1
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Karayol R, Borroto MC, Haghshenas S, Namasivayam A, Reilly J, Levy MA, Relator R, Kerkhof J, McConkey H, Shvedunova M, Petersen AK, Magnussen K, Zweier C, Vasileiou G, Reis A, Savatt JM, Mulligan MR, Bicknell LS, Poke G, Abu-El-Haija A, Duis J, Hannig V, Srivastava S, Barkoudah E, Hauser NS, van den Born M, Hamiel U, Henig N, Baris Feldman H, McKee S, Krapels IPC, Lei Y, Todorova A, Yordanova R, Atemin S, Rogac M, McConnell V, Chassevent A, Barañano KW, Shashi V, Sullivan JA, Peron A, Iascone M, Canevini MP, Friedman J, Reyes IA, Kierstein J, Shen JJ, Ahmed FN, Mao X, Almoguera B, Blanco-Kelly F, Platzer K, Treu AB, Quilichini J, Bourgois A, Chatron N, Januel L, Rougeot C, Carere DA, Monaghan KG, Rousseau J, Myers KA, Sadikovic B, Akhtar A, Campeau PM. MSL2 variants lead to a neurodevelopmental syndrome with lack of coordination, epilepsy, specific dysmorphisms, and a distinct episignature. Am J Hum Genet 2024; 111:1330-1351. [PMID: 38815585 DOI: 10.1016/j.ajhg.2024.05.001] [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: 09/23/2023] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024] Open
Abstract
Epigenetic dysregulation has emerged as an important etiological mechanism of neurodevelopmental disorders (NDDs). Pathogenic variation in epigenetic regulators can impair deposition of histone post-translational modifications leading to aberrant spatiotemporal gene expression during neurodevelopment. The male-specific lethal (MSL) complex is a prominent multi-subunit epigenetic regulator of gene expression and is responsible for histone 4 lysine 16 acetylation (H4K16ac). Using exome sequencing, here we identify a cohort of 25 individuals with heterozygous de novo variants in MSL complex member MSL2. MSL2 variants were associated with NDD phenotypes including global developmental delay, intellectual disability, hypotonia, and motor issues such as coordination problems, feeding difficulties, and gait disturbance. Dysmorphisms and behavioral and/or psychiatric conditions, including autism spectrum disorder, and to a lesser extent, seizures, connective tissue disease signs, sleep disturbance, vision problems, and other organ anomalies, were observed in affected individuals. As a molecular biomarker, a sensitive and specific DNA methylation episignature has been established. Induced pluripotent stem cells (iPSCs) derived from three members of our cohort exhibited reduced MSL2 levels. Remarkably, while NDD-associated variants in two other members of the MSL complex (MOF and MSL3) result in reduced H4K16ac, global H4K16ac levels are unchanged in iPSCs with MSL2 variants. Regardless, MSL2 variants altered the expression of MSL2 targets in iPSCs and upon their differentiation to early germ layers. Our study defines an MSL2-related disorder as an NDD with distinguishable clinical features, a specific blood DNA episignature, and a distinct, MSL2-specific molecular etiology compared to other MSL complex-related disorders.
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Affiliation(s)
- Remzi Karayol
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Maria Carla Borroto
- Centre de recherche Azrieli du CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Anoja Namasivayam
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Jack Reilly
- Department of Pediatrics, Clinical Neurological Sciences and Epidemiology, Western University, London, ON N6A 3K7, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Maria Shvedunova
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Andrea K Petersen
- Department of Genetics and Metabolism, Randall Children's and Legacy Emanuel Hospitals, Portland, OR 97227, USA
| | - Kari Magnussen
- Department of Genetics and Metabolism, Randall Children's and Legacy Emanuel Hospitals, Portland, OR 97227, USA
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Georgia Vasileiou
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Juliann M Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Meghan R Mulligan
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Louise S Bicknell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Gemma Poke
- Genetic Health Service New Zealand, Wellington, New Zealand
| | - Aya Abu-El-Haija
- Division of Genetics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Jessica Duis
- Section of Genetics & Metabolism, Department of Pediatrics, University of Colorado, Children's Hospital Colorado, Aurora, CO, USA
| | - Vickie Hannig
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Siddharth Srivastava
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Natalie S Hauser
- Medical Genetics, Inova Fairfax Hospital, Falls Church, VA 22042, USA
| | - Myrthe van den Born
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Uri Hamiel
- Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center & Faculty of Medicine, Tel Aviv University, Tel Aviv 6423906, Israel
| | - Noa Henig
- Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Hagit Baris Feldman
- Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center & Faculty of Medicine, Tel Aviv University, Tel Aviv 6423906, Israel
| | - Shane McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast Health & Social Care Trust, Belfast BT9 7AB, UK
| | - Ingrid P C Krapels
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Albena Todorova
- Department of Medical Chemistry and Biochemistry, Medical University Sofia, Sofia, Bulgaria; Genetic Medico-Diagnostic Laboratory "Genica", Sofia, Bulgaria
| | - Ralitsa Yordanova
- Department of pediatrics "Prof. Ivan Andreev", Medical university - Plovdiv, Plovdiv, Bulgaria; Department of Pediatrics, University Hospital "St. George", Plovdiv, Bulgaria
| | - Slavena Atemin
- Genetic Medico-Diagnostic Laboratory "Genica", Sofia, Bulgaria
| | - Mihael Rogac
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vivienne McConnell
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast Health & Social Care Trust, Belfast BT9 7AB, UK
| | - Anna Chassevent
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Kristin W Barañano
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Angela Peron
- SOC Genetica Medica, Meyer Children's Hospital IRCCS, Florence, Italy; Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", Università degli Studi di Firenze, Florence, Italy
| | - Maria Iascone
- Department of Medical Genetics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Maria P Canevini
- Epilepsy Center - Sleep Medicine Center, Childhood and Adolescence Neuropsychiatry Unit, ASST Santi Paolo e Carlo, San Paolo Hospital, Milan, Italy; Department of Health Sciences, University of Milan, Milan, Italy
| | - Jennifer Friedman
- Departments of Neurosciences and Pediatrics, University of California, San Diego, La Jolla, CA, USA; Rady Children's Institute for Genomic Medicine and Rady Children's Hospital, San Diego, CA, USA
| | - Iris A Reyes
- Rady Children's Institute for Genomic Medicine and Rady Children's Hospital, San Diego, CA, USA
| | - Janell Kierstein
- Section of Genetics & Metabolism, Department of Pediatrics, University of Colorado, Children's Hospital Colorado, Aurora, CO, USA
| | - Joseph J Shen
- Division of Genomic Medicine, Department of Pediatrics, MIND Institute, UC Davis, Sacramento, CA 95817, USA
| | - Faria N Ahmed
- Division of Genomic Medicine, Department of Pediatrics, UC Davis, Sacramento, CA 95817, USA
| | - Xiao Mao
- National Health Commission Key Laboratory of Birth Defects Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Hunan, China; Nanhua University, Chiayi County, Taiwan
| | - Berta Almoguera
- Department of Genetics and Genomics, Fundacion Jimenez Diaz University Hospital, Health Research Institute-Fundacion Jimenez Diaz, Universidad Autonoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics and Genomics, Fundacion Jimenez Diaz University Hospital, Health Research Institute-Fundacion Jimenez Diaz, Universidad Autonoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, German
| | | | - Juliette Quilichini
- Service de Médecine Génomique des maladies de système et d'organe, APHP, Centre Université Paris Cité, Paris, France
| | - Alexia Bourgois
- Normandy University, UNICAEN, Caen University Hospital, Department of Genetics, UR 7450 BioTARGen, FHU G4 Genomics, Caen, France
| | - Nicolas Chatron
- Department of Genetics, Lyon University Hospital, Lyon, France; Pathophysiology and Genetics of Neuron and Muscle (PGNM, UCBL - CNRS UMR5261 - INSERM U1315), Université Claude Bernard Lyon 1, Lyon, France
| | - Louis Januel
- Department of Genetics, Lyon University Hospital, Lyon, France
| | | | | | | | - Justine Rousseau
- Centre de recherche Azrieli du CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada
| | - Kenneth A Myers
- Child Health and Human Development, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada.
| | - Asifa Akhtar
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| | - Philippe M Campeau
- Centre de recherche Azrieli du CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, University of Montreal, Montreal, QC H3T 1C5, Canada
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2
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Bi S, Huang L, Chen Y, Hu Z, Li S, Wang Y, Huang B, Zhang L, Huang Y, Dai B, Du L, Tu Z, Wang Y, Xu D, Xu X, Sun W, Kzhyshkowska J, Wang H, Chen D, Wang F, Zhang S. KAT8-mediated H4K16ac is essential for sustaining trophoblast self-renewal and proliferation via regulating CDX2. Nat Commun 2024; 15:5602. [PMID: 38961108 PMCID: PMC11222414 DOI: 10.1038/s41467-024-49930-6] [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: 12/04/2023] [Accepted: 06/24/2024] [Indexed: 07/05/2024] Open
Abstract
Abnormal trophoblast self-renewal and differentiation during early gestation is the major cause of miscarriage, yet the underlying regulatory mechanisms remain elusive. Here, we show that trophoblast specific deletion of Kat8, a MYST family histone acetyltransferase, leads to extraembryonic ectoderm abnormalities and embryonic lethality. Employing RNA-seq and CUT&Tag analyses on trophoblast stem cells (TSCs), we further discover that KAT8 regulates the transcriptional activation of the trophoblast stemness marker, CDX2, via acetylating H4K16. Remarkably, CDX2 overexpression partially rescues the defects arising from Kat8 knockout. Moreover, increasing H4K16ac via using deacetylase SIRT1 inhibitor, EX527, restores CDX2 levels and promoted placental development. Clinical analysis shows reduced KAT8, CDX2 and H4K16ac expression are associated with recurrent pregnancy loss (RPL). Trophoblast organoids derived from these patients exhibit impaired TSC self-renewal and growth, which are significantly ameliorated with EX527 treatment. These findings suggest the therapeutic potential of targeting the KAT8-H4K16ac-CDX2 axis for mitigating RPL, shedding light on early gestational abnormalities.
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Affiliation(s)
- Shilei Bi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Lijun Huang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Yongjie Chen
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University. Beijing Maternal and Child Health Care Hospital, Beijing, 100026, China
| | - Zhenhua Hu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Shanze Li
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Yifan Wang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Baoying Huang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Lizi Zhang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Yuanyuan Huang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Beibei Dai
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Lili Du
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Zhaowei Tu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Yijing Wang
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Dan Xu
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Xiaotong Xu
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Wen Sun
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Julia Kzhyshkowska
- Institute of Transfusion Medicine and Immunology, Mannheim Institute of Innate Immunosciences (MI3), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
- German Red Cross Blood Service Baden-Württemberg-Hessen, 68167, Mannheim, Germany
- Laboratory of Translational Cellular and Molecular Biomedicine, National Research Tomsk State University, Tomsk, Russia
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361102, China.
| | - Dunjin Chen
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Fengchao Wang
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China.
| | - Shuang Zhang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
- Guangdong-Hong Kong-Macao Great Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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Yoo L, Mendoza D, Richard AJ, Stephens JM. KAT8 beyond Acetylation: A Survey of Its Epigenetic Regulation, Genetic Variability, and Implications for Human Health. Genes (Basel) 2024; 15:639. [PMID: 38790268 PMCID: PMC11121512 DOI: 10.3390/genes15050639] [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: 04/20/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Lysine acetyltransferase 8, also known as KAT8, is an enzyme involved in epigenetic regulation, primarily recognized for its ability to modulate histone acetylation. This review presents an overview of KAT8, emphasizing its biological functions, which impact many cellular processes and range from chromatin remodeling to genetic and epigenetic regulation. In many model systems, KAT8's acetylation of histone H4 lysine 16 (H4K16) is critical for chromatin structure modification, which influences gene expression, cell proliferation, differentiation, and apoptosis. Furthermore, this review summarizes the observed genetic variability within the KAT8 gene, underscoring the implications of various single nucleotide polymorphisms (SNPs) that affect its functional efficacy and are linked to diverse phenotypic outcomes, ranging from metabolic traits to neurological disorders. Advanced insights into the structural biology of KAT8 reveal its interaction with multiprotein assemblies, such as the male-specific lethal (MSL) and non-specific lethal (NSL) complexes, which regulate a wide range of transcriptional activities and developmental functions. Additionally, this review focuses on KAT8's roles in cellular homeostasis, stem cell identity, DNA damage repair, and immune response, highlighting its potential as a therapeutic target. The implications of KAT8 in health and disease, as evidenced by recent studies, affirm its importance in cellular physiology and human pathology.
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Affiliation(s)
- Lindsey Yoo
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - David Mendoza
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Allison J. Richard
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
| | - Jacqueline M. Stephens
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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Salzler HR, Vandadi V, Matera AG. Set2 and H3K36 regulate the Drosophila male X chromosome in a context-specific manner, independent from MSL complex spreading. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592390. [PMID: 38766267 PMCID: PMC11100620 DOI: 10.1101/2024.05.03.592390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Dosage compensation in Drosophila involves upregulating male X-genes two-fold. This process is carried out by the MSL (male-specific lethal) complex, which binds high-affinity sites and spreads to surrounding genes. Current models of MSL spreading focus on interactions of MSL3 (male-specific lethal 3) with histone marks; in particular, Set2-dependent H3 lysine-36 trimethylation (H3K36me3). However, Set2 might affect DC via another target, or there could be redundancy between canonical H3.2 and variant H3.3 histones. Further, it is difficult to parse male-specific effects from those that are simply X-specific. To discriminate among these possibilities, we employed genomic approaches in H3K36 (residue) and Set2 (writer) mutants. The results confirm a role for Set2 in X-gene regulation, but show that expression trends in males are often mirrored in females. Instead of global male-specific reduction of X-genes in Set2/H3K36 mutants, the effects were heterogeneous. We identified cohorts of genes whose expression was significantly altered following loss of H3K36 or Set2, but the changes were in opposite directions, suggesting that H3K36me states have reciprocal functions. In contrast to H4K16R controls, analysis of combined H3.2K36R/H3.3K36R mutants neither showed consistent reduction in X-gene expression, nor any correlation with MSL3 binding. Examination of other developmental stages/tissues revealed additional layers of context-dependence. Our studies implicate BEAF-32 and other insulator proteins in Set2/H3K36-dependent regulation. Overall, the data are inconsistent with the prevailing model wherein H3K36me3 directly recruits the MSL complex. We propose that Set2 and H3K36 support DC indirectly, via processes that are utilized by MSL but common to both sexes.
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Affiliation(s)
- Harmony R. Salzler
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Vasudha Vandadi
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - A. Gregory Matera
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- RNA Discovery and Lineberger Comprehensive Cancer Centers, University of North Carolina, Chapel Hill, NC, USA
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5
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Jalloh B, Lancaster CL, Rounds JC, Brown BE, Leung SW, Banerjee A, Morton DJ, Bienkowski RS, Fasken MB, Kremsky IJ, Tegowski M, Meyer K, Corbett A, Moberg K. The Drosophila Nab2 RNA binding protein inhibits m 6A methylation and male-specific splicing of Sex lethal transcript in female neuronal tissue. eLife 2023; 12:e64904. [PMID: 37458420 PMCID: PMC10351920 DOI: 10.7554/elife.64904] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 06/23/2023] [Indexed: 07/20/2023] Open
Abstract
The Drosophila polyadenosine RNA binding protein Nab2, which is orthologous to a human protein lost in a form of inherited intellectual disability, controls adult locomotion, axon projection, dendritic arborization, and memory through a largely undefined set of target RNAs. Here, we show a specific role for Nab2 in regulating splicing of ~150 exons/introns in the head transcriptome and focus on retention of a male-specific exon in the sex determination factor Sex-lethal (Sxl) that is enriched in female neurons. Previous studies have revealed that this splicing event is regulated in females by N6-methyladenosine (m6A) modification by the Mettl3 complex. At a molecular level, Nab2 associates with Sxl pre-mRNA in neurons and limits Sxl m6A methylation at specific sites. In parallel, reducing expression of the Mettl3, Mettl3 complex components, or the m6A reader Ythdc1 rescues mutant phenotypes in Nab2 flies. Overall, these data identify Nab2 as an inhibitor of m6A methylation and imply significant overlap between Nab2 and Mettl3 regulated RNAs in neuronal tissue.
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Affiliation(s)
- Binta Jalloh
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Carly L Lancaster
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory UniversityAtlantaUnited States
| | - J Christopher Rounds
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Brianna E Brown
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
| | - Sara W Leung
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Ayan Banerjee
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Derrick J Morton
- Department of Biology, Emory UniversityAtlantaUnited States
- Emory Institutional Research and Academic Career Development Award (IRACDA), Fellowships in Research and Science Teaching (FIRST) Postdoctoral FellowshipAtlantaUnited States
| | - Rick S Bienkowski
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Milo B Fasken
- Department of Biology, Emory UniversityAtlantaUnited States
| | | | - Matthew Tegowski
- Department of Biochemistry, Duke University School of MedicineDurhamUnited States
| | - Kate Meyer
- Department of Biochemistry, Duke University School of MedicineDurhamUnited States
- Department of Neurobiology, Duke University School of MedicineDurhamUnited States
| | - Anita Corbett
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Ken Moberg
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
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6
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Wu T, Zhao B, Cai C, Chen Y, Miao Y, Chu J, Sui Y, Li F, Chen W, Cai Y, Wang F, Jin J. The Males Absent on the First (MOF) Mediated Acetylation Alters the Protein Stability and Transcriptional Activity of YY1 in HCT116 Cells. Int J Mol Sci 2023; 24:ijms24108719. [PMID: 37240065 DOI: 10.3390/ijms24108719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Yin Yang 1 (YY1) is a well-known transcription factor that controls the expression of many genes and plays an important role in the occurrence and development of various cancers. We previously found that the human males absent on the first (MOF)-containing histone acetyltransferase (HAT) complex may be involved in regulating YY1 transcriptional activity; however, the precise interaction between MOF-HAT and YY1, as well as whether the acetylation activity of MOF impacts the function of YY1, has not been reported. Here, we present evidence that the MOF-containing male-specific lethal (MSL) HAT complex regulates YY1 stability and transcriptional activity in an acetylation-dependent manner. First, the MOF/MSL HAT complex was bound to and acetylated YY1, and this acetylation further promoted the ubiquitin-proteasome degradation pathway of YY1. The MOF-mediated degradation of YY1 was mainly related to the 146-270 amino acid residues of YY1. Further research clarified that acetylation-mediated ubiquitin degradation of YY1 mainly occurred through lysine 183. A mutation at the YY1K183 site was sufficient to alter the expression level of p53-mediated downstream target genes, such as CDKN1A (encoding p21), and it also suppressed the transactivation of YY1 on CDC6. Furthermore, a YY1K183R mutant and MOF remarkably antagonized the clone-forming ability of HCT116 and SW480 cells facilitated by YY1, suggesting that the acetylation-ubiquitin mode of YY1 plays an important role in tumor cell proliferation. These data may provide new strategies for the development of therapeutic drugs for tumors with high expression of YY1.
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Affiliation(s)
- Tingting Wu
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Bingxin Zhao
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Chengyu Cai
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yuyang Chen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yujuan Miao
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Jinmeng Chu
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yi Sui
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Fuqiang Li
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Wenqi Chen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yong Cai
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Fei Wang
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Jingji Jin
- School of Life Sciences, Jilin University, Changchun 130012, China
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7
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Laslo M, Just J, Angelini DR. Theme and variation in the evolution of insect sex determination. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:162-181. [PMID: 35239250 PMCID: PMC10078687 DOI: 10.1002/jez.b.23125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 11/24/2021] [Accepted: 01/03/2022] [Indexed: 11/07/2022]
Abstract
The development of dimorphic adult sexes is a critical process for most animals, one that is subject to intense selection. Work in vertebrate and insect model species has revealed that sex determination mechanisms vary widely among animal groups. However, this variation is not uniform, with a limited number of conserved factors. Therefore, sex determination offers an excellent context to consider themes and variations in gene network evolution. Here we review the literature describing sex determination in diverse insects. We have screened public genomic sequence databases for orthologs and duplicates of 25 genes involved in insect sex determination, identifying patterns of presence and absence. These genes and a 3.5 reference set of 43 others were used to infer phylogenies and compared to accepted organismal relationships to examine patterns of congruence and divergence. The function of candidate genes for roles in sex determination (virilizer, female-lethal-2-d, transformer-2) and sex chromosome dosage compensation (male specific lethal-1, msl-2, msl-3) were tested using RNA interference in the milkweed bug, Oncopeltus fasciatus. None of these candidate genes exhibited conserved roles in these processes. Amidst this variation we wish to highlight the following themes for the evolution of sex determination: (1) Unique features within taxa influence network evolution. (2) Their position in the network influences a component's evolution. Our analyses also suggest an inverse association of protein sequence conservation with functional conservation.
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Affiliation(s)
- Mara Laslo
- Department of Cell Biology, Curriculum Fellows ProgramHarvard Medical School25 Shattuck StBostonMassachusettsUSA
| | - Josefine Just
- Department of Organismic and Evolutionary BiologyHarvard University26 Oxford StCambridgeMassachusettsUSA
- Department of BiologyColby College5734 Mayflower Hill DrWatervilleMaineUSA
| | - David R. Angelini
- Department of BiologyColby College5734 Mayflower Hill DrWatervilleMaineUSA
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8
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Nikolenko JV, Georgieva SG, Kopytova DV. Diversity of MLE Helicase Functions in the Regulation of Gene Expression in Higher Eukaryotes. Mol Biol 2023. [DOI: 10.1134/s0026893323010107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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9
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Su J, Zhang Y, Su H, Wang C, Wang D, Yang Y, Li X, Qi W, Li H, Li X, Song Y, Cao G. Dosage Compensation of the X Chromosome during Sheep Testis Development Revealed by Single-Cell RNA Sequencing. Animals (Basel) 2022; 12:ani12172169. [PMID: 36077890 PMCID: PMC9454834 DOI: 10.3390/ani12172169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/09/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Male and female mammals carry the same complement of autosomes but differ with respect to their sex chromosomes: females carry XX chromosomes and males carry XY chromosomes. The evolutionary loss of genes from the Y chromosome led to a disparity in the dosage of X chromosomes versus autosomal genes, with males becoming monosomic for X-linked gene products. An imbalance in gene expression may have detrimental consequences. In males, X-linked genes need to be upregulated to levels equal to those of females, which is called dosage compensation. The existence of dosage compensation in germ cells is controversial. In testis, dosage compensation is thought to cease during meiosis. Some studies showed that the X chromosome is inactivated during meiosis and premature transcriptional inactivation of the X and Y chromosome during mid-spermatogenesis is essential for fertility. However, some studies failed to find support for male germline X inactivation. Using single-cell RNA seq data, in this study, we presented a comprehensive transcriptional map of sheep testes at different developmental stages and found that germ cell types in sheep testes show X-chromosome expression similar to that in the autosomes. The dosage compensation of germ cells at different stages was analyzed. MSL complex members are expressed in female flies and orthologs exist in many species, where dosage compensation mechanisms are absent or fundamentally different. This suggests that the MSL complex members also function outside of the dosage compensation machinery. Studies have shown that MSL complex can regulate mammalian X inactivation and activation. Abstract Dosage compensation is a mechanism first proposed by Susumu Ohno, whereby X inactivation balances X gene output between males (XY) and females (XX), while X upregulation balances X genes with autosomal gene output. These mechanisms have been actively studied in Drosophila and mice, but research regarding them lags behind in domestic species. It is unclear how the X chromosome is regulated in the sheep male germline. To address this, using single-cell RNA sequencing, we analyzed testes in three important developmental stages of sheep. We observed that the total RNA per cell from X and autosomes peaked in SSCs and spermatogonia and was then reduced in early spermatocytes. Furthermore, we counted the detected reads per gene in each cell type for X and autosomes. In cells experiencing dose compensation, close proximity to MSL (male-specific lethal), which is regulated the active X chromosome and was observed. Our results suggest that there is no dose compensation in the pre-meiotic germ cells of sheep testes and, in addition, MSL1 and MSL2 are expressed in early germ cells and involved in regulating mammalian X-chromosome inactivation and activation.
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Affiliation(s)
- Jie Su
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
- Department of Psychosomatic Medicine, Inner Mongolia Medical University, Hohhot 010030, China
| | - Yue Zhang
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
| | - Hong Su
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
| | - Caiyun Wang
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
| | - Daqing Wang
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
| | - Yanyan Yang
- Inner Mongolia Academy of Agriculture & Animal Husbandry Sciences, Hohhot 010000, China
| | - Xiunan Li
- Inner Mongolia Academy of Agriculture & Animal Husbandry Sciences, Hohhot 010000, China
| | - Wangmei Qi
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
| | - Haijun Li
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
| | - Xihe Li
- Inner Mongolia Saikexing Institutes of Breeding and Reproductive Biotechnologies in Domestic Animal, Hohhot 011517, China
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Science, Inner Mongolia University, Hohhot 010021, China
| | - Yongli Song
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Science, Inner Mongolia University, Hohhot 010021, China
- Correspondence: (Y.S.); (G.C.); Tel.: +86-133-6601-7565 (Y.S.); +86-138-4812-0488 (G.C.)
| | - Guifang Cao
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
- Correspondence: (Y.S.); (G.C.); Tel.: +86-133-6601-7565 (Y.S.); +86-138-4812-0488 (G.C.)
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10
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Wei T, Liu H, Zhu H, Chen W, Wu T, Bai Y, Zhang X, Miao Y, Wang F, Cai Y, Jin J. Two distinct males absent on the first (MOF)-containing histone acetyltransferases are involved in the epithelial-mesenchymal transition in different ways in human cells. Cell Mol Life Sci 2022; 79:238. [PMID: 35416545 PMCID: PMC11073432 DOI: 10.1007/s00018-022-04258-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/02/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022]
Abstract
Human males absent on the first (MOF), a histone acetyltransferase (HAT), forms male-specific lethal (MSL) and non-specific lethal (NSL), two multiprotein HATs, in cells. MSL was originally discovered in dosage compensation study in Drosophila that can specifically acetylate H4K16, while NSL can simultaneously catalyze the H4 at K5, K8, and K16 sites. However, comparative studies of the two HATs in regulating specific biological functions are rarely reported. Here, we present evidence to argue that MSL and NSL function in different ways in the epithelial-to-mesenchymal transition (EMT) process. At first, CRISPR/Cas9-mediated MSL1 (a key subunit of the MSL)-knockout (KO) and NSL3 (a key subunit of the NSL)-KO cells seem to prefer to grow in clusters. Interestingly, the former promotes cell survival and clonal formation, while the latter has the opposite effect on it. Cell staining revealed that MSL1-KO leads to multipolarized spindles, while NSL3-KO causes more lumen-like cells. Furthermore, in Transwell experiments, silencing of MSL1 promotes cell invasion in 293 T, MCF-7, and MDA-MB-231 cells. In contrast, the inhibitory effects on cell invasion are observed in the same NSL3-silenced cells. Consistent with this, mesenchymal biomarkers, like N-cadherin, vimentin, and snail, are negatively correlated with the expression level of MSL1; however, a positive relationship between these proteins and NSL3 in cells has been found. Further studies have clarified that MSL1, but not NSL3, can specifically bind to the E-box-containing Snail promoter region and thereby negatively regulate Snail transactivation. Also, silencing of MSL1 promotes the lung metastasis of B16F10 melanoma cells in mice. Finally, ChIP-Seq analysis indicated that the NSL may be mainly involved in phosphoinositide-mediated signaling pathways. Taken together, the MOF-containing MSL and NSL HATs may regulate the EMT process in different ways in order to respond to different stimuli.
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Affiliation(s)
- Tao Wei
- School of Life Sciences, Jilin University, Changchun, 130012, China
- School of Basic Medicine, Mudanjiang Medical University, Mudanjiang, 157000, China
| | - Hongsen Liu
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Huihui Zhu
- School of Life Sciences, Jilin University, Changchun, 130012, China
- School of Basic Medicine, Mudanjiang Medical University, Mudanjiang, 157000, China
| | - Wenqi Chen
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Tingting Wu
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Yuerong Bai
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Xueyan Zhang
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Yujuan Miao
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Fei Wang
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Yong Cai
- School of Life Sciences, Jilin University, Changchun, 130012, China.
- National Engineering Laboratory for AIDS Vaccine, The Ministry of Education, Jilin University, Changchun, 130012, China.
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, Jilin University, Changchun, 130012, China.
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117, China.
| | - Jingji Jin
- School of Life Sciences, Jilin University, Changchun, 130012, China.
- National Engineering Laboratory for AIDS Vaccine, The Ministry of Education, Jilin University, Changchun, 130012, China.
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117, China.
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11
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Kunisky AK, Anyaeche VI, Herron RS, Park CY, Hwang HW. Shift in MSL1 alternative polyadenylation in response to DNA damage protects cancer cells from chemotherapeutic agent-induced apoptosis. Cell Rep 2021; 37:109815. [PMID: 34644577 PMCID: PMC8580136 DOI: 10.1016/j.celrep.2021.109815] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 07/26/2021] [Accepted: 09/17/2021] [Indexed: 12/13/2022] Open
Abstract
DNA damage reshapes the cellular transcriptome by modulating RNA transcription and processing. In cancer cells, these changes can alter the expression of genes in the immune surveillance and cell death pathways. Here, we investigate how DNA damage impacts alternative polyadenylation (APA) using the PAPERCLIP technique. We find that APA shifts are a coordinated response for hundreds of genes to DNA damage, and we identify PCF11 as an important contributor of DNA damage-induced APA shifts. One of these APA shifts results in upregulation of the full-length MSL1 mRNA isoform, which protects cells from DNA damage-induced apoptosis and promotes cell survival from DNA-damaging agents. Importantly, blocking MSL1 upregulation enhances cytotoxicity of chemotherapeutic agents even in the absence of p53 and overcomes chemoresistance. Our study demonstrates that characterizing adaptive APA shifts to DNA damage has therapeutic implications and reveals a link between PCF11, the MSL complex, and DNA damage-induced apoptosis. Kunisky et al. use PAPERCLIP profiling to identify a DNA damage-induced shift in mRNA alternative polyadenylation in the MSL1 gene. Blocking this response promotes apoptosis and amplifies the cytotoxic effects of DNA-damaging chemotherapeutic agents in cancer cells.
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Affiliation(s)
- Alexander K Kunisky
- Department of Pathology, University of Pittsburgh, School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Vivian I Anyaeche
- Department of Pathology, University of Pittsburgh, School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - R Samuel Herron
- Department of Pathology, University of Pittsburgh, School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Christopher Y Park
- Flatiron Institute, Simons Foundation, 162 Fifth Avenue, New York, NY 10010, USA
| | - Hun-Way Hwang
- Department of Pathology, University of Pittsburgh, School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15261, USA.
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12
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Interaction of Male Specific Lethal complex and genomic imbalance on global gene expression in Drosophila. Sci Rep 2021; 11:19679. [PMID: 34608252 PMCID: PMC8490464 DOI: 10.1038/s41598-021-99268-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/20/2021] [Indexed: 02/04/2023] Open
Abstract
The inverse dosage effect caused by chromosome number variations shows global consequences in genomic imbalance including sexual dimorphism and an X chromosome-specific response. To investigate the relationship of the MSL complex to genomic imbalance, we over-expressed MSL2 in autosomal and sex chromosomal aneuploids, and analyzed the different transcriptomes. Some candidate genes involved in regulatory mechanisms have also been tested during embryogenesis using TSA-FISH. Here we show that the de novo MSL complex assembled on the X chromosomes in females further reduced the global expression level on the basis of 2/3 down-regulation caused by the inverse dosage effect in trisomy through epigenetic modulations rather than induced dosage compensation. Plus, the sexual dimorphism effect in unbalanced genomes was further examined due to the pre-existing of the MSL complex in males. All these results demonstrate the dynamic functions of the MSL complex on global gene expression in different aneuploid genomes.
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13
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Keller Valsecchi CI, Marois E, Basilicata MF, Georgiev P, Akhtar A. Distinct mechanisms mediate X chromosome dosage compensation in Anopheles and Drosophila. Life Sci Alliance 2021; 4:4/9/e202000996. [PMID: 34266874 PMCID: PMC8321682 DOI: 10.26508/lsa.202000996] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 12/14/2022] Open
Abstract
CRISPR knockout of msl-2 and epigenome analyses in Anopheles reveal that X chromosome dosage compensation in mosquitos and Drosophila is achieved by two different molecular mechanisms. Sex chromosomes induce potentially deleterious gene expression imbalances that are frequently corrected by dosage compensation (DC). Three distinct molecular strategies to achieve DC have been previously described in nematodes, fruit flies, and mammals. Is this a consequence of distinct genomes, functional or ecological constraints, or random initial commitment to an evolutionary trajectory? Here, we study DC in the malaria mosquito Anopheles gambiae. The Anopheles and Drosophila X chromosomes evolved independently but share a high degree of homology. We find that Anopheles achieves DC by a mechanism distinct from the Drosophila MSL complex–histone H4 lysine 16 acetylation pathway. CRISPR knockout of Anopheles msl-2 leads to embryonic lethality in both sexes. Transcriptome analyses indicate that this phenotype is not a consequence of defective X chromosome DC. By immunofluorescence and ChIP, H4K16ac does not preferentially enrich on the male X. Instead, the mosquito MSL pathway regulates conserved developmental genes. We conclude that a novel mechanism confers X chromosome up-regulation in Anopheles. Our findings highlight the pluralism of gene-dosage buffering mechanisms even under similar genomic and functional constraints.
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Affiliation(s)
| | - Eric Marois
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS) UPR9022, Inserm U1257, Strasbourg, France
| | - M Felicia Basilicata
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Institute of Molecular Biology (IMB), Mainz, Germany
| | - Plamen Georgiev
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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14
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Monserrat J, Morales Torres C, Richardson L, Wilson TS, Patel H, Domart MC, Horswell S, Song OR, Jiang M, Crawford M, Bui M, Dalal Y, Scaffidi P. Disruption of the MSL complex inhibits tumour maintenance by exacerbating chromosomal instability. Nat Cell Biol 2021; 23:401-412. [PMID: 33837287 PMCID: PMC7610593 DOI: 10.1038/s41556-021-00657-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 02/26/2021] [Indexed: 02/01/2023]
Abstract
Rewiring of cellular programmes in malignant cells generates cancer-specific vulnerabilities. Here, using an unbiased screening strategy aimed at identifying non-essential genes required by tumour cells to sustain unlimited proliferative capacity, we identify the male-specific lethal (MSL) acetyltransferase complex as a vulnerability of genetically unstable cancers. We find that disruption of the MSL complex and consequent loss of the associated H4K16ac mark do not substantially alter transcriptional programmes but compromise chromosome integrity and promote chromosomal instability (CIN) that progressively exhausts the proliferative potential of cancer cells through a p53-independent mechanism. This effect is dependent on pre-existing genomic instability, and normal cells are insensitive to MSL disruption. Using cell- and patient-derived xenografts from multiple cancer types, we show that excessive CIN induced by MSL disruption inhibits tumour maintenance. Our findings suggest that targeting MSL may be a valuable means to increase CIN beyond the level tolerated by cancer cells without inducing severe adverse effects in normal tissues.
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Affiliation(s)
- Josep Monserrat
- Cancer Epigenetics Laboratory, Francis Crick Institute, London, UK
| | | | | | | | - Harshil Patel
- Bioinformatics and Biostatistics, Francis Crick Institute, London, UK
| | | | - Stuart Horswell
- Bioinformatics and Biostatistics, Francis Crick Institute, London, UK
| | - Ok-Ryul Song
- High Throughput Screening, Francis Crick Institute, London, UK
| | - Ming Jiang
- High Throughput Screening, Francis Crick Institute, London, UK
| | | | - Minh Bui
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yamini Dalal
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paola Scaffidi
- Cancer Epigenetics Laboratory, Francis Crick Institute, London, UK.
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15
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Burrell JA, Stephens JM. KAT8, lysine acetyltransferase 8, is required for adipocyte differentiation in vitro. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166103. [PMID: 33617987 DOI: 10.1016/j.bbadis.2021.166103] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 02/07/2021] [Accepted: 02/16/2021] [Indexed: 10/22/2022]
Abstract
KAT8 is a lysine acetyltransferase (KAT) that plays a role in a variety of cellular functions ranging from DNA damage repair to apoptosis. The role of KAT8 in adipocyte development and function has not been studied. Notably, a large genome-wide association study identified KAT8 as part of a novel locus that significantly contributed to body mass index and other metabolic phenotypes. Hence, we examined the expression and regulation of KAT8 during adipocyte development. KAT8 mRNA and protein levels were examined over a time course of adipocyte development, and KAT8 was found to be present in both the cytosol and nucleus of 3T3-L1 adipocytes. Although KAT8 expression was not highly regulated by adipogenesis, its expression was required for the adipogenesis of 3T3-L1 cells. Loss of KAT8 expression in preadipocytes inhibited their ability to differentiate as judged by both lipid accumulation and adipocyte marker gene expression. However, if KAT8 was knocked down after clonal expansion, its absence did not inhibit adipocyte differentiation. Also, loss of KAT8 in adipocytes did not impact lipid accumulation or the expression of adiponectin or other fat markers. Although our data demonstrate that KAT8 is required for adipocyte differentiation, further studies are necessary to determine the functions and regulation of KAT8 in adipose tissue.
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Affiliation(s)
- Jasmine A Burrell
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States of America
| | - Jacqueline M Stephens
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, United States of America; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States of America.
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16
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Brunet T, McWalter K, Mayerhanser K, Anbouba GM, Armstrong-Javors A, Bader I, Baugh E, Begtrup A, Bupp CP, Callewaert BL, Cereda A, Cousin MA, Del Rey Jimenez JC, Demmer L, Dsouza NR, Fleischer N, Gavrilova RH, Ghate S, Graf E, Green A, Green SR, Iascone M, Kdissa A, Klee D, Klee EW, Lancaster E, Lindstrom K, Mayr JA, McEntagart M, Meeks NJL, Mittag D, Moore H, Olsen AK, Ortiz D, Parsons G, Pena LDM, Person RE, Punj S, Ramos-Rivera GA, Sacoto MJG, Bradley Schaefer G, Schnur RE, Scott TM, Scott DA, Serbinski CR, Shashi V, Siu VM, Stadheim BF, Sullivan JA, Švantnerová J, Velsher L, Wargowski DS, Wentzensen IM, Wieczorek D, Winkelmann J, Yap P, Zech M, Zimmermann MT, Meitinger T, Distelmaier F, Wagner M. Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder. Genet Med 2020; 23:384-395. [PMID: 33173220 PMCID: PMC7862064 DOI: 10.1038/s41436-020-00993-y] [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: 06/16/2020] [Accepted: 09/23/2020] [Indexed: 12/01/2022] Open
Abstract
Purpose We sought to delineate the genotypic and phenotypic spectrum of female and male individuals with X-linked, MSL3-related disorder (Basilicata–Akhtar syndrome). Methods Twenty-five individuals (15 males, 10 females) with causative variants in MSL3 were ascertained through exome or genome sequencing at ten different sequencing centers. Results We identified multiple variant types in MSL3 (ten nonsense, six frameshift, four splice site, three missense, one in-frame-deletion, one multi-exon deletion), most proven to be de novo, and clustering in the terminal eight exons suggesting that truncating variants in the first five exons might be compensated by an alternative MSL3 transcript. Three-dimensional modeling of missense and splice variants indicated that these have a deleterious effect. The main clinical findings comprised developmental delay and intellectual disability ranging from mild to severe. Autism spectrum disorder, muscle tone abnormalities, and macrocephaly were common as well as hearing impairment and gastrointestinal problems. Hypoplasia of the cerebellar vermis emerged as a consistent magnetic resonance image (MRI) finding. Females and males were equally affected. Using facial analysis technology, a recognizable facial gestalt was determined. Conclusion Our aggregated data illustrate the genotypic and phenotypic spectrum of X-linked, MSL3-related disorder (Basilicata–Akhtar syndrome). Our cohort improves the understanding of disease related morbidity and allows us to propose detailed surveillance guidelines for affected individuals.
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Affiliation(s)
- Theresa Brunet
- Institute of Human Genetics, Technical University Munich, Munich, Germany.
| | | | | | - Grace M Anbouba
- Division of Genetics and Metabolism, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Amy Armstrong-Javors
- Department of Pediatric Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Ingrid Bader
- Department of Clinical Genetics, University Children's Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Evan Baugh
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | | | - Caleb P Bupp
- Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, MI, USA.,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Bert L Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Anna Cereda
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Laurie Demmer
- Medical Genetics, Atrium Health Levine Children's Hospital, Charlotte, NC, USA
| | - Nikita R Dsouza
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Ralitza H Gavrilova
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Sumedha Ghate
- St Vincent Hospital Medical Genetics Clinic, Green Bay, WI, USA
| | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Andrew Green
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Sarah R Green
- University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Springdale, AR, USA
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | | | - Dirk Klee
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Emily Lancaster
- UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kristin Lindstrom
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Johannes A Mayr
- Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University, Salzburg, Austria
| | - Meriel McEntagart
- Medical Genetics, St George's University Hospitals NHS FT, London, UK
| | - Naomi J L Meeks
- Department of Pediatrics, Section of Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dana Mittag
- Medical Genetics, Atrium Health Levine Children's Hospital, Charlotte, NC, USA
| | - Harrison Moore
- INTEGRIS Pediatric Specialties/Medical Genetics, Oklahoma City, OK, USA
| | - Anne K Olsen
- Department of Pediatric, Soerlandet Sykehus Kristiansand, Kristiansand, Norway
| | - Damara Ortiz
- UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Gretchen Parsons
- Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Loren D M Pena
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | | | | | | | - G Bradley Schaefer
- University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Springdale, AR, USA
| | | | - Tiana M Scott
- Texas Children's Hospital, Houston, TX, USA.,Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Daryl A Scott
- Texas Children's Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Carolyn R Serbinski
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - Victoria M Siu
- Department of Pediatrics, Western University, London, ON, Canada
| | | | - Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - Jana Švantnerová
- Second Department of Neurology, Faculty of Medicine, Comenius University, University Hospital Bratislava, Bratislava, Slovakia
| | - Lea Velsher
- Genetics Program, North York General Hospital, Toronto, ON, Canada
| | - David S Wargowski
- Division of Genetics and Metabolism, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,St Vincent Hospital Medical Genetics Clinic, Green Bay, WI, USA
| | | | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, Technical University Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,Neurogenetics, Technische Universität München, Munich, Germany
| | - Patrick Yap
- Genetic Health Service New Zealand (Northern Hub), Auckland, New Zealand.,Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Michael Zech
- Institute of Human Genetics, Technical University Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Thomas Meitinger
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Matias Wagner
- Institute of Human Genetics, Technical University Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
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17
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Dor L, Shirak A, Curzon AY, Rosenfeld H, Ashkenazi IM, Nixon O, Seroussi E, Weller JI, Ron M. Preferential Mapping of Sex-Biased Differentially-Expressed Genes of Larvae to the Sex-Determining Region of Flathead Grey Mullet ( Mugil cephalus). Front Genet 2020; 11:839. [PMID: 32973865 PMCID: PMC7472742 DOI: 10.3389/fgene.2020.00839] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/10/2020] [Indexed: 12/23/2022] Open
Abstract
Flathead gray mullet (Mugil cephalus) is a cosmopolitan mugilid species popular in fishery and aquaculture with an economic preference for all-female population. However, it displays neither sexual dimorphisms nor heteromorphic sex chromosomes. We have previously presented a microsatellite-based linkage map for this species locating a single sex determination region (SDR) on linkage group 9 (LG9) with evidence for XX/XY sex determination (SD) mechanism. In this work, we refine the critical SDR on LG9, and propose positional- and functional- candidate genes for SD. To elucidate the genetic mechanism of SD, we assembled and compared male and female genomic sequences of 19 syntenic genes within the putative SDR on mullet's LG9, based on orthology to tilapia's LG8 (tLG8) physical map. A total of 25 sequence-based markers in 12 genes were developed. For all markers, we observed association with sex in at least one of the two analyzed M. cephalus full-sib families, but not in the wild-type population. Recombination events were inferred within families thus setting the SDR boundaries to a region orthologous to ∼0.9 Mbp with 27 genes on tLG8. As the sexual phenotype is evident only in adults, larvae were assigned into two putative sex-groups according to their paternal haplotypes, following a model of XY/XX SD-system. A total of 107 sex-biased differentially expressed genes in larvae were observed, of which 51 were mapped to tLG8 (48% enrichment), as compared to 5% in random control. Furthermore, 23 of the 107 genes displayed sex-specific expression; and 22 of these genes were positioned to tLG8, indicating 96% enrichment. Of the 27 SDR genes, BCCIP, DHX32A, DOCK1, and FSHR (GTH-RI) are suggested as positional and functional gene candidates for SD.
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Affiliation(s)
- Lior Dor
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan, Israel
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Andrey Shirak
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Arie Y. Curzon
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan, Israel
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Hana Rosenfeld
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat, Israel
| | - Iris M. Ashkenazi
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat, Israel
| | - Oriya Nixon
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat, Israel
| | - Eyal Seroussi
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan, Israel
| | - Joel I. Weller
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan, Israel
| | - Micha Ron
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan, Israel
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18
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Pal K, Forcato M, Jost D, Sexton T, Vaillant C, Salviato E, Mazza EMC, Lugli E, Cavalli G, Ferrari F. Global chromatin conformation differences in the Drosophila dosage compensated chromosome X. Nat Commun 2019; 10:5355. [PMID: 31767860 PMCID: PMC6877619 DOI: 10.1038/s41467-019-13350-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/01/2019] [Indexed: 01/08/2023] Open
Abstract
In Drosophila melanogaster the single male chromosome X undergoes an average twofold transcriptional upregulation for balancing the transcriptional output between sexes. Previous literature hypothesised that a global change in chromosome structure may accompany this process. However, recent studies based on Hi-C failed to detect these differences. Here we show that global conformational differences are specifically present in the male chromosome X and detectable using Hi-C data on sex-sorted embryos, as well as male and female cell lines, by leveraging custom data analysis solutions. We find the male chromosome X has more mid-/long-range interactions. We also identify differences at structural domain boundaries containing BEAF-32 in conjunction with CP190 or Chromator. Weakening of these domain boundaries in male chromosome X co-localizes with the binding of the dosage compensation complex and its co-factor CLAMP, reported to enhance chromatin accessibility. Together, our data strongly indicate that chromosome X dosage compensation affects global chromosome structure.
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Affiliation(s)
- Koustav Pal
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 287, 41125, Modena, Italy
| | - Daniel Jost
- University of Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
- Laboratory of Biology and Modelling of the Cell, University of Lyon, ENS de Lyon, University of Claude Bernard, CNRS UMR 5239, Inserm U1210, F-69007, Lyon, France
| | - Thomas Sexton
- IGH, Institute of Human Genetics, CNRS UPR1142, 141 rue de la Cardonille, 34090, Montpellier, France
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch, France
| | - Cédric Vaillant
- University of Lyon, ENS de Lyon, University of Claude Bernard, CNRS, Laboratoire de Physique, 46 allée d'Italie, 69007, Lyon, France
| | - Elisa Salviato
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Emilia Maria Cristina Mazza
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, Via A. Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Enrico Lugli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, Via A. Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Giacomo Cavalli
- IGH, Institute of Human Genetics, CNRS UPR1142, 141 rue de la Cardonille, 34090, Montpellier, France
| | - Francesco Ferrari
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy.
- Institute of Molecular Genetics, National Research Council, Via Abbiategrasso 207, 27100, Pavia, Italy.
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19
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The NSL complex maintains nuclear architecture stability via lamin A/C acetylation. Nat Cell Biol 2019; 21:1248-1260. [PMID: 31576060 DOI: 10.1038/s41556-019-0397-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 08/21/2019] [Indexed: 12/26/2022]
Abstract
While nuclear lamina abnormalities are hallmarks of human diseases, their interplay with epigenetic regulators and precise epigenetic landscape remain poorly understood. Here, we show that loss of the lysine acetyltransferase MOF or its associated NSL-complex members KANSL2 or KANSL3 leads to a stochastic accumulation of nuclear abnormalities with genomic instability patterns including chromothripsis. SILAC-based MOF and KANSL2 acetylomes identified lamin A/C as an acetylation target of MOF. HDAC inhibition or acetylation-mimicking lamin A derivatives rescue nuclear abnormalities observed in MOF-deficient cells. Mechanistically, loss of lamin A/C acetylation resulted in its increased solubility, defective phosphorylation dynamics and impaired nuclear mechanostability. We found that nuclear abnormalities include EZH2-dependent histone H3 Lys 27 trimethylation and loss of nascent transcription. We term this altered epigenetic landscape "heterochromatin enrichment in nuclear abnormalities" (HENA). Collectively, the NSL-complex-dependent lamin A/C acetylation provides a mechanism that maintains nuclear architecture and genome integrity.
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20
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Albig C, Tikhonova E, Krause S, Maksimenko O, Regnard C, Becker PB. Factor cooperation for chromosome discrimination in Drosophila. Nucleic Acids Res 2019; 47:1706-1724. [PMID: 30541149 PMCID: PMC6393291 DOI: 10.1093/nar/gky1238] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/05/2018] [Accepted: 11/29/2018] [Indexed: 12/27/2022] Open
Abstract
Transcription regulators select their genomic binding sites from a large pool of similar, non-functional sequences. Although general principles that allow such discrimination are known, the complexity of DNA elements often precludes a prediction of functional sites. The process of dosage compensation in Drosophila allows exploring the rules underlying binding site selectivity. The male-specific-lethal (MSL) Dosage Compensation Complex (DCC) selectively binds to some 300 X chromosomal ‘High Affinity Sites’ (HAS) containing GA-rich ‘MSL recognition elements’ (MREs), but disregards thousands of other MRE sequences in the genome. The DNA-binding subunit MSL2 alone identifies a subset of MREs, but fails to recognize most MREs within HAS. The ‘Chromatin-linked adaptor for MSL proteins’ (CLAMP) also interacts with many MREs genome-wide and promotes DCC binding to HAS. Using genome-wide DNA-immunoprecipitation we describe extensive cooperativity between both factors, depending on the nature of the binding sites. These are explained by physical interaction between MSL2 and CLAMP. In vivo, both factors cooperate to compete with nucleosome formation at HAS. The male-specific MSL2 thus synergises with a ubiquitous GA-repeat binding protein for refined X/autosome discrimination.
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Affiliation(s)
- Christian Albig
- Molecular Biology Division, Biomedical Center, Faculty of Medicine and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität Munich, 82151 Martinsried, Germany.,Graduate School for Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität Munich, 81377 Munich, Germany
| | - Evgeniya Tikhonova
- Group of Molecular Organization of Genome, Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Silke Krause
- Molecular Biology Division, Biomedical Center, Faculty of Medicine and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität Munich, 82151 Martinsried, Germany
| | - Oksana Maksimenko
- Group of Molecular Organization of Genome, Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Catherine Regnard
- Molecular Biology Division, Biomedical Center, Faculty of Medicine and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität Munich, 82151 Martinsried, Germany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, Faculty of Medicine and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität Munich, 82151 Martinsried, Germany
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21
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Bhardwaj V, Semplicio G, Erdogdu NU, Manke T, Akhtar A. MAPCap allows high-resolution detection and differential expression analysis of transcription start sites. Nat Commun 2019; 10:3219. [PMID: 31363093 PMCID: PMC6667505 DOI: 10.1038/s41467-019-11115-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/20/2019] [Indexed: 01/06/2023] Open
Abstract
The position, shape and number of transcription start sites (TSS) are critical determinants of gene regulation. Most methods developed to detect TSSs and study promoter usage are, however, of limited use in studies that demand quantification of expression changes between two or more groups. In this study, we combine high-resolution detection of transcription start sites and differential expression analysis using a simplified TSS quantification protocol, MAPCap (Multiplexed Affinity Purification of Capped RNA) along with the software icetea. Applying MAPCap on developing Drosophila melanogaster embryos and larvae, we detected stage and sex-specific promoter and enhancer activity and quantify the effect of mutants of maleless (MLE) helicase at X-chromosomal promoters. We observe that MLE mutation leads to a median 1.9 fold drop in expression of X-chromosome promoters and affects the expression of several TSSs with a sexually dimorphic expression on autosomes. Our results provide quantitative insights into promoter activity during dosage compensation. The position, shape and number of transcription start sites (TSS) regulate gene expression. Here authors present MAPCap, a method for high-resolution detection and differential expression analysis of TSS, and apply MAPCap to early fly development, detecting stage and sex-specific promoter and enhancer activity.
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Affiliation(s)
- Vivek Bhardwaj
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Giuseppe Semplicio
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Niyazi Umut Erdogdu
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Thomas Manke
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany.
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22
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Sheikh BN, Guhathakurta S, Akhtar A. The non-specific lethal (NSL) complex at the crossroads of transcriptional control and cellular homeostasis. EMBO Rep 2019; 20:e47630. [PMID: 31267707 PMCID: PMC6607013 DOI: 10.15252/embr.201847630] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/10/2019] [Accepted: 03/19/2019] [Indexed: 12/14/2022] Open
Abstract
The functionality of chromatin is tightly regulated by post-translational modifications that modulate transcriptional output from target loci. Among the post-translational modifications of chromatin, reversible ε-lysine acetylation of histone proteins is prominent at transcriptionally active genes. Lysine acetylation is catalyzed by lysine acetyltransferases (KATs), which utilize the central cellular metabolite acetyl-CoA as their substrate. Among the KATs that mediate lysine acetylation, males absent on the first (MOF/KAT8) is particularly notable for its ability to acetylate histone 4 lysine 16 (H4K16ac), a modification that decompacts chromatin structure. MOF and its non-specific lethal (NSL) complex members have been shown to localize to gene promoters and enhancers in the nucleus, as well as to microtubules and mitochondria to regulate key cellular processes. Highlighting their importance, mutations or deregulation of NSL complex members has been reported in both human neurodevelopmental disorders and cancer. Based on insight gained from studies in human, mouse, and Drosophila model systems, this review discusses the role of NSL-mediated lysine acetylation in a myriad of cellular functions in both health and disease. Through these studies, the importance of the NSL complex in regulating core transcriptional and signaling networks required for normal development and cellular homeostasis is beginning to emerge.
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Affiliation(s)
- Bilal N Sheikh
- Max Planck Institute for Immunobiology and EpigeneticsFreiburg im BreisgauGermany
| | - Sukanya Guhathakurta
- Max Planck Institute for Immunobiology and EpigeneticsFreiburg im BreisgauGermany
- Faculty of BiologyAlbert Ludwig University of FreiburgFreiburgGermany
| | - Asifa Akhtar
- Max Planck Institute for Immunobiology and EpigeneticsFreiburg im BreisgauGermany
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23
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Investigating the structural features of chromodomain proteins in the human genome and predictive impacts of their mutations in cancers. Int J Biol Macromol 2019; 131:1101-1116. [PMID: 30917913 DOI: 10.1016/j.ijbiomac.2019.03.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/20/2019] [Accepted: 03/22/2019] [Indexed: 11/22/2022]
Abstract
Epigenetic readers are specific proteins which recognize histone marks and represents the underlying mechanism for chromatin regulation. Histone H3 lysine methylation is a potential epigenetic code for the chromatin organization and transcriptional control. Recognition of histone methylation is achieved by evolutionary conserved reader modules known as chromodomain, identified in several proteins, and is involved in transcriptional silencing and chromatin remodelling. Genetic perturbations within the structurally conserved chromodomain could potentially mistarget the reader protein and impair their regulatory pathways, ultimately leading to cellular chaos by setting the stage for tumor development and progression. Here, we report the structural conservations associated with diverse functions, prognostic significance and functional consequences of mutations within chromodomain of human proteins in distinct cancers. We have extensively analysed chromodomain containing human proteins in terms of their structural-functional ability to act as a molecular switch in the recognition of methyl-lysine recognition. We further investigated the combinatorial potential, target promiscuity and binding specificity associated with their underlying mechanisms. Indeed, the molecular mechanism of epigenetic silencing significantly underlies a newer cancer therapy approach. We hope that a critical understanding of chromodomains will pave the way for novel paths of research providing newer insights into the designing of effective anti-cancer therapies.
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24
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Zhang Y, Jang Y, Lee JE, Ahn J, Xu L, Holden MR, Cornett EM, Krajewski K, Klein BJ, Wang SP, Dou Y, Roeder RG, Strahl BD, Rothbart SB, Shi X, Ge K, Kutateladze TG. Selective binding of the PHD6 finger of MLL4 to histone H4K16ac links MLL4 and MOF. Nat Commun 2019; 10:2314. [PMID: 31127101 PMCID: PMC6534582 DOI: 10.1038/s41467-019-10324-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/30/2019] [Indexed: 01/01/2023] Open
Abstract
Histone methyltransferase MLL4 is centrally involved in transcriptional regulation and is often mutated in human diseases, including cancer and developmental disorders. MLL4 contains a catalytic SET domain that mono-methylates histone H3K4 and seven PHD fingers of unclear function. Here, we identify the PHD6 finger of MLL4 (MLL4-PHD6) as a selective reader of the epigenetic modification H4K16ac. The solution NMR structure of MLL4-PHD6 in complex with a H4K16ac peptide along with binding and mutational analyses reveal unique mechanistic features underlying recognition of H4K16ac. Genomic studies show that one third of MLL4 chromatin binding sites overlap with H4K16ac-enriched regions in vivo and that MLL4 occupancy in a set of genomic targets depends on the acetyltransferase activity of MOF, a H4K16ac-specific acetyltransferase. The recognition of H4K16ac is conserved in the PHD7 finger of paralogous MLL3. Together, our findings reveal a previously uncharacterized acetyllysine reader and suggest that selective targeting of H4K16ac by MLL4 provides a direct functional link between MLL4, MOF and H4K16 acetylation.
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Affiliation(s)
- Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Younghoon Jang
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA
| | - Ji-Eun Lee
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA
| | - JaeWoo Ahn
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Longxia Xu
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Michael R Holden
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Evan M Cornett
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Krzysztof Krajewski
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Shu-Ping Wang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Xiaobing Shi
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Kai Ge
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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25
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The Drosophila Dot Chromosome: Where Genes Flourish Amidst Repeats. Genetics 2019; 210:757-772. [PMID: 30401762 PMCID: PMC6218221 DOI: 10.1534/genetics.118.301146] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/17/2018] [Indexed: 11/18/2022] Open
Abstract
The F element of the Drosophila karyotype (the fourth chromosome in Drosophila melanogaster) is often referred to as the "dot chromosome" because of its appearance in a metaphase chromosome spread. This chromosome is distinct from other Drosophila autosomes in possessing both a high level of repetitious sequences (in particular, remnants of transposable elements) and a gene density similar to that found in the other chromosome arms, ∼80 genes distributed throughout its 1.3-Mb "long arm." The dot chromosome is notorious for its lack of recombination and is often neglected as a consequence. This and other features suggest that the F element is packaged as heterochromatin throughout. F element genes have distinct characteristics (e.g, low codon bias, and larger size due both to larger introns and an increased number of exons), but exhibit expression levels comparable to genes found in euchromatin. Mapping experiments show the presence of appropriate chromatin modifications for the formation of DNaseI hypersensitive sites and transcript initiation at the 5' ends of active genes, but, in most cases, high levels of heterochromatin proteins are observed over the body of these genes. These various features raise many interesting questions about the relationships of chromatin structures with gene and chromosome function. The apparent evolution of the F element as an autosome from an ancestral sex chromosome also raises intriguing questions. The findings argue that the F element is a unique chromosome that occupies its own space in the nucleus. Further study of the F element should provide new insights into chromosome structure and function.
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26
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Basilicata MF, Bruel AL, Semplicio G, Valsecchi CIK, Aktaş T, Duffourd Y, Rumpf T, Morton J, Bache I, Szymanski WG, Gilissen C, Vanakker O, Õunap K, Mittler G, van der Burgt I, El Chehadeh S, Cho MT, Pfundt R, Tan TY, Kirchhoff M, Menten B, Vergult S, Lindstrom K, Reis A, Johnson DS, Fryer A, McKay V, Fisher RB, Thauvin-Robinet C, Francis D, Roscioli T, Pajusalu S, Radtke K, Ganesh J, Brunner HG, Wilson M, Faivre L, Kalscheuer VM, Thevenon J, Akhtar A. De novo mutations in MSL3 cause an X-linked syndrome marked by impaired histone H4 lysine 16 acetylation. Nat Genet 2018; 50:1442-1451. [PMID: 30224647 DOI: 10.1038/s41588-018-0220-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 08/01/2018] [Indexed: 12/15/2022]
Abstract
The etiological spectrum of ultra-rare developmental disorders remains to be fully defined. Chromatin regulatory mechanisms maintain cellular identity and function, where misregulation may lead to developmental defects. Here, we report pathogenic variations in MSL3, which encodes a member of the chromatin-associated male-specific lethal (MSL) complex responsible for bulk histone H4 lysine 16 acetylation (H4K16ac) in flies and mammals. These variants cause an X-linked syndrome affecting both sexes. Clinical features of the syndrome include global developmental delay, progressive gait disturbance, and recognizable facial dysmorphism. MSL3 mutations affect MSL complex assembly and activity, accompanied by a pronounced loss of H4K16ac levels in vivo. Patient-derived cells display global transcriptome alterations of pathways involved in morphogenesis and cell migration. Finally, we use histone deacetylase inhibitors to rebalance acetylation levels, alleviating some of the molecular and cellular phenotypes of patient cells. Taken together, we characterize a syndrome that allowed us to decipher the developmental importance of MSL3 in humans.
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Affiliation(s)
- M Felicia Basilicata
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Ange-Line Bruel
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France
| | - Giuseppe Semplicio
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | | | - Tuğçe Aktaş
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Yannis Duffourd
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France
| | - Tobias Rumpf
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Jenny Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's Hospital NHS Foundation Trust, Birmingham, UK
| | - Iben Bache
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Witold G Szymanski
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Olivier Vanakker
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Ineke van der Burgt
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Salima El Chehadeh
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France.,Service de Génétique Médicale, Hôpital de Hautepierre, Strasbourg, France
| | | | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne Department of Paediatrics, Parkville, VIC, Australia
| | - Maria Kirchhoff
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kristin Lindstrom
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Diana S Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Alan Fryer
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Victoria McKay
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | | | - Richard B Fisher
- Northern Genetics Service, Teesside Genetics Unit, The James Cook University Hospital, Middlesbrough, UK
| | - Christel Thauvin-Robinet
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France
| | - David Francis
- Cytogenetic Laboratory, Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Tony Roscioli
- Neuroscience Research Australia, Sydney, New South Wales, Australia.,Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia.,Department of Medical Genetics, Sydney Children's Hospital, Sydney, New South Wales, Australia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Kelly Radtke
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Jaya Ganesh
- Division of Genetics, Cooper University Hospital and Cooper Medical School at Rowan University, Camden, NJ, USA
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, Disciplines of Genetic Medicine and Child and Adolescent Health, University of Sydney, Sydney, New South Wales, Australia
| | - Laurence Faivre
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Julien Thevenon
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France. .,CNRS UMR 5309, INSERM, U1209, Institute of Advanced Biosciences, Université Grenoble-Alpes CHU Grenoble, Grenoble, France.
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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27
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Facultative dosage compensation of developmental genes on autosomes in Drosophila and mouse embryonic stem cells. Nat Commun 2018; 9:3626. [PMID: 30194291 PMCID: PMC6128902 DOI: 10.1038/s41467-018-05642-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/04/2018] [Indexed: 12/25/2022] Open
Abstract
Haploinsufficiency and aneuploidy are two phenomena, where gene dosage alterations cause severe defects ultimately resulting in developmental failures and disease. One remarkable exception is the X chromosome, where copy number differences between sexes are buffered by dosage compensation systems. In Drosophila, the Male-Specific Lethal complex (MSLc) mediates upregulation of the single male X chromosome. The evolutionary origin and conservation of this process orchestrated by MSL2, the only male-specific protein within the fly MSLc, have remained unclear. Here, we report that MSL2, in addition to regulating the X chromosome, targets autosomal genes involved in patterning and morphogenesis. Precise regulation of these genes by MSL2 is required for proper development. This set of dosage-sensitive genes maintains such regulation during evolution, as MSL2 binds and similarly regulates mouse orthologues via Histone H4 lysine 16 acetylation. We propose that this gene-by-gene dosage compensation mechanism was co-opted during evolution for chromosome-wide regulation of the Drosophila male X. In Drosophila the Male-Specific Lethal complex (MSLc) mediates upregulation of the single male X chromosome. Here the authors provide evidence that MSL2 also targets autosomal genes required for proper development and that MSL2 binds and similarly regulates mouse orthologues.
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28
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Lakhotia SC. From Heterochromatin to Long Noncoding RNAs in Drosophila: Expanding the Arena of Gene Function and Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:75-118. [PMID: 28815537 DOI: 10.1007/978-981-10-5203-3_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc. There has been a rapid increase in the number of identified lncRNAs, although a much larger number still remains unknown. The diversity of modes of actions and functions of the limited number of Drosophila lncRNAs, which have been examined, already reflects the profound roles of such RNAs in generating and sustaining the biological complexities of eukaryotes. Several of the known Drosophila lncRNAs originate as independent sense or antisense transcripts from promoter or intergenic, intronic, or 5'/3'-UTR regions, while many of them are independent genes that produce only lncRNAs or coding as well as noncoding RNAs. The different lncRNAs affect chromatin organization (local or large-scale pan-chromosomal), transcription, RNA processing/stability, or translation either directly through interaction with their target DNA sequences or indirectly by acting as intermediary molecules for specific regulatory proteins or may act as decoys/sinks, or storage sites for specific proteins or groups of proteins, or may provide a structural framework for the assembly of substructures in nucleus/cytoplasm. It is interesting that many of the "functions" alluded to heterochromatin in earlier cytogenetic studies appear to find correlates with the known subtle as well as far-reaching actions of the different small and long noncoding RNAs. Further studies exploiting the very rich and powerful genetic and molecular resources available for the Drosophila model are expected to unravel the mystery underlying the long reach of ncRNAs.
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Affiliation(s)
- Subhash C Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.
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29
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Cheetham SW, Brand AH. RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites. Nat Struct Mol Biol 2017; 25:109-114. [PMID: 29323275 PMCID: PMC5813796 DOI: 10.1038/s41594-017-0006-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/09/2017] [Indexed: 02/08/2023]
Abstract
Thousands of long noncoding RNAs (lncRNAs) have been identified in eukaryotic genomes, many of which are expressed in spatially and temporally restricted patterns. Nonetheless, the roles of the majority of these transcripts are still unknown. One of the mechanisms by which lncRNAs function is through the modulation of chromatin state. To assess the functions of lncRNAs we developed RNA-DamID, a novel approach that detects lncRNA-genome interactions in a cell-type specific manner in vivo with high sensitivity and accuracy. Identifying the cell-type-specific genome occupancy of lncRNAs is key to understanding their mechanisms of action in development and disease. We used RNA-DamID to investigate targeting of the lncRNAs in the Drosophila dosage compensation complex (DCC) and show that initial targeting is cell-type-specific.
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Affiliation(s)
- Seth W Cheetham
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.,Mater Research Institute, University of Queensland, Wooloongabba, Queensland, Australia
| | - Andrea H Brand
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
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30
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Drosophila Dosage Compensation Loci Associate with a Boundary-Forming Insulator Complex. Mol Cell Biol 2017; 37:MCB.00253-17. [PMID: 28784719 DOI: 10.1128/mcb.00253-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/10/2017] [Indexed: 12/18/2022] Open
Abstract
Chromatin entry sites (CES) are 100- to 1,500-bp elements that recruit male-specific lethal (MSL) complexes to the X chromosome to upregulate expression of X-linked genes in male flies. CES contain one or more ∼20-bp GA-rich sequences called MSL recognition elements (MREs) that are critical for dosage compensation. Recent studies indicate that CES also correspond to boundaries of X-chromosomal topologically associated domains (TADs). Here, we show that an ∼1,000-kDa complex called the late boundary complex (LBC), which is required for the functioning of the Bithorax complex boundary Fab-7, interacts specifically with a special class of CES that contain multiple MREs. Mutations in the MRE sequences of three of these CES that disrupt function in vivo abrogate interactions with the LBC. Moreover, reducing the levels of two LBC components compromises MSL recruitment. Finally, we show that several of the CES that are physically linked to each other in vivo are LBC interactors.
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31
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Wong JT, Akhbar F, Ng AYE, Tay MLI, Loi GJE, Pek JW. DIP1 modulates stem cell homeostasis in Drosophila through regulation of sisR-1. Nat Commun 2017; 8:759. [PMID: 28970471 PMCID: PMC5624886 DOI: 10.1038/s41467-017-00684-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/19/2017] [Indexed: 01/09/2023] Open
Abstract
Stable intronic sequence RNAs (sisRNAs) are by-products of splicing and regulate gene expression. How sisRNAs are regulated is unclear. Here we report that a double-stranded RNA binding protein, Disco-interacting protein 1 (DIP1) regulates sisRNAs in Drosophila. DIP1 negatively regulates the abundance of sisR-1 and INE-1 sisRNAs. Fine-tuning of sisR-1 by DIP1 is important to maintain female germline stem cell homeostasis by modulating germline stem cell differentiation and niche adhesion. Drosophila DIP1 localizes to a nuclear body (satellite body) and associates with the fourth chromosome, which contains a very high density of INE-1 transposable element sequences that are processed into sisRNAs. DIP1 presumably acts outside the satellite bodies to regulate sisR-1, which is not on the fourth chromosome. Thus, our study identifies DIP1 as a sisRNA regulatory protein that controls germline stem cell self-renewal in Drosophila. Stable intronic sequence RNAs (sisRNAs) are by-products of splicing from introns with roles in embryonic development in Drosophila. Here, the authors show that the RNA binding protein DIP1 regulates sisRNAs in Drosophila, which is necessary for germline stem cell homeostasis.
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Affiliation(s)
- Jing Ting Wong
- Ngee Ann Polytechnic, 535 Clementi Road, Singapore, 599489, Singapore
| | - Farzanah Akhbar
- Temasek Polytechnic, 21 Tampines Avenue 1, Singapore, 529757, Singapore
| | - Amanda Yunn Ee Ng
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore
| | - Mandy Li-Ian Tay
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore
| | - Gladys Jing En Loi
- National University of Singapore, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore.
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32
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Schauer T, Ghavi‐Helm Y, Sexton T, Albig C, Regnard C, Cavalli G, Furlong EEM, Becker PB. Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation. EMBO Rep 2017; 18:1854-1868. [PMID: 28794204 PMCID: PMC5623837 DOI: 10.15252/embr.201744292] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/30/2017] [Accepted: 07/04/2017] [Indexed: 11/09/2022] Open
Abstract
X chromosome dosage compensation in Drosophila requires chromosome-wide coordination of gene activation. The male-specific lethal dosage compensation complex (DCC) identifies and binds to X-chromosomal high-affinity sites (HAS) from which it boosts transcription. A sub-class of HAS, PionX sites, represent first contacts on the X. Here, we explored the chromosomal interactions of representative PionX sites by high-resolution 4C and determined the global chromosome conformation by Hi-C in sex-sorted embryos. Male and female X chromosomes display similar nuclear architecture, concordant with clustered, constitutively active genes. PionX sites, like HAS, are evenly distributed in the active compartment and engage in short- and long-range interactions beyond compartment boundaries. Long-range, inter-domain interactions between DCC binding sites are stronger in males, suggesting that the complex refines chromatin organization. By de novo induction of DCC in female cells, we monitored the extent of activation surrounding PionX sites. This revealed a remarkable range of DCC action not only in linear proximity, but also at megabase distance if close in space, suggesting that DCC profits from pre-existing chromosome folding to activate genes.
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Affiliation(s)
- Tamás Schauer
- Molecular Biology DivisionBiomedical Center and Center for Integrated Protein Science Ludwig‐Maximilians‐UniversityMunichGermany
| | - Yad Ghavi‐Helm
- European Molecular Biology LaboratoryGenome Biology UnitHeidelbergGermany
| | - Tom Sexton
- Institute of Genetics and Molecular and Cellular BiologyIllkirchFrance
| | - Christian Albig
- Molecular Biology DivisionBiomedical Center and Center for Integrated Protein Science Ludwig‐Maximilians‐UniversityMunichGermany
| | - Catherine Regnard
- Molecular Biology DivisionBiomedical Center and Center for Integrated Protein Science Ludwig‐Maximilians‐UniversityMunichGermany
| | - Giacomo Cavalli
- Institute of Human GeneticsCNRSMontpellierFrance
- University of MontpellierMontpellierFrance
| | - Eileen EM Furlong
- European Molecular Biology LaboratoryGenome Biology UnitHeidelbergGermany
| | - Peter B Becker
- Molecular Biology DivisionBiomedical Center and Center for Integrated Protein Science Ludwig‐Maximilians‐UniversityMunichGermany
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33
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The Drosophila DAXX-Like Protein (DLP) Cooperates with ASF1 for H3.3 Deposition and Heterochromatin Formation. Mol Cell Biol 2017; 37:MCB.00597-16. [PMID: 28320872 DOI: 10.1128/mcb.00597-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/09/2017] [Indexed: 01/22/2023] Open
Abstract
Histone variants are nonallelic isoforms of canonical histones, and they are deposited, in contrast to canonical histones, in a replication-independent (RI) manner. RI deposition of H3.3, a histone variant from the H3.3 family, is mediated in mammals by distinct pathways involving either the histone regulator A (HIRA) complex or the death-associated protein (DAXX)/α-thalassemia X-linked mental retardation protein (ATRX) complex. Here, we investigated the function of the Drosophila DAXX-like protein (DLP) by using both fly genetic approaches and protein biochemistry. DLP specifically interacts with H3.3 and shows a prominent localization on the base of the X chromosome, where it appears to act in concert with XNP, the Drosophila homolog of ATRX, in heterochromatin assembly and maintenance. The functional association between DLP and XNP is further supported by a series of experiments that illustrate genetic interactions and the DLP-XNP-dependent localization of specific chromosomal proteins. In addition, DLP both participates in the RI deposition of H3.3 and associates with anti-silencing factor 1 (ASF1). We suggest, in agreement with a recently proposed model, that DLP and ASF1 are part of a predeposition complex, which is recruited by XNP and is necessary to prevent DNA exposure in the nucleus.
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34
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Dosage Compensation in Drosophila-a Model for the Coordinate Regulation of Transcription. Genetics 2017; 204:435-450. [PMID: 27729494 DOI: 10.1534/genetics.115.185108] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/25/2016] [Indexed: 12/20/2022] Open
Abstract
The sex chromosomes have special significance in the history of genetics. The chromosomal basis of inheritance was firmly established when Calvin Bridges demonstrated that exceptions to Mendel's laws of segregation were accompanied at the cytological level by exceptional sex chromosome segregation. The morphological differences between X and Y exploited in Bridges' experiments arose as a consequence of the evolution of the sex chromosomes. Originally a homologous chromosome pair, the degeneration of the Y chromosome has been accompanied by a requirement for increased expression of the single X chromosome in males. Drosophila has been a model for the study of this dosage compensation and has brought key strengths, including classical genetics, the exceptional cytology of polytene chromosomes, and more recently, comprehensive genomics. The impact of these studies goes beyond sex chromosome regulation, providing valuable insights into mechanisms for the establishment and maintenance of chromatin domains, and for the coordinate regulation of transcription.
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35
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adélaide J, cervera N, carbuccia N, garnier S, guille A, mozziconnaci MJ, devillier R, chaffanet M, vey N, birnbaum D, gelsi-boyer V. Epigenetically centered evolution in an example of myeloid malignancy. Am J Hematol 2016; 91:E361-2. [PMID: 27299509 DOI: 10.1002/ajh.24450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/08/2016] [Accepted: 06/11/2016] [Indexed: 11/07/2022]
Affiliation(s)
- josé adélaide
- Centre de Recherche en Cancérologie de Marseille, Laboratoire D'Oncologie Moléculaire; UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR725; Marseille France
| | - nathalie cervera
- Centre de Recherche en Cancérologie de Marseille, Laboratoire D'Oncologie Moléculaire; UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR725; Marseille France
| | - nadine carbuccia
- Centre de Recherche en Cancérologie de Marseille, Laboratoire D'Oncologie Moléculaire; UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR725; Marseille France
| | - séverine garnier
- Centre de Recherche en Cancérologie de Marseille, Laboratoire D'Oncologie Moléculaire; UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR725; Marseille France
| | - arnaud guille
- Centre de Recherche en Cancérologie de Marseille, Laboratoire D'Oncologie Moléculaire; UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR725; Marseille France
| | | | - raynier devillier
- Aix-Marseille Université; Marseille France
- Département d'Hématologie; Institut Paoli-Calmettes; Marseille France
| | - max chaffanet
- Centre de Recherche en Cancérologie de Marseille, Laboratoire D'Oncologie Moléculaire; UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR725; Marseille France
| | - norbert vey
- Aix-Marseille Université; Marseille France
- Département d'Hématologie; Institut Paoli-Calmettes; Marseille France
| | - daniel birnbaum
- Centre de Recherche en Cancérologie de Marseille, Laboratoire D'Oncologie Moléculaire; UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR725; Marseille France
| | - véronique gelsi-boyer
- Centre de Recherche en Cancérologie de Marseille, Laboratoire D'Oncologie Moléculaire; UMR1068 Inserm, Institut Paoli-Calmettes, CNRS UMR725; Marseille France
- Département de BioPathologie; Institut Paoli-Calmettes; Marseille France
- Aix-Marseille Université; Marseille France
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36
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Leone S, Santoro R. Challenges in the analysis of long noncoding RNA functionality. FEBS Lett 2016; 590:2342-53. [DOI: 10.1002/1873-3468.12308] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 01/23/2023]
Affiliation(s)
- Sergio Leone
- Department of Molecular Mechanisms of Disease; University of Zurich; Switzerland
- Molecular Life Science Program; Life Science Zurich Graduate School; University of Zurich; Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease; University of Zurich; Switzerland
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Chlamydas S, Holz H, Samata M, Chelmicki T, Georgiev P, Pelechano V, Dündar F, Dasmeh P, Mittler G, Cadete FT, Ramírez F, Conrad T, Wei W, Raja S, Manke T, Luscombe NM, Steinmetz LM, Akhtar A. Functional interplay between MSL1 and CDK7 controls RNA polymerase II Ser5 phosphorylation. Nat Struct Mol Biol 2016; 23:580-9. [PMID: 27183194 DOI: 10.1038/nsmb.3233] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/21/2016] [Indexed: 01/09/2023]
Abstract
Proper gene expression requires coordinated interplay among transcriptional coactivators, transcription factors and the general transcription machinery. We report here that MSL1, a central component of the dosage compensation complex in Drosophila melanogaster and Drosophila virilis, displays evolutionarily conserved sex-independent binding to promoters. Genetic and biochemical analyses reveal a functional interaction of MSL1 with CDK7, a subunit of the Cdk-activating kinase (CAK) complex of the general transcription factor TFIIH. Importantly, MSL1 depletion leads to decreased phosphorylation of Ser5 of RNA polymerase II. In addition, we demonstrate that MSL1 is a phosphoprotein, and transgenic flies expressing MSL1 phosphomutants show mislocalization of the histone acetyltransferase MOF and histone H4 K16 acetylation, thus ultimately causing male lethality due to a failure of dosage compensation. We propose that, by virtue of its interaction with components of the general transcription machinery, MSL1 exists in different phosphorylation states, thereby modulating transcription in flies.
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Affiliation(s)
- Sarantis Chlamydas
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Herbert Holz
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Maria Samata
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- University of Freiburg, Faculty of Biology, Freiburg im Breisgau, Germany
| | - Tomasz Chelmicki
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Plamen Georgiev
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Vicent Pelechano
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Friederike Dündar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- University of Freiburg, Faculty of Biology, Freiburg im Breisgau, Germany
| | - Pouria Dasmeh
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | | | - Fidel Ramírez
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Thomas Conrad
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Wu Wei
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
| | - Sunil Raja
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Nicholas M Luscombe
- The Francis Crick Institute, London, UK
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
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38
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Prabu JR, Müller M, Thomae AW, Schüssler S, Bonneau F, Becker PB, Conti E. Structure of the RNA Helicase MLE Reveals the Molecular Mechanisms for Uridine Specificity and RNA-ATP Coupling. Mol Cell 2016; 60:487-99. [PMID: 26545078 DOI: 10.1016/j.molcel.2015.10.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/10/2015] [Accepted: 10/02/2015] [Indexed: 10/22/2022]
Abstract
The MLE helicase remodels the roX lncRNAs, enabling the lncRNA-mediated assembly of the Drosophila dosage compensation complex. We identified a stable MLE core comprising the DExH helicase module and two auxiliary domains: a dsRBD and an OB-like fold. MLEcore is an unusual DExH helicase that can unwind blunt-ended RNA duplexes and has specificity for uridine nucleotides. We determined the 2.1 Å resolution structure of MLEcore bound to a U10 RNA and ADP-AlF4. The OB-like and dsRBD folds bind the DExH module and contribute to form the entrance of the helicase channel. Four uridine nucleotides engage in base-specific interactions, rationalizing the conservation of uridine-rich sequences in critical roX substrates. roX2 binding is orchestrated by MLE's auxiliary domains, which is prerequisite for MLE localization to the male X chromosome. The structure visualizes a transition-state mimic of the reaction and suggests how eukaryotic DEAH/RHA helicases couple ATP hydrolysis to RNA translocation.
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Affiliation(s)
- J Rajan Prabu
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Marisa Müller
- Biomedical Center and Center for Integrated Protein Science, Ludwig-Maximilians-University, 82152 Martinsried, Germany
| | - Andreas W Thomae
- Biomedical Center and Center for Integrated Protein Science, Ludwig-Maximilians-University, 82152 Martinsried, Germany
| | - Steffen Schüssler
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Fabien Bonneau
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Peter B Becker
- Biomedical Center and Center for Integrated Protein Science, Ludwig-Maximilians-University, 82152 Martinsried, Germany.
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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Ramírez F, Lingg T, Toscano S, Lam KC, Georgiev P, Chung HR, Lajoie BR, de Wit E, Zhan Y, de Laat W, Dekker J, Manke T, Akhtar A. High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila. Mol Cell 2016; 60:146-62. [PMID: 26431028 DOI: 10.1016/j.molcel.2015.08.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 07/20/2015] [Accepted: 08/25/2015] [Indexed: 01/08/2023]
Abstract
Dosage compensation mechanisms provide a paradigm to study the contribution of chromosomal conformation toward targeting and spreading of epigenetic regulators over a specific chromosome. By using Hi-C and 4C analyses, we show that high-affinity sites (HAS), landing platforms of the male-specific lethal (MSL) complex, are enriched around topologically associating domain (TAD) boundaries on the X chromosome and harbor more long-range contacts in a sex-independent manner. Ectopically expressed roX1 and roX2 RNAs target HAS on the X chromosome in trans and, via spatial proximity, induce spreading of the MSL complex in cis, leading to increased expression of neighboring autosomal genes. We show that the MSL complex regulates nucleosome positioning at HAS, therefore acting locally rather than influencing the overall chromosomal architecture. We propose that the sex-independent, three-dimensional conformation of the X chromosome poises it for exploitation by the MSL complex, thereby facilitating spreading in males.
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Affiliation(s)
- Fidel Ramírez
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Lingg
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Sarah Toscano
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Kin Chung Lam
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Plamen Georgiev
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Ho-Ryun Chung
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Bryan R Lajoie
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Elzo de Wit
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Wouter de Laat
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA; Howard Hughes Medical Institute
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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40
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LAKHOTIA SUBHASHC. Divergent actions of long noncoding RNAs on X-chromosome remodelling in mammals and Drosophila achieve the same end result: dosage compensation. J Genet 2015; 94:575-84. [DOI: 10.1007/s12041-015-0566-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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41
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Abstract
MOF was first identified in Drosophila melanogaster as an important component of the dosage compensation complex. As a member of MYST family of histone acetyltransferase, MOF specifically deposits the acetyl groups to histone H4 lysine 16. Throughout evolution, MOF and its mammalian ortholog have retained highly conserved substrate specificity and similar enzymatic activities. MOF plays important roles in dosage compensation, ESC self-renewal, DNA damage and repair, cell survival, and gene expression regulation. Dysregulation of MOF has been implicated in tumor formation and progression of many types of human cancers. This review will discuss the structure and activity of mammalian hMOF as well as its function in H4K16 acetylation, DNA damage response, stem cell pluripotency, and carcinogenesis.
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Affiliation(s)
- Qiao Yi Chen
- Department of Environmental Medicine, NYU School of Medicine, Tuxedo, NY, USA
| | - Max Costa
- Department of Environmental Medicine, NYU School of Medicine, Tuxedo, NY, USA
| | - Hong Sun
- Department of Environmental Medicine, NYU School of Medicine, Tuxedo, NY, USA
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