulation to alter the epigenome of skeletal muscle in rats. J Appl Physiol (1985) 2018; 125:1097-1104. [PMID: 30070609 DOI: 10.1152/japplphysiol.00074.2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Long-term running training causes epigenetic changes in the skeletal muscles. Here we tested the effects of the total amount or duration of running training on the distribution of histones in the rat plantaris muscle. Post-weaned young rats were assigned to 3 different training groups: Run-1, 30 min/day running exercise for 8 wk using an animal treadmill at 24 m/min; Run-2, 15 min/day for 8 wk; and Run-3, 60 min/day for 4 wk. Citrate synthase activity was not significantly changed by running training, although the slight increase was observed in Run-3. Genes that were previously defined as showing the typical responses to running training were targeted to measure the distribution of histones using chromatin immunoprecipitation. The distribution of acetylated histone 3 was elevated in Run-2 and Run-3, but not in Run-1. Incorporation of H3.3 into the nucleosome was stimulated in Run-1, whereas H3.3 distribution was unchanged in Run-2 or downregulated in Run-3. Significant downregulation of H3.3 expression was also detected in Run-3. We further checked the responses of the target genes during acute running. Target genes were transcriptionally activated and histone acetylation was stimulated at the loci in response to acute running. These results suggested that the exchange of the histone component to H3.3 was stimulated by running training, inhibiting the accumulation of acetylated histones in Run-1. Additionally, it was further suggested that the enhanced daily amount of running caused changes in the H3.3 expression, affecting the rate of the histone exchange in Run-3. NEW & NOTEWORTHY Chromatin remodeling in the skeletal muscle is a potent mechanism preventing disuse atrophy in later life that can be acquired via long-term exercise training. Here we demonstrated in rats that daily exercise amount is a key factor in the development of epigenetic changes in the skeletal muscle. To acquire a health benefit, our research suggests the importance of considering the time endurance for daily exercise bouts.
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Affiliation(s)
- Ikumi Ohsawa
- Department of Sports and Health Science, Faculty of Human Health and Science, Matsumoto University, Matsumoto City, Japan
| | - Ryotaro Konno
- Department of Sports and Health Science, Faculty of Human Health and Science, Matsumoto University, Matsumoto City, Japan
| | - Ryo Masuzawa
- Graduate School of Health Sciences, Matsumoto University, Matsumoto City, Japan
| | - Fuminori Kawano
- Department of Sports and Health Science, Faculty of Human Health and Science, Matsumoto University, Matsumoto City, Japan.,Graduate School of Health Sciences, Matsumoto University, Matsumoto City, Japan
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45
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G-quadruplexes in the BAP1 promoter positively regulate its expression. Exp Cell Res 2018; 369:147-157. [DOI: 10.1016/j.yexcr.2018.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/23/2018] [Accepted: 05/17/2018] [Indexed: 12/13/2022]
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46
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Lamar KMJ, Carvill GL. Chromatin Remodeling Proteins in Epilepsy: Lessons From CHD2-Associated Epilepsy. Front Mol Neurosci 2018; 11:208. [PMID: 29962935 PMCID: PMC6013553 DOI: 10.3389/fnmol.2018.00208] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/25/2018] [Indexed: 12/24/2022] Open
Abstract
The chromodomain helicase DNA-binding (CHD) family of proteins are ATP-dependent chromatin remodelers that contribute to the reorganization of chromatin structure and deposition of histone variants necessary to regulate gene expression. CHD proteins play an important role in neurodevelopment, as pathogenic variants in CHD1, CHD2, CHD4, CHD7 and CHD8 have been associated with a range of neurological phenotypes, including autism spectrum disorder (ASD), intellectual disability (ID) and epilepsy. Pathogenic variants in CHD2 are associated with developmental epileptic encephalopathy (DEE) in humans, however little is known about how these variants contribute to this disorder. Of the nine CHD family members, CHD2 is the only one that leads to a brain-restricted phenotype when disrupted in humans. This suggests that despite being expressed ubiquitously, CHD2 has a unique role in human brain development and function. In this review, we will discuss the phenotypic spectrum of patients with pathogenic variants in CHD2, current animal models of CHD2 deficiency, and the role of CHD2 in proliferation, neurogenesis, neuronal differentiation, chromatin remodeling and DNA-repair. We also consider how CHD2 depletion can affect each of these biological mechanisms and how these defects may underpin neurodevelopmental disorders including epilepsy.
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Affiliation(s)
- Kay-Marie J Lamar
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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47
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Sartorelli V, Puri PL. Shaping Gene Expression by Landscaping Chromatin Architecture: Lessons from a Master. Mol Cell 2018; 71:375-388. [PMID: 29887393 DOI: 10.1016/j.molcel.2018.04.025] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/05/2018] [Accepted: 04/27/2018] [Indexed: 01/14/2023]
Abstract
Since its discovery as a skeletal muscle-specific transcription factor able to reprogram somatic cells into differentiated myofibers, MyoD has provided an instructive model to understand how transcription factors regulate gene expression. Reciprocally, studies of other transcriptional regulators have provided testable hypotheses to further understand how MyoD activates transcription. Using MyoD as a reference, in this review, we discuss the similarities and differences in the regulatory mechanisms employed by tissue-specific transcription factors to access DNA and regulate gene expression by cooperatively shaping the chromatin landscape within the context of cellular differentiation.
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Affiliation(s)
- Vittorio Sartorelli
- Laboratory of Muscle Stem Cells & Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA.
| | - Pier Lorenzo Puri
- Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, La Jolla, CA 92037, USA; Epigenetics and Regenerative Medicine, IRCCS Fondazione Santa Lucia, Rome, Italy.
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48
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Kudou K, Komatsu T, Nogami J, Maehara K, Harada A, Saeki H, Oki E, Maehara Y, Ohkawa Y. The requirement of Mettl3-promoted MyoD mRNA maintenance in proliferative myoblasts for skeletal muscle differentiation. Open Biol 2018; 7:rsob.170119. [PMID: 28878038 PMCID: PMC5627051 DOI: 10.1098/rsob.170119] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/27/2017] [Indexed: 12/21/2022] Open
Abstract
Myogenic progenitor/stem cells retain their skeletal muscle differentiation potential by maintaining myogenic transcription factors such as MyoD. However, the mechanism of how MyoD expression is maintained in proliferative progenitor cells has not been elucidated. Here, we found that MyoD expression was reduced at the mRNA level by cell cycle arrest in S and G2 phases, which in turn led to the absence of skeletal muscle differentiation. The reduction of MyoD mRNA was correlated with the reduced expression of factors regulating RNA metabolism, including methyltransferase like 3 (Mettl3), which induces N6-methyladenosine (m6A) modifications of RNA. Knockdown of Mettl3 revealed that MyoD RNA was specifically downregulated and that this was caused by a decrease in processed, but not unprocessed, mRNA. Potential m6A modification sites were profiled by m6A sequencing and identified within the 5' untranslated region (UTR) of MyoD mRNA. Deletion of the 5' UTR revealed that it has a role in MyoD mRNA processing. These data showed that Mettl3 is required for MyoD mRNA expression in proliferative myoblasts.
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Affiliation(s)
- Kensuke Kudou
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, JST-CREST, Fukuoka 812-8582, Japan.,Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Tetsuro Komatsu
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, JST-CREST, Fukuoka 812-8582, Japan
| | - Jumpei Nogami
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, JST-CREST, Fukuoka 812-8582, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, JST-CREST, Fukuoka 812-8582, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, JST-CREST, Fukuoka 812-8582, Japan
| | - Hiroshi Saeki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yoshihiko Maehara
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, JST-CREST, Fukuoka 812-8582, Japan
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49
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Harada A, Maehara K, Ono Y, Taguchi H, Yoshioka K, Kitajima Y, Xie Y, Sato Y, Iwasaki T, Nogami J, Okada S, Komatsu T, Semba Y, Takemoto T, Kimura H, Kurumizaka H, Ohkawa Y. Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration. Nat Commun 2018; 9:1400. [PMID: 29643389 PMCID: PMC5895627 DOI: 10.1038/s41467-018-03845-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/16/2018] [Indexed: 12/12/2022] Open
Abstract
Regulation of gene expression requires selective incorporation of histone H3 variant H3.3 into chromatin. Histone H3.3 has several subsidiary variants but their functions are unclear. Here we characterize the function of histone H3.3 sub-variant, H3mm7, which is expressed in skeletal muscle satellite cells. H3mm7 knockout mice demonstrate an essential role of H3mm7 in skeletal muscle regeneration. Chromatin analysis reveals that H3mm7 facilitates transcription by forming an open chromatin structure around promoter regions including those of myogenic genes. The crystal structure of the nucleosome containing H3mm7 reveals that, unlike the S57 residue of other H3 proteins, the H3mm7-specific A57 residue cannot form a hydrogen bond with the R40 residue of the cognate H4 molecule. Consequently, the H3mm7 nucleosome is unstable in vitro and exhibited higher mobility in vivo compared with the H3.3 nucleosome. We conclude that the unstable H3mm7 nucleosome may be required for proper skeletal muscle differentiation. Incorporation of histone H3 variant H3.3 into chromatin regulates transcription. Here the authors find that H3.3 sub-variant H3mm7 is required for skeletal muscle regeneration and that H3mm7 nucleosomes are unstable and exhibit higher mobility, with H3mm7 promoting open chromatin around promoters.
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Affiliation(s)
- Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan
| | - Yusuke Ono
- Graduate School of Biomedical Science, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Hiroyuki Taguchi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Research Institute for Science and Engineering, and Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Kiyoshi Yoshioka
- Graduate School of Biomedical Science, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Yasuo Kitajima
- Graduate School of Biomedical Science, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Yan Xie
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Research Institute for Science and Engineering, and Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Yuko Sato
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Yokohama, 226-8503, Japan
| | - Takeshi Iwasaki
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan
| | - Jumpei Nogami
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan
| | - Seiji Okada
- Department of Advanced Medical Initiatives, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tetsuro Komatsu
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan
| | - Yuichiro Semba
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan
| | - Tatsuya Takemoto
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Yokohama, 226-8503, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Research Institute for Science and Engineering, and Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan.
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Mansouri L, Wierzbinska JA, Plass C, Rosenquist R. Epigenetic deregulation in chronic lymphocytic leukemia: Clinical and biological impact. Semin Cancer Biol 2018; 51:1-11. [PMID: 29427646 DOI: 10.1016/j.semcancer.2018.02.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 12/12/2017] [Accepted: 02/05/2018] [Indexed: 01/01/2023]
Abstract
Deregulated transcriptional control caused by aberrant DNA methylation and/or histone modifications is a hallmark of cancer cells. In chronic lymphocytic leukemia (CLL), the most common adult leukemia, the epigenetic 'landscape' has added a new layer of complexity to our understanding of this clinically and biologically heterogeneous disease. Early studies identified aberrant DNA methylation, often based on single gene promoter analysis with both biological and clinical impact. Subsequent genome-wide profiling studies revealed differential DNA methylation between CLLs and controls and in prognostics subgroups of the disease. From these studies, it became apparent that DNA methylation in regions outside of promoters, such as enhancers, is important for the regulation of coding genes as well as for the regulation of non-coding RNAs. Although DNA methylation profiles are reportedly stable over time and in relation to therapy, a higher epigenetic heterogeneity or 'burden' is seen in more aggressive CLL subgroups, albeit as non-recurrent 'passenger' events. More recently, DNA methylation profiles in CLL analyzed in relation to differentiating normal B-cell populations revealed that the majority of the CLL epigenome reflects the epigenomes present in the cell of origin and that only a small fraction of the epigenetic alterations represents truly CLL-specific changes. Furthermore, CLL patients can be grouped into at least three clinically relevant epigenetic subgroups, potentially originating from different cells at various stages of differentiation and associated with distinct outcomes. In this review, we summarize the current understanding of the DNA methylome in CLL, the role of histone modifying enzymes, highlight insights derived from animal models and attempts made to target epigenetic regulators in CLL along with the future directions of this rapidly advancing field.
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Affiliation(s)
- Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Sweden
| | - Justyna Anna Wierzbinska
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Sweden.
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