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Lekkos K, Bhuiyan AA, Albloshi AMK, Brooks PM, Coate TM, Lionikas A. Validation of positional candidates Rps6ka6 and Pou3f4 for a locus associated with skeletal muscle mass variability. G3 (BETHESDA, MD.) 2024; 14:jkae046. [PMID: 38577978 PMCID: PMC11075558 DOI: 10.1093/g3journal/jkae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/17/2024] [Indexed: 04/06/2024]
Abstract
Genetic variability significantly contributes to individual differences in skeletal muscle mass; however, the specific genes involved in that process remain elusive. In this study, we examined the role of positional candidates, Rps6ka6 and Pou3f4, of a chromosome X locus, implicated in muscle mass variability in CFW laboratory mice. Histology of hindlimb muscles was studied in CFW male mice carrying the muscle "increasing" allele C (n = 15) or "decreasing" allele T (n = 15) at the peak marker of the locus, rs31308852, and in the Pou3f4y/- and their wild-type male littermates. To study the role of the Rps6ka6 gene, we deleted exon 7 (Rps6ka6-ΔE7) using clustered regularly interspaced palindromic repeats-Cas9 based method in H2Kb myogenic cells creating a severely truncated RSK4 protein. We then tested whether that mutation affected myoblast proliferation, migration, and/or differentiation. The extensor digitorum longus muscle was 7% larger (P < 0.0001) due to 10% more muscle fibers (P = 0.0176) in the carriers of the "increasing" compared with the "decreasing" CFW allele. The number of fibers was reduced by 15% (P = 0.0268) in the slow-twitch soleus but not in the fast-twitch extensor digitorum longus (P = 0.2947) of Pou3f4y/- mice. The proliferation and migration did not differ between the Rps6ka6-ΔE7 and wild-type H2Kb myoblasts. However, indices of differentiation (myosin expression, P < 0.0001; size of myosin-expressing cells, P < 0.0001; and fusion index, P = 0.0013) were significantly reduced in Rps6ka6-ΔE7 cells. This study suggests that the effect of the X chromosome locus on muscle fiber numbers in the fast-twitch extensor digitorum longus is mediated by the Rps6ka6 gene, whereas the Pou3f4 gene affects fiber number in slow-twitch soleus.
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Affiliation(s)
- Konstantinos Lekkos
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Afra A Bhuiyan
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Abdullah M K Albloshi
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
- Department of Anatomy and Histology, School of Medicine, University of Albaha, Alaqiq 65779, Saudi Arabia
| | - Paige M Brooks
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Thomas M Coate
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Arimantas Lionikas
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
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2
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Langouët M, Jolicoeur C, Javed A, Mattar P, Gearhart MD, Daiger SP, Bertelsen M, Tranebjærg L, Rendtorff ND, Grønskov K, Jespersgaard C, Chen R, Sun Z, Li H, Alirezaie N, Majewski J, Bardwell VJ, Sui R, Koenekoop RK, Cayouette M. Mutations in BCOR, a co-repressor of CRX/OTX2, are associated with early-onset retinal degeneration. SCIENCE ADVANCES 2022; 8:eabh2868. [PMID: 36070393 PMCID: PMC9451151 DOI: 10.1126/sciadv.abh2868] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/21/2022] [Indexed: 06/10/2023]
Abstract
Many transcription factors regulating the production, survival, and function of photoreceptor cells have been identified, but little is known about transcriptional co-regulators in retinal health and disease. Here, we show that BCL6 co-repressor (BCOR), a Polycomb repressive complex 1 factor mutated in various cancers, is involved in photoreceptor degenerative diseases. Using proteomics and transcription assays, we report that BCOR interacts with the transcription factors CRX and OTX2 and reduces their ability to activate the promoters of photoreceptor-specific genes. CUT&RUN sequencing further shows that BCOR shares genome-wide binding profiles with CRX/OTX2, consistent with a general co-repression activity. We also identify missense mutations in human BCOR in five families that have no evidence of cancer but present severe early-onset X-linked retinal degeneration. Last, we show that the human BCOR mutants cause degeneration when expressed in the mouse retina and have enhanced repressive activity on OTX2. These results uncover a role for BCOR in photoreceptors in both health and disease.
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Affiliation(s)
- Maéva Langouët
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Christine Jolicoeur
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Awais Javed
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Pierre Mattar
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Micah D. Gearhart
- Department of Genetics, Cell Biology and Development, Development Biology Center, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Stephen P. Daiger
- EHGED Department, Human Genetics Center, School of Public Health, University of Texas HSC, Houston, TX 77030, USA
| | - Mette Bertelsen
- Department of Clinical Genetics, Rigshospitalet, The Kennedy Centre, Copenhagen, Denmark
- Department of Ophthalmology, Rigshospitalet, The Kennedy Centre, Glostrup, Denmark
| | - Lisbeth Tranebjærg
- Department of Clinical Genetics, Rigshospitalet, The Kennedy Centre, Copenhagen, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Denmark
| | - Nanna D. Rendtorff
- Department of Clinical Genetics, Rigshospitalet, The Kennedy Centre, Copenhagen, Denmark
| | - Karen Grønskov
- Department of Clinical Genetics, Rigshospitalet, The Kennedy Centre, Copenhagen, Denmark
| | - Catherine Jespersgaard
- Department of Clinical Genetics, Rigshospitalet, The Kennedy Centre, Copenhagen, Denmark
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Zixi Sun
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Hui Li
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Najmeh Alirezaie
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Vivian J. Bardwell
- Department of Genetics, Cell Biology and Development, Development Biology Center, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ruifang Sui
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Robert K. Koenekoop
- Departments of Pediatric Surgery, Human Genetics, Adult Ophthalmology and the McGill Ocular Genetics Laboratory, McGill University Health Center Research Institute, Montreal, QC, Canada
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Anatomy and Cell Biology, Division of Experimental Medicine, McGill University, Montreal, QC, Canada
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3
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Protasova MS, Gusev FE, Andreeva TV, Klyushnikov SA, Illarioshkin SN, Rogaev EI. Novel genes bearing mutations in rare cases of early-onset ataxia with cerebellar hypoplasia. Eur J Hum Genet 2022; 30:703-711. [PMID: 35351988 DOI: 10.1038/s41431-022-01088-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/09/2022] [Accepted: 03/10/2022] [Indexed: 12/13/2022] Open
Abstract
We propose an approach for the identification of mutant genes for rare diseases in single cases of unknown etiology. All genes with rare biologically significant variants sorted from individual exome data are tested further for profiling of their spatial-temporal and cell/tissue specific expression compared to that of their paralogs. We developed a simple bioinformatics tool ("Essential Paralogue by Expression" (EPbE)) for such analysis. Here, we present rare clinical forms of early ataxia with cerebellar hypoplasia. Using whole-exome sequencing and the EPbE tool, we identified two novel mutant genes previously not associated with congenital human diseases. In Family I, the unique missense mutation (p.Lys258Glu) was found in the LRCH2 gene inherited in an X-linked manner. p.Lys258Glu occurs in the evolutionarily invariant site of the leucine-rich repeat domain of LRCH2. In Family II and Family III, the identical genetic variant was found in the CSMD1 gene inherited as an autosomal-recessive trait. The variant leads to amino acid substitution p.Gly2979Ser in a highly conserved region of the complement-interacting domain of CSMD1. The LRCH2 gene for Family I patients (in which congenital cerebellar hypoplasia was associated with demyelinating polyneuropathy) is expressed in Schwann and precursor Schwann cells and predominantly over its paralogous genes in the developing cerebellar cortex. The CSMD1 gene is predominantly expressed over its paralogous genes in the cerebellum, specifically in the period of late childhood. Thus, the comparative spatial-temporal expression of the selected genes corresponds to the neurological manifestations of the disease.
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Affiliation(s)
- Maria S Protasova
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, 119333, Moscow, Russia
| | - Fedor E Gusev
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, 119333, Moscow, Russia
| | - Tatiana V Andreeva
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, 119333, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Sergey A Klyushnikov
- Department of Neurogenetics, Research Center of Neurology, 123367, Moscow, Russia
| | | | - Evgeny I Rogaev
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, 119333, Moscow, Russia. .,Center for Genetics and Life Science, Sirius University of Science and Technology, 354340, Sochi, Russia. .,Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA, 01545, USA.
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4
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Deubiquitinases in cell death and inflammation. Biochem J 2022; 479:1103-1119. [PMID: 35608338 PMCID: PMC9162465 DOI: 10.1042/bcj20210735] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/07/2022] [Accepted: 05/10/2022] [Indexed: 11/20/2022]
Abstract
Apoptosis, pyroptosis, and necroptosis are distinct forms of programmed cell death that eliminate infected, damaged, or obsolete cells. Many proteins that regulate or are a part of the cell death machinery undergo ubiquitination, a post-translational modification made by ubiquitin ligases that modulates protein abundance, localization, and/or activity. For example, some ubiquitin chains target proteins for degradation, while others function as scaffolds for the assembly of signaling complexes. Deubiquitinases (DUBs) are the proteases that counteract ubiquitin ligases by cleaving ubiquitin from their protein substrates. Here, we review the DUBs that have been found to suppress or promote apoptosis, pyroptosis, or necroptosis.
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5
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Lambert N, Moïse M, Nguyen L. E3 Ubiquitin ligases and cerebral cortex development in health and disease. Dev Neurobiol 2022; 82:392-407. [PMID: 35476229 DOI: 10.1002/dneu.22877] [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: 01/17/2022] [Revised: 02/24/2022] [Accepted: 03/30/2022] [Indexed: 11/08/2022]
Abstract
Cerebral cortex development involves the sequential progression of biological steps driven by molecular pathways whose tight regulation often relies on ubiquitination. Ubiquitination is a post-translational modification involved in all aspects of cellular homeostasis through the attachment of a ubiquitin moiety on proteins. Over the past years, an increasing amount of research has highlighted the crucial role played by ubiquitin ligases in every step of cortical development and whose impairment often leads to various neurodevelopmental disorders. In this review, we focus on the key contributions of E3 ubiquitin ligases for the progression of the different steps of corticogenesis, as well as the pathological consequences of their mutations, often resulting in malformations of cortical development. Finally, we discuss some promising targeted treatment strategies for these diseases based on recent advances in the field. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Nicolas Lambert
- Laboratory of molecular regulation of neurogenesis, GIGA-Stem Cells and GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, CHU Sart Tilman, Liège, 4000, Belgium.,Department of Neurology, University Hospital of Liège, Liège, Belgium
| | - Martin Moïse
- Laboratory of molecular regulation of neurogenesis, GIGA-Stem Cells and GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, CHU Sart Tilman, Liège, 4000, Belgium.,Department of Radiology, University Hospital of Liège, Liège, Belgium
| | - Laurent Nguyen
- Laboratory of molecular regulation of neurogenesis, GIGA-Stem Cells and GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, CHU Sart Tilman, Liège, 4000, Belgium
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6
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Zhuang J, Chen C, Chen Y, Zeng S, Jiang Y, Wang Y, Chen X, Xie Y, Wang G. Case Report: Prenatal Diagnosis of a Novel Variant c.251dupT (p.N87Kfs*6) in BCOR Resulting in Oculofaciocardiodental Syndrome Using Whole-Exome Sequencing. Front Genet 2022; 13:829613. [PMID: 35401667 PMCID: PMC8990034 DOI: 10.3389/fgene.2022.829613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Oculofaciocardiodental (OFCD) syndrome is an X-linked dominant syndrome caused by BCOR variants, which manifests only in females and presumed leading to male lethality. Herein, we aim to present a prenatal diagnosis for OFCD syndrome associated with a novel hemizygous variant in BCOR gene. Case presentation: A 29-year-old pregnant woman from Quanzhou Fujian Province, China, with fetal ultrasound anomalies, was enrolled in this study. A normal 46, XY karyotype with no abnormalities was observed in the fetus detected on microarray. Furthermore, a whole-exome sequencing (WES) detection result demonstrated that a novel hemizygous variant of c.251dupT (p.N87Kfs*6) in the BCOR gene was identified in the fetus, which was a frameshift mutation and classified as a likely pathogenic variant, and may lead to OFCD syndrome according to the clinical feature of the fetus. In this case, male lethality had not occurred by the end of the second trimester, then termination of the pregnancy was conducted at a gestational age of 26 weeks. Sanger sequencing of parental samples revealed that the variant was maternally transmitted, which was consistent with the OFCD syndrome phenotypic features observed in her. Conclusions: In the study, we first present the affected male with a novel variant in BCOR that leads to the OFCD syndrome. Additionally, our study broadened the spectrum of BCOR results in the OFCD syndrome and provided the valuable references for prenatal genetic consultation.
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Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women’s and Children’s Hospital, Quanzhou, China
| | - Chunnuan Chen
- Department of Neurology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Yu’e Chen
- Ultrasonography, Quanzhou Women’s and Children’s Hospital, Quanzhou, China
| | - Shuhong Zeng
- Prenatal Diagnosis Center, Quanzhou Women’s and Children’s Hospital, Quanzhou, China
| | - Yuying Jiang
- Prenatal Diagnosis Center, Quanzhou Women’s and Children’s Hospital, Quanzhou, China
| | - Yuanbai Wang
- Prenatal Diagnosis Center, Quanzhou Women’s and Children’s Hospital, Quanzhou, China
| | - Xinying Chen
- Prenatal Diagnosis Center, Quanzhou Women’s and Children’s Hospital, Quanzhou, China
| | - Yingjun Xie
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Gaoxiong Wang, ; Yingjun Xie,
| | - Gaoxiong Wang
- Quanzhou Women’s and Children’s Hospital, Quanzhou, China
- *Correspondence: Gaoxiong Wang, ; Yingjun Xie,
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7
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Murine allele and transgene symbols: ensuring unique, concise, and informative nomenclature. Mamm Genome 2021; 33:108-119. [PMID: 34389871 PMCID: PMC8913455 DOI: 10.1007/s00335-021-09902-3] [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: 05/28/2021] [Accepted: 08/03/2021] [Indexed: 11/15/2022]
Abstract
In addition to naturally occurring sequence variation and spontaneous mutations, a wide array of technologies exist for modifying the mouse genome. Standardized nomenclature, including allele, transgene, and other mutation nomenclature, as well as persistent unique identifiers (PUID) are critical for effective scientific communication, comparison of results, and integration of data into knowledgebases such as Mouse Genome Informatics (MGI), Alliance for Genome Resources, and International Mouse Strain Resource (IMSR). As well as being the authoritative source for mouse gene, allele, and strain nomenclature, MGI integrates published and unpublished genomic, phenotypic, and expression data while linking to other online resources for a complete view of the mouse as a valuable model organism. The International Committee on Standardized Genetic Nomenclature for Mice has developed allele nomenclature rules and guidelines that take into account the number of genes impacted, the method of allele generation, and the nature of the sequence alteration. To capture details that cannot be included in allele symbols, MGI has further developed allele to gene relationships using sequence ontology (SO) definitions for mutations that provide links between alleles and the genes affected. MGI is also using (HGVS) variant nomenclature for variants associated with alleles that will enhance searching for mutations and will improve cross-species comparison. With the ability to assign unique and informative symbols as well as to link alleles with more than one gene, allele and transgene nomenclature rules and guidelines provide an unambiguous way to represent alterations in the mouse genome and facilitate data integration among multiple resources such the Alliance of Genome Resources and International Mouse Strain Resource.
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Macrae TA, Ramalho-Santos M. The deubiquitinase Usp9x regulates PRC2-mediated chromatin reprogramming during mouse development. Nat Commun 2021; 12:1865. [PMID: 33767158 PMCID: PMC7994559 DOI: 10.1038/s41467-021-21910-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
Pluripotent cells of the mammalian embryo undergo extensive chromatin rewiring to prepare for lineage commitment after implantation. Repressive H3K27me3, deposited by Polycomb Repressive Complex 2 (PRC2), is reallocated from large blankets in pre-implantation embryos to mark promoters of developmental genes. The regulation of this global redistribution of H3K27me3 is poorly understood. Here we report a post-translational mechanism that destabilizes PRC2 to constrict H3K27me3 during lineage commitment. Using an auxin-inducible degron system, we show that the deubiquitinase Usp9x is required for mouse embryonic stem (ES) cell self-renewal. Usp9x-high ES cells have high PRC2 levels and bear a chromatin and transcriptional signature of the pre-implantation embryo, whereas Usp9x-low ES cells resemble the post-implantation, gastrulating epiblast. We show that Usp9x interacts with, deubiquitinates and stabilizes PRC2. Deletion of Usp9x in post-implantation embryos results in the derepression of genes that normally gain H3K27me3 after gastrulation, followed by the appearance of morphological abnormalities at E9.5, pointing to a recurrent link between Usp9x and PRC2 during development. Usp9x is a marker of "stemness" and is mutated in various neurological disorders and cancers. Our results unveil a Usp9x-PRC2 regulatory axis that is critical at peri-implantation and may be redeployed in other stem cell fate transitions and disease states.
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Affiliation(s)
- Trisha A Macrae
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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9
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Basar MA, Beck DB, Werner A. Deubiquitylases in developmental ubiquitin signaling and congenital diseases. Cell Death Differ 2021; 28:538-556. [PMID: 33335288 PMCID: PMC7862630 DOI: 10.1038/s41418-020-00697-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Metazoan development from a one-cell zygote to a fully formed organism requires complex cellular differentiation and communication pathways. To coordinate these processes, embryos frequently encode signaling information with the small protein modifier ubiquitin, which is typically attached to lysine residues within substrates. During ubiquitin signaling, a three-step enzymatic cascade modifies specific substrates with topologically unique ubiquitin modifications, which mediate changes in the substrate's stability, activity, localization, or interacting proteins. Ubiquitin signaling is critically regulated by deubiquitylases (DUBs), a class of ~100 human enzymes that oppose the conjugation of ubiquitin. DUBs control many essential cellular functions and various aspects of human physiology and development. Recent genetic studies have identified mutations in several DUBs that cause developmental disorders. Here we review principles controlling DUB activity and substrate recruitment that allow these enzymes to regulate ubiquitin signaling during development. We summarize key mechanisms of how DUBs control embryonic and postnatal differentiation processes, highlight developmental disorders that are caused by mutations in particular DUB members, and describe our current understanding of how these mutations disrupt development. Finally, we discuss how emerging tools from human disease genetics will enable the identification and study of novel congenital disease-causing DUBs.
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Affiliation(s)
- Mohammed A Basar
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David B Beck
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
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10
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Roles of HIF and 2-Oxoglutarate-Dependent Dioxygenases in Controlling Gene Expression in Hypoxia. Cancers (Basel) 2021; 13:cancers13020350. [PMID: 33477877 PMCID: PMC7832865 DOI: 10.3390/cancers13020350] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Hypoxia—reduction in oxygen availability—plays key roles in both physiological and pathological processes. Given the importance of oxygen for cell and organism viability, mechanisms to sense and respond to hypoxia are in place. A variety of enzymes utilise molecular oxygen, but of particular importance to oxygen sensing are the 2-oxoglutarate (2-OG) dependent dioxygenases (2-OGDs). Of these, Prolyl-hydroxylases have long been recognised to control the levels and function of Hypoxia Inducible Factor (HIF), a master transcriptional regulator in hypoxia, via their hydroxylase activity. However, recent studies are revealing that such dioxygenases are involved in almost all aspects of gene regulation, including chromatin organisation, transcription and translation. Abstract Hypoxia—reduction in oxygen availability—plays key roles in both physiological and pathological processes. Given the importance of oxygen for cell and organism viability, mechanisms to sense and respond to hypoxia are in place. A variety of enzymes utilise molecular oxygen, but of particular importance to oxygen sensing are the 2-oxoglutarate (2-OG) dependent dioxygenases (2-OGDs). Of these, Prolyl-hydroxylases have long been recognised to control the levels and function of Hypoxia Inducible Factor (HIF), a master transcriptional regulator in hypoxia, via their hydroxylase activity. However, recent studies are revealing that dioxygenases are involved in almost all aspects of gene regulation, including chromatin organisation, transcription and translation. We highlight the relevance of HIF and 2-OGDs in the control of gene expression in response to hypoxia and their relevance to human biology and health.
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Beck DB, Basar MA, Asmar AJ, Thompson JJ, Oda H, Uehara DT, Saida K, Pajusalu S, Talvik I, D'Souza P, Bodurtha J, Mu W, Barañano KW, Miyake N, Wang R, Kempers M, Tamada T, Nishimura Y, Okada S, Kosho T, Dale R, Mitra A, Macnamara E, Matsumoto N, Inazawa J, Walkiewicz M, Õunap K, Tifft CJ, Aksentijevich I, Kastner DL, Rocha PP, Werner A. Linkage-specific deubiquitylation by OTUD5 defines an embryonic pathway intolerant to genomic variation. SCIENCE ADVANCES 2021; 7:7/4/eabe2116. [PMID: 33523931 PMCID: PMC7817106 DOI: 10.1126/sciadv.abe2116] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/07/2020] [Indexed: 05/09/2023]
Abstract
Reversible modification of proteins with linkage-specific ubiquitin chains is critical for intracellular signaling. Information on physiological roles and underlying mechanisms of particular ubiquitin linkages during human development are limited. Here, relying on genomic constraint scores, we identify 10 patients with multiple congenital anomalies caused by hemizygous variants in OTUD5, encoding a K48/K63 linkage-specific deubiquitylase. By studying these mutations, we find that OTUD5 controls neuroectodermal differentiation through cleaving K48-linked ubiquitin chains to counteract degradation of select chromatin regulators (e.g., ARID1A/B, histone deacetylase 2, and HCF1), mutations of which underlie diseases that exhibit phenotypic overlap with OTUD5 patients. Loss of OTUD5 during differentiation leads to less accessible chromatin at neuroectodermal enhancers and aberrant gene expression. Our study describes a previously unidentified disorder we name LINKED (LINKage-specific deubiquitylation deficiency-induced Embryonic Defects) syndrome and reveals linkage-specific ubiquitin cleavage from chromatin remodelers as an essential signaling mode that coordinates chromatin remodeling during embryogenesis.
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Affiliation(s)
- David B Beck
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mohammed A Basar
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony J Asmar
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joyce J Thompson
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hirotsugu Oda
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniela T Uehara
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Inga Talvik
- Department of Neurology and Rehabilitation, Tallinn Children's Hospital, Tallinn, Estonia
| | - Precilla D'Souza
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joann Bodurtha
- Department of Genetic Medicine, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - Weiyi Mu
- Department of Genetic Medicine, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - Kristin W Barañano
- Department of Neurology, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Raymond Wang
- Division of Metabolic Disorders, CHOC Children's Specialists, Orange, CA 92868, USA
- Department of Pediatrics, University of California Irvine School of Medicine, Orange, CA 92967, USA
| | - Marlies Kempers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Tomoko Tamada
- Department of Pediatrics, Hiroshima Prefectural Rehabilitation Center, Hiroshima, Japan
| | - Yutaka Nishimura
- Department of General Perinatology, Hiroshima City Hiroshima Citizens Hospital, Hiroshima, Japan
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Nagano, Japan
| | - Ryan Dale
- Bioinformatics and Scientific Programming Core, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Apratim Mitra
- Bioinformatics and Scientific Programming Core, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ellen Macnamara
- Undiagnosed Diseases Program, The Common Fund, Office of the Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Magdalena Walkiewicz
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Cynthia J Tifft
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Undiagnosed Diseases Program, The Common Fund, Office of the Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivona Aksentijevich
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel L Kastner
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pedro P Rocha
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA.
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12
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Hamline MY, Corcoran CM, Wamstad JA, Miletich I, Feng J, Lohr JL, Hemberger M, Sharpe PT, Gearhart MD, Bardwell VJ. OFCD syndrome and extraembryonic defects are revealed by conditional mutation of the Polycomb-group repressive complex 1.1 (PRC1.1) gene BCOR. Dev Biol 2020; 468:110-132. [PMID: 32692983 PMCID: PMC9583620 DOI: 10.1016/j.ydbio.2020.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/16/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022]
Abstract
BCOR is a critical regulator of human development. Heterozygous mutations of BCOR in females cause the X-linked developmental disorder Oculofaciocardiodental syndrome (OFCD), and hemizygous mutations of BCOR in males cause gestational lethality. BCOR associates with Polycomb group proteins to form one subfamily of the diverse Polycomb repressive complex 1 (PRC1) complexes, designated PRC1.1. Currently there is limited understanding of differing developmental roles of the various PRC1 complexes. We therefore generated a conditional exon 9-10 knockout Bcor allele and a transgenic conditional Bcor expression allele and used these to define multiple roles of Bcor, and by implication PRC1.1, in mouse development. Females heterozygous for Bcor exhibiting mosaic expression due to the X-linkage of the gene showed reduced postnatal viability and had OFCD-like defects. By contrast, Bcor hemizygosity in the entire male embryo resulted in embryonic lethality by E9.5. We further dissected the roles of Bcor, focusing on some of the tissues affected in OFCD through use of cell type specific Cre alleles. Mutation of Bcor in neural crest cells caused cleft palate, shortening of the mandible and tympanic bone, ectopic salivary glands and abnormal tongue musculature. We found that defects in the mandibular region, rather than in the palate itself, led to palatal clefting. Mutation of Bcor in hindlimb progenitor cells of the lateral mesoderm resulted in 2/3 syndactyly. Mutation of Bcor in Isl1-expressing lineages that contribute to the heart caused defects including persistent truncus arteriosus, ventricular septal defect and fetal lethality. Mutation of Bcor in extraembryonic lineages resulted in placental defects and midgestation lethality. Ubiquitous over expression of transgenic Bcor isoform A during development resulted in embryonic defects and midgestation lethality. The defects we have found in Bcor mutants provide insights into the etiology of the OFCD syndrome and how BCOR-containing PRC1 complexes function in development.
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Affiliation(s)
- Michelle Y Hamline
- The Molecular, Cellular, Developmental Biology and Genetics Graduate Program, University of Minnesota, Minneapolis, MN, 55455, USA; University of Minnesota Medical Scientist Training Program, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Connie M Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Joseph A Wamstad
- The Molecular, Cellular, Developmental Biology and Genetics Graduate Program, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Isabelle Miletich
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Jifan Feng
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Jamie L Lohr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Myriam Hemberger
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Paul T Sharpe
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, SE1 9RT, UK; Medical Research Council Centre for Transplantation, King's College London, London, SE1 9RT, UK
| | - Micah D Gearhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Vivian J Bardwell
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN, 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
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13
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Novel clinical and genetic insight into CXorf56-associated intellectual disability. Eur J Hum Genet 2019; 28:367-372. [PMID: 31822863 PMCID: PMC7028711 DOI: 10.1038/s41431-019-0558-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/18/2019] [Accepted: 11/26/2019] [Indexed: 11/08/2022] Open
Abstract
Intellectual disability (ID) is one of most frequent reasons for genetic consultation. The complex molecular anatomy of ID ranges from complete chromosomal imbalances to single nucleotide variant changes occurring de novo, with thousands of genes identified. This extreme genetic heterogeneity challenges the molecular diagnosis, which mostly requires a genomic approach. CXorf56 is largely uncharacterized and was recently proposed as a candidate ID gene based on findings in a single Dutch family. Here, we describe nine cases (six males and three females) from three unrelated families. Exome sequencing and combined database analyses, identified family-specific CXorf56 variants (NM_022101.3:c.498_503del, p.(Glu167_Glu168del) and c.303_304delCTinsACCC, p.(Phe101Leufs*20)) that segregated with the ID phenotype. These variants are presumably leading to loss-of-function, which is the proposed disease mechanism. Clinically, CXorf56-related disease is a slowly progressive neurological disorder. The phenotype is more severe in hemizygote males, but might also manifests in heterozygote females, which showed skewed X-inactivation patterns in blood. Male patients might present previously unreported neurological features such as epilepsy, abnormal gait, tremor, and clonus, which extends the clinical spectrum of the disorder. In conclusion, we confirm the causative role of variants in CXorf56 for an X-linked form of intellectual disability with additional neurological features. The gene should be considered for molecular diagnostics of patients with ID, specifically when family history is suggestive of X-linked inheritance. Further work is needed to understand the role of this gene in neurodevelopment and intellectual disability.
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14
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Hupalowska A, Jedrusik A, Zhu M, Bedford MT, Glover DM, Zernicka-Goetz M. CARM1 and Paraspeckles Regulate Pre-implantation Mouse Embryo Development. Cell 2019; 175:1902-1916.e13. [PMID: 30550788 PMCID: PMC6292842 DOI: 10.1016/j.cell.2018.11.027] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 07/29/2018] [Accepted: 11/16/2018] [Indexed: 01/20/2023]
Abstract
Nuclear architecture has never been carefully examined during early mammalian development at the stages leading to establishment of the embryonic and extra-embryonic lineages. Heterogeneous activity of the methyltransferase CARM1 during these stages results in differential methylation of histone H3R26 to modulate establishment of these two lineages. Here we show that CARM1 accumulates in nuclear granules at the 2- to 4-cell stage transition in the mouse embryo, with the majority corresponding to paraspeckles. The paraspeckle component Neat1 and its partner p54nrb are required for CARM1's association with paraspeckles and for H3R26 methylation. Conversely, CARM1 also influences paraspeckle organization. Depletion of Neat1 or p54nrb results in arrest at the 16- to 32-cell stage, with elevated expression of transcription factor Cdx2, promoting differentiation into the extra-embryonic lineage. This developmental arrest occurs at an earlier stage than following CARM1 depletion, indicating that paraspeckles act upstream of CARM1 but also have additional earlier roles in fate choice.
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Affiliation(s)
- Anna Hupalowska
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Agnieszka Jedrusik
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Meng Zhu
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, MD Anderson Cancer Center, The University of Texas, 1808 Park Road 1C, Smithville, TX 78957, USA
| | - David M Glover
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
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15
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Chen CY, Yu IS, Pai CH, Lin CY, Lin SR, Chen YT, Lin SW. Embryonic Cul4b is important for epiblast growth and location of primitive streak layer cells. PLoS One 2019; 14:e0219221. [PMID: 31260508 PMCID: PMC6602292 DOI: 10.1371/journal.pone.0219221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 06/19/2019] [Indexed: 11/18/2022] Open
Abstract
Cul4b-null (Cul4bΔ/Y) mice undergo growth arrest and degeneration during the early embryonic stages and die at E9.5. The pathogenic causes of this lethality remain incompletely characterized. However, it has been hypothesized that the loss of Cul4b function in extraembryonic tissues plays a key role. In this study, we investigated possible causes of death for Cul4b-null embryos, particularly in regard to the role of embryonic Cul4b. First, we show that the loss of embryonic Cul4b affects the growth of the inner cell mass in vitro and delays epiblast development during the gastrulation period at E6.5~E7.5 in vivo, as highlighted by the absence of the epiblastic transcription factor Brachyury from E6.5~E7.5. Additionally, at E7.5, strong and laterally expanded expression of Eomes and Fgf8 signaling was detected. Sectioning of these embryos showed disorganized primitive streak layer cells. Second, we observed that Mash2-expressing cells were present in the extraembryonic tissues of Cul4b-deficient embryos at E6.5 but were absent at E7.5. In addition, the loss of Cul4b resulted in decreased expression of cyclin proteins, which are required for the cell cycle transition from G1 to S. Taken together, these observations suggest that the embryonic expression of Cul4b is important for epiblast growth during E6.5~E7.5, and the loss of Cul4b results in either delayed growth of the epiblast or defective localization of primitive streak layer cells. As a result, the signaling activity mediated by the epiblast for subsequent ectoplacental cone development is affected, with the potential to induce growth retardation and lethality in Cul4bΔ/Y embryos.
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Affiliation(s)
- Chun-Yu Chen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - I-Shing Yu
- Laboratory Animal Center, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chen-Hsueh Pai
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chien-Yu Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shu-Rung Lin
- Department of Bioscience Technology, College of Science, Chung-Yuan Christian University, Taoyuan, Taiwan
- Center for Nanotechnology and Center for Biomedical Technology, Chung-Yuan Christian University, Taoyuan, Taiwan
| | - You-Tzung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shu-Wha Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
- Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
- * E-mail:
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16
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From Flies to Mice: The Emerging Role of Non-Canonical PRC1 Members in Mammalian Development. EPIGENOMES 2018. [DOI: 10.3390/epigenomes2010004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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17
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Verkerk AJMH, Zeidler S, Breedveld G, Overbeek L, Huigh D, Koster L, van der Linde H, de Esch C, Severijnen LA, de Vries BBA, Swagemakers SMA, Willemsen R, Hoogeboom AJM, van der Spek PJ, Oostra BA. CXorf56, a dendritic neuronal protein, identified as a new candidate gene for X-linked intellectual disability. Eur J Hum Genet 2018; 26:552-560. [PMID: 29374277 DOI: 10.1038/s41431-017-0051-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 11/20/2017] [Accepted: 11/23/2017] [Indexed: 11/09/2022] Open
Abstract
Intellectual disability (ID) comprises a large group of heterogeneous disorders, often without a known molecular cause. X-linked ID accounts for 5-10% of male ID cases. We investigated a large, three-generation family with mild ID and behavior problems in five males and one female, with a segregation suggestive for X-linked inheritance. Linkage analysis mapped a disease locus to a 7.6 Mb candidate region on the X-chromosome (LOD score 3.3). Whole-genome sequencing identified a 2 bp insertion in exon 2 of the chromosome X open reading frame 56 gene (CXorf56), resulting in a premature stop codon. This insertion was present in all intellectually impaired individuals and carrier females. Additionally, X-inactivation status showed skewed methylation patterns favoring the inactivation of the mutated allele in the unaffected carrier females. We demonstrate that the insertion leads to nonsense-mediated decay and that CXorf56 mRNA expression is reduced in the impaired males and female. In murine brain slices and primary hippocampal neuronal cultures, CXorf56 protein was present and localized in the nucleus, cell soma, dendrites, and dendritic spines. Although no other families have been identified with pathogenic variants in CXorf56, these results suggest that CXorf56 is the causative gene in this family, and thus a novel candidate gene for X-linked ID with behavior problems.
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Affiliation(s)
- Annemieke J M H Verkerk
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands. .,Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Shimriet Zeidler
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Guido Breedveld
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lydia Overbeek
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Daphne Huigh
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Linda Koster
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Herma van der Linde
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Celine de Esch
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lies-Anne Severijnen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Rob Willemsen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Peter J van der Spek
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ben A Oostra
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
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18
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Facompre ND, Harmeyer KM, Sahu V, Gimotty PA, Rustgi AK, Nakagawa H, Basu D. Targeting JARID1B's demethylase activity blocks a subset of its functions in oral cancer. Oncotarget 2017; 9:8985-8998. [PMID: 29507668 PMCID: PMC5823649 DOI: 10.18632/oncotarget.23739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/13/2017] [Indexed: 12/14/2022] Open
Abstract
Upregulation of the H3K4me3 demethylase JARID1B is linked to acquisition of aggressive, stem cell-like features by many cancer types. However, the utility of emerging JARID1 family inhibitors remains uncertain, in part because JARID1B’s functions in normal development and malignancy are diverse and highly context-specific. In this study, responses of oral squamous cell carcinomas (OSCCs) to catalytic inhibition of JARID1B were assessed using CPI-455, the first tool compound with true JARID1 family selectivity. CPI-455 attenuated clonal sphere and tumor formation by stem-like cells that highly express JARID1B while also depleting the CD44-positive and Aldefluor-high fractions conventionally used to designate OSCC stem cells. Silencing JARID1B abrogated CPI-455’s effects on sphere formation, supporting that the drug acted through this isoform. To further delineate CPI-455’s capacity to block JARID1B’s functions, its biologic effects were compared against those indicated by pathway analysis of the transcriptional profile produced by JARID1B knockdown. Downregulation of multiple gene sets related to stem cell function was consistent with the drug’s observed actions. However, strong E-Cadherin upregulation seen upon silencing JARID1B surprisingly could not be reproduced using CPI-455. Expressing a demethylase-inactive mutant of JARID1B demonstrated suppression of this transcript to be demethylase-independent, and the capacity of mutant JARID1B but not CPI-455 to modulate invasion provided a functional correlate of this finding. These results show that JARID1B catalytic inhibition effectively targets some stem cell-like features of malignancy but also reveal demethylase-independent actions refractory to inhibition. Future application of JARID1 inhibitors in combinatorial use for cancer therapy may be guided by these findings.
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Affiliation(s)
- Nicole D Facompre
- Department of Otorhinolaryngology, Head and Neck Surgery, The University of Pennsylvania, Philadelphia, PA, USA
| | - Kayla M Harmeyer
- Department of Otorhinolaryngology, Head and Neck Surgery, The University of Pennsylvania, Philadelphia, PA, USA
| | - Varun Sahu
- Department of Otorhinolaryngology, Head and Neck Surgery, The University of Pennsylvania, Philadelphia, PA, USA
| | - Phyllis A Gimotty
- Department of Biostatistics Epidemiology and Informatics, The University of Pennsylvania, Philadelphia, PA, USA
| | - Anil K Rustgi
- Department of Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - Hiroshi Nakagawa
- Department of Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - Devraj Basu
- Department of Otorhinolaryngology, Head and Neck Surgery, The University of Pennsylvania, Philadelphia, PA, USA.,Philadelphia VA Medical Center, Philadelphia, PA, USA.,The Wistar Institute, Philadelphia, PA, USA
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19
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Morgan MAJ, Rickels RA, Collings CK, He X, Cao K, Herz HM, Cozzolino KA, Abshiru NA, Marshall SA, Rendleman EJ, Sze CC, Piunti A, Kelleher NL, Savas JN, Shilatifard A. A cryptic Tudor domain links BRWD2/PHIP to COMPASS-mediated histone H3K4 methylation. Genes Dev 2017; 31:2003-2014. [PMID: 29089422 PMCID: PMC5710144 DOI: 10.1101/gad.305201.117] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/05/2017] [Indexed: 01/22/2023]
Abstract
In this study, Morgan et al. identify an evolutionarily conserved factor, BRWD2/PHIP, that localizes with histone H3K4 methylation genome-wide in human cells, mouse embryonic stem cells, and Drosophila. Depletion of the Drosophila sole homolog dBRWD3 results in altered histone H3 Lys27 acetylation patterns at enhancers and promoters and changes in gene expression, suggesting a cross-talk between these epigenetic modifications and transcription through the BRWD family. Histone H3 Lys4 (H3K4) methylation is a chromatin feature enriched at gene cis-regulatory sequences such as promoters and enhancers. Here we identify an evolutionarily conserved factor, BRWD2/PHIP, which colocalizes with histone H3K4 methylation genome-wide in human cells, mouse embryonic stem cells, and Drosophila. Biochemical analysis of BRWD2 demonstrated an association with the Cullin-4–RING ubiquitin E3 ligase-4 (CRL4) complex, nucleosomes, and chromatin remodelers. BRWD2/PHIP binds directly to H3K4 methylation through a previously unidentified chromatin-binding module related to Royal Family Tudor domains, which we named the CryptoTudor domain. Using CRISPR–Cas9 genetic knockouts, we demonstrate that COMPASS H3K4 methyltransferase family members differentially regulate BRWD2/PHIP chromatin occupancy. Finally, we demonstrate that depletion of the single Drosophila homolog dBRWD3 results in altered gene expression and aberrant patterns of histone H3 Lys27 acetylation at enhancers and promoters, suggesting a cross-talk between these chromatin modifications and transcription through the BRWD protein family.
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Affiliation(s)
- Marc A J Morgan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Ryan A Rickels
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Clayton K Collings
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Xiaolin He
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Kaixiang Cao
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Hans-Martin Herz
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | | | - Nebiyu A Abshiru
- Department of Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Emily J Rendleman
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Christie C Sze
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Andrea Piunti
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Neil L Kelleher
- Department of Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | | | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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20
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Harmeyer KM, Facompre ND, Herlyn M, Basu D. JARID1 Histone Demethylases: Emerging Targets in Cancer. Trends Cancer 2017; 3:713-725. [PMID: 28958389 DOI: 10.1016/j.trecan.2017.08.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 01/04/2023]
Abstract
JARID1 proteins are histone demethylases that both regulate normal cell fates during development and contribute to the epigenetic plasticity that underlies malignant transformation. This H3K4 demethylase family participates in multiple repressive transcriptional complexes at promoters and has broader regulatory effects on chromatin that remain ill-defined. There is growing understanding of the oncogenic and tumor suppressive functions of JARID1 proteins, which are contingent on cell context and the protein isoform. Their contributions to stem cell-like dedifferentiation, tumor aggressiveness, and therapy resistance in cancer have sustained interest in the development of JARID1 inhibitors. Here we review the diverse and context-specific functions of the JARID1 proteins that may impact the utilization of emerging targeted inhibitors of this histone demethylase family in cancer therapy.
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Affiliation(s)
- Kayla M Harmeyer
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicole D Facompre
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Devraj Basu
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104, USA; The Wistar Institute, Philadelphia, PA 19104, USA; Philadelphia VA Medical Center, Philadelphia, PA 19104, USA.
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21
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Shen H, Xu W, Lan F. Histone lysine demethylases in mammalian embryonic development. Exp Mol Med 2017; 49:e325. [PMID: 28450736 PMCID: PMC6130211 DOI: 10.1038/emm.2017.57] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 01/19/2017] [Indexed: 12/18/2022] Open
Abstract
Post-translational modifications, such as methylation, acetylation and phosphorylation, of histone proteins play important roles in regulating dynamic chromatin structure. Histone demethylation has become one of the most active research areas of epigenetics in the past decade. To date, with the exception of histone H3 lysine 79 methylation, the demethylases for all major lysine methylation sites have been discovered. These enzymes have been shown to be involved in various biological processes, with embryonic development being an exciting emerging area. This review will primarily discuss the involvement of these demethylases in the regulation of mammalian embryonic development, including their roles in embryonic stem cell pluripotency, primordial germ cell (PGC) formation and maternal-to-zygotic transition.
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Affiliation(s)
- Hongjie Shen
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics, Shanghai Ministry of Education, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Wenqi Xu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics, Shanghai Ministry of Education, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Fei Lan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Epigenetics, Shanghai Ministry of Education, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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22
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Toriyama M, Toriyama M, Wallingford JB, Finnell RH. Folate-dependent methylation of septins governs ciliogenesis during neural tube closure. FASEB J 2017; 31:3622-3635. [PMID: 28432198 DOI: 10.1096/fj.201700092r] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/11/2017] [Indexed: 12/15/2022]
Abstract
Periconception maternal folic acid (vitamin B9) supplementation can reduce the prevalence of neural tube defects (NTDs), although just how folates benefit the developing embryo and promote closing of the neural tube and other morphologic processes during development remains unknown. Folate contributes to a 1-carbon metabolism, which is essential for purine biosynthesis and methionine recycling and affects methylation of DNA, histones, and nonhistone proteins. Herein, we used animal models and cultured mammalian cells to demonstrate that disruption of the methylation pathway mediated by folate compromises normal neural tube closure (NTC) and ciliogenesis. We demonstrate that the embryos with NTD failed to adequately methylate septin2, a key regulator of cilium structure and function. We report that methylation of septin2 affected its GTP binding activity and formation of the septin2-6-7 complex. We propose that folic acid promotes normal NTC in some embryos by regulating the methylation of septin2, which is critical for normal cilium formation during early embryonic development.-Toriyama, M., Toriyama, M., Wallingford, J. B., Finnell, R. H. Folate-dependent methylation of septins governs ciliogenesis during neural tube closure.
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Affiliation(s)
- Manami Toriyama
- Department of Pediatrics, Dell Pediatric Research Institute, The University of Texas at Austin Dell Medical School, Austin, Texas, USA
| | - Michinori Toriyama
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - John B Wallingford
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Richard H Finnell
- Department of Pediatrics, Dell Pediatric Research Institute, The University of Texas at Austin Dell Medical School, Austin, Texas, USA;
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23
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Jia L, Yan F, Cao W, Chen Z, Zheng H, Li H, Pan Y, Narula N, Ren X, Li H, Zhou P. Dysregulation of CUL4A and CUL4B Ubiquitin Ligases in Lung Cancer. J Biol Chem 2016; 292:2966-2978. [PMID: 27974468 DOI: 10.1074/jbc.m116.765230] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/29/2016] [Indexed: 01/11/2023] Open
Abstract
The Cullin-RING ubiquitin ligase 4 (CRL4) is implicated in controlling cell cycle, DNA damage repair, and checkpoint response based on studies employing cell lines and mouse models. CRL4 proteins, including CUL4A and CUL4B, are often highly accumulated in human malignancies. Elevated CRL4 attenuates DNA damage repair and increases genome instability that is believed to facilitate tumorigenesis. However, this has yet to be evaluated in human patients with cancer. In our study, 352 lung cancer and 62 normal lung specimens of Asian origin were constructed into tissue microarrays of four distinct lung cancer subtypes. Expression of CUL4A, CUL4B, and their substrates was detected by immunohistochemistry and analyzed statistically for their prognostic value and association with DNA damage response and genomic instability. Our results show that both CUL4A and CUL4B are overexpressed in the majority of lung carcinomas (PCUL4A <0.001 and PCUL4B <0.001) and significantly associated with tumor size (PCUL4A <0.001 and PCUL4B = 0.002), lymphatic invasion (PCUL4A = 0.004 and PCUL4B <0.001), metastasis (PCUL4A = 0.019 and PCUL4B = 0.006), and advanced TNM stage (PCUL4A <0.001 and PCUL4B <0.001), which parallels gene amplification and abnormal activation of the canonical WNT signaling. Moreover, overexpression of CUL4A, but not CUL4B, is significantly associated with tobacco smoking (p = 0.01) and is inversely correlated with XPC and P21, both of which are substrates of CUL4A (PCUL4A = 0.019 and PCUL4B = 0.006). Higher levels of CUL4A or CUL4B are significantly associated with the overall survival of patients (PCUL4A <0.001 and PCUL4B <0.001) and progression-free survival (PCUL4A <0.001 and PCUL4B = 0.001). Our findings revealed that CUL4A and CUL4B are differentially associated with etiologic factors for pulmonary malignancies and are independent prognostic markers for the survival of distinct lung cancer subtypes.
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Affiliation(s)
- Lei Jia
- From the Department of Immunology, Key Laboratory of Cancer Immunology and Biotherapy
| | - Fan Yan
- From the Department of Immunology, Key Laboratory of Cancer Immunology and Biotherapy.,the Departments of Pathology and Laboratory Medicine and
| | - Wenfeng Cao
- Department of Pathology, Key Laboratory of Tianjin Cancer Prevention and Treatment
| | - Zhengming Chen
- Healthcare Policy and Research, Weill Cornell Medical College, New York, New York 10065
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, and
| | - Haixin Li
- Department of Epidemiology and Biostatistics, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, and
| | - Yi Pan
- Department of Pathology, Key Laboratory of Tianjin Cancer Prevention and Treatment
| | - Navneet Narula
- the Departments of Pathology and Laboratory Medicine and
| | - Xiubao Ren
- From the Department of Immunology, Key Laboratory of Cancer Immunology and Biotherapy,
| | - Hui Li
- From the Department of Immunology, Key Laboratory of Cancer Immunology and Biotherapy, .,the Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China and
| | - Pengbo Zhou
- From the Department of Immunology, Key Laboratory of Cancer Immunology and Biotherapy, .,the Departments of Pathology and Laboratory Medicine and
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24
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Farah O, Biechele S, Rossant J, Dufort D. Porcupine-dependent Wnt signaling controls stromal proliferation and endometrial gland maintenance through the action of distinct WNTs. Dev Biol 2016; 422:58-69. [PMID: 27965056 DOI: 10.1016/j.ydbio.2016.11.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/07/2016] [Accepted: 11/30/2016] [Indexed: 01/03/2023]
Abstract
Wnt signaling has been shown to be important in orchestrating proper development of the female reproductive tract. In the uterus, six members of the Wnt family are expressed in the neonatal endometrium and deletion of individual Wnt genes often leads to similar phenotypes, suggesting an interaction of these genes in uterine development and function. Furthermore, Wnts may have complementary functions, which could mask the identification of their individual functional role in single gene deletions. To circumvent this issue, we have generated a deletion of the Porcupine homolog within the female reproductive tract using progesterone receptor-Cre mice (PgrCre/+); preventing Wnt secretion from the producing cells. We show that Porcupine-dependent Wnt signaling, unlike previously reported, is dispensable for postnatal gland formation but is required for post-pubertal gland maintenance as well as for stromal cell proliferation. Furthermore, our results demonstrate that WNT7a is sufficient to restore post-pubertal endometrial gland formation. Although WNT5a did not restore gland formation, it rescued stromal cell proliferation; up-regulating several secreted factors including Fgf10 and Ihh. Our results further elucidate the roles of Wnt signaling in uterine development and function as well as provide an ideal system to address individual Wnt functions in the uterus.
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Affiliation(s)
- Omar Farah
- Department of Obstetrics and Gynecology, McGill University Health Centre, Montreal, Quebec, Canada; Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Steffen Biechele
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Janet Rossant
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Daniel Dufort
- Department of Obstetrics and Gynecology, McGill University Health Centre, Montreal, Quebec, Canada; Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada; Department of Biology, McGill University, Montreal, Quebec, Canada.
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25
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Towards Functional Annotation of the Preimplantation Transcriptome: An RNAi Screen in Mammalian Embryos. Sci Rep 2016; 6:37396. [PMID: 27869233 PMCID: PMC5116644 DOI: 10.1038/srep37396] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 10/27/2016] [Indexed: 12/19/2022] Open
Abstract
With readily available transcriptome-wide data, understanding the role of each expressed gene is an essential next step. Although RNAi technologies allow for genome-wide screens in cell culture, these approaches cannot replace strategies for discovery in the embryo. Here we present, for the first time, a knockdown screen in mouse preimplantation embryos. Early mammalian development encompasses dynamic cellular, molecular and epigenetic events that are largely conserved from mouse to man. We assayed 712 genes for requirements during preimplantation. We identified 59 genes required for successful development or outgrowth and implantation. We have characterized each phenotype and revealed cellular, molecular, and lineage specific defects following knockdown of transcript. Induced network analyses demonstrate this as a valid approach to identify networks of genes that play important roles during preimplantation. Our approach provides a robust and efficient strategy towards identification of novel phenotypes during mouse preimplantation and facilitates functional annotation of the mammalian transcriptome.
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26
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FGF treatment of host embryos injected with ES cells increases rates of chimaerism. Transgenic Res 2016; 26:237-246. [PMID: 27873161 PMCID: PMC5350236 DOI: 10.1007/s11248-016-9997-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 11/04/2016] [Indexed: 11/23/2022]
Abstract
In spite of the emergence of genome editing tools, ES cell mediated transgenesis remains the most controllable way of creating genetically modified animals. Although tetraploid (4N) complementation of 4N host embryos and ES cells, is the only method guaranteeing that offspring are entirely ES cell derived, this technique is challenging, not always successful and difficult to implement in some laboratory settings. The current study shows that pretreatment of host blastocysts with FGF4 prior to ES cell injection can provide an alternative method for the generation of animals displaying high rates of chimaerism. Chimaerism assessment in E11 fetuses and born pups shows that a large percentage of resulting conceptuses show a high ES cell contribution from implantation onwards and that developing pups do not necessitate c-section for delivery.
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27
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High-throughput discovery of novel developmental phenotypes. Nature 2016; 537:508-514. [PMID: 27626380 PMCID: PMC5295821 DOI: 10.1038/nature19356] [Citation(s) in RCA: 772] [Impact Index Per Article: 96.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 08/10/2016] [Indexed: 12/29/2022]
Abstract
Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. Using a standardized phenotyping platform that incorporates high-resolution 3D imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in clinical sequencing efforts.
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28
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Chu LF, Leng N, Zhang J, Hou Z, Mamott D, Vereide DT, Choi J, Kendziorski C, Stewart R, Thomson JA. Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm. Genome Biol 2016; 17:173. [PMID: 27534536 PMCID: PMC4989499 DOI: 10.1186/s13059-016-1033-x] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 07/27/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Human pluripotent stem cells offer the best available model to study the underlying cellular and molecular mechanisms of human embryonic lineage specification. However, it is not fully understood how individual stem cells exit the pluripotent state and transition towards their respective progenitor states. RESULTS Here, we analyze the transcriptomes of human embryonic stem cell-derived lineage-specific progenitors by single-cell RNA-sequencing (scRNA-seq). We identify a definitive endoderm (DE) transcriptomic signature that leads us to pinpoint a critical time window when DE differentiation is enhanced by hypoxia. The molecular mechanisms governing the emergence of DE are further examined by time course scRNA-seq experiments, employing two new statistical tools to identify stage-specific genes over time (SCPattern) and to reconstruct the differentiation trajectory from the pluripotent state through mesendoderm to DE (Wave-Crest). Importantly, presumptive DE cells can be detected during the transitory phase from Brachyury (T) (+) mesendoderm toward a CXCR4 (+) DE state. Novel regulators are identified within this time window and are functionally validated on a screening platform with a T-2A-EGFP knock-in reporter engineered by CRISPR/Cas9. Through loss-of-function and gain-of-function experiments, we demonstrate that KLF8 plays a pivotal role modulating mesendoderm to DE differentiation. CONCLUSIONS We report the analysis of 1776 cells by scRNA-seq covering distinct human embryonic stem cell-derived progenitor states. By reconstructing a differentiation trajectory at single-cell resolution, novel regulators of the mesendoderm transition to DE are elucidated and validated. Our strategy of combining single-cell analysis and genetic approaches can be applied to uncover novel regulators governing cell fate decisions in a variety of systems.
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Affiliation(s)
- Li-Fang Chu
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA.
| | - Ning Leng
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA.,Present address: Genentech, Inc., South San Francisco, CA, USA
| | - Jue Zhang
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Zhonggang Hou
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA.,Present address: Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Daniel Mamott
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - David T Vereide
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Jeea Choi
- Department of Statistics, University of Wisconsin, Madison, WI, USA
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, 53715, USA. .,Department of Cell & Regenerative Biology, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, CA, USA.
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29
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Schmitt D, Funk N, Blum R, Asan E, Andersen L, Rülicke T, Sendtner M, Buchner E. Initial characterization of a Syap1 knock-out mouse and distribution of Syap1 in mouse brain and cultured motoneurons. Histochem Cell Biol 2016; 146:489-512. [PMID: 27344443 PMCID: PMC5037158 DOI: 10.1007/s00418-016-1457-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2016] [Indexed: 02/07/2023]
Abstract
Synapse-associated protein 1 (Syap1/BSTA) is the mammalian homologue of Sap47 (synapse-associated protein of 47 kDa) in Drosophila. Sap47 null mutant larvae show reduced short-term synaptic plasticity and a defect in associative behavioral plasticity. In cultured adipocytes, Syap1 functions as part of a complex that phosphorylates protein kinase Bα/Akt1 (Akt1) at Ser(473) and promotes differentiation. The role of Syap1 in the vertebrate nervous system is unknown. Here, we generated a Syap1 knock-out mouse and show that lack of Syap1 is compatible with viability and fertility. Adult knock-out mice show no overt defects in brain morphology. In wild-type brain, Syap1 is found widely distributed in synaptic neuropil, notably in regions rich in glutamatergic synapses, but also in perinuclear structures associated with the Golgi apparatus of specific groups of neuronal cell bodies. In cultured motoneurons, Syap1 is located in axons and growth cones and is enriched in a perinuclear region partially overlapping with Golgi markers. We studied in detail the influence of Syap1 knockdown and knockout on structure and development of these cells. Importantly, Syap1 knockout does not affect motoneuron survival or axon growth. Unexpectedly, neither knockdown nor knockout of Syap1 in cultured motoneurons is associated with reduced Ser(473) or Thr(308) phosphorylation of Akt. Our findings demonstrate a widespread expression of Syap1 in the mouse central nervous system with regionally specific distribution patterns as illustrated in particular for olfactory bulb, hippocampus, and cerebellum.
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Affiliation(s)
- Dominique Schmitt
- Institute of Clinical Neurobiology, University of Würzburg, Versbacher Str. 5, 97078, Würzburg, Germany
| | - Natalia Funk
- Institute of Clinical Neurobiology, University of Würzburg, Versbacher Str. 5, 97078, Würzburg, Germany
| | - Robert Blum
- Institute of Clinical Neurobiology, University of Würzburg, Versbacher Str. 5, 97078, Würzburg, Germany
| | - Esther Asan
- Institute of Anatomy and Cell Biology, University of Würzburg, 97070, Würzburg, Germany
| | - Lill Andersen
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Thomas Rülicke
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University of Würzburg, Versbacher Str. 5, 97078, Würzburg, Germany
| | - Erich Buchner
- Institute of Clinical Neurobiology, University of Würzburg, Versbacher Str. 5, 97078, Würzburg, Germany.
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30
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Mariani L, Lussi YC, Vandamme J, Riveiro A, Salcini AE. The H3K4me3/2 histone demethylase RBR-2 controls axon guidance by repressing the actin-remodeling gene wsp-1. Development 2016; 143:851-63. [PMID: 26811384 DOI: 10.1242/dev.132985] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/16/2016] [Indexed: 12/25/2022]
Abstract
The dynamic regulation of histone modifications is important for modulating transcriptional programs during development. Aberrant H3K4 methylation is associated with neurological disorders, but how the levels and the recognition of this modification affect specific neuronal processes is unclear. Here, we show that RBR-2, the sole homolog of the KDM5 family of H3K4me3/2 demethylases in Caenorhabditis elegans, ensures correct axon guidance by controlling the expression of the actin regulator wsp-1. Loss of rbr-2 results in increased levels of H3K4me3 at the transcriptional start site of wsp-1, with concomitant higher wsp-1 expression responsible for defective axon guidance. In agreement, overexpression of WSP-1 mimics rbr-2 loss, and its depletion restores normal axon guidance in rbr-2 mutants. NURF-1, an H3K4me3-binding protein and member of the chromatin-remodeling complex NURF, is required for promoting aberrant wsp-1 transcription in rbr-2 mutants and its ablation restores wild-type expression of wsp-1 and axon guidance. Thus, our results establish a precise role for epigenetic regulation in neuronal development by demonstrating a functional link between RBR-2 activity, H3K4me3 levels, the NURF complex and the expression of WSP-1.
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Affiliation(s)
- Luca Mariani
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Yvonne C Lussi
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Julien Vandamme
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alba Riveiro
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anna Elisabetta Salcini
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
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31
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Zha Z, Han X, Smith MD, Liu Y, Giguère PM, Kopanja D, Raychaudhuri P, Siderovski DP, Guan KL, Lei QY, Xiong Y. A Non-Canonical Function of Gβ as a Subunit of E3 Ligase in Targeting GRK2 Ubiquitylation. Mol Cell 2015; 58:794-803. [PMID: 25982117 DOI: 10.1016/j.molcel.2015.04.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 02/17/2015] [Accepted: 04/09/2015] [Indexed: 01/08/2023]
Abstract
G protein-coupled receptors (GPCRs) comprise the largest family of cell surface receptors, regulate a wide range of physiological processes, and are the major targets of pharmaceutical drugs. Canonical signaling from GPCRs is relayed to intracellular effector proteins by trimeric G proteins, composed of α, β, and γ subunits (Gαβγ). Here, we report that G protein β subunits (Gβ) bind to DDB1 and that Gβ2 targets GRK2 for ubiquitylation by the DDB1-CUL4A-ROC1 ubiquitin ligase. Activation of GPCR results in PKA-mediated phosphorylation of DDB1 at Ser645 and its dissociation from Gβ2, leading to increase of GRK2 protein. Deletion of Cul4a results in cardiac hypertrophy in male mice that can be partially rescued by the deletion of one Grk2 allele. These results reveal a non-canonical function of the Gβ protein as a ubiquitin ligase component and a mechanism of feedback regulation of GPCR signaling.
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Affiliation(s)
- Zhengyu Zha
- Key Laboratory of Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200032, People's Republic of China; Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, People's Republic of China; School of Life Sciences, Fudan University 200032, People's Republic of China; Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xiaoran Han
- Key Laboratory of Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200032, People's Republic of China; Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, People's Republic of China; School of Life Sciences, Fudan University 200032, People's Republic of China
| | - Matthew D Smith
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yang Liu
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Patrick M Giguère
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dragana Kopanja
- Department of Biochemistry and Molecular Genetics, University of Illinois, College of Medicine, Chicago, IL 60607, USA
| | - Pradip Raychaudhuri
- Department of Biochemistry and Molecular Genetics, University of Illinois, College of Medicine, Chicago, IL 60607, USA
| | - David P Siderovski
- Department of Pharmacology, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kun-Liang Guan
- Key Laboratory of Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200032, People's Republic of China; Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, People's Republic of China; Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Qun-Ying Lei
- Key Laboratory of Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200032, People's Republic of China; Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, People's Republic of China.
| | - Yue Xiong
- Key Laboratory of Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200032, People's Republic of China; Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, People's Republic of China; Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA.
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32
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Rasmussen PB, Staller P. The KDM5 family of histone demethylases as targets in oncology drug discovery. Epigenomics 2015; 6:277-86. [PMID: 25111482 DOI: 10.2217/epi.14.14] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
There is growing evidence for a causal role of the KDM5 family of histone demethylases in human cancer. In particular, KDM5A (JARID1A/RBP2) and KDM5B (JARID1B/PLU1) contribute to cancer cell proliferation, reduce the expression of tumor suppressor genes, promote the development of drug tolerance and maintain tumor-initiating cells. KDM5 enzymes remove tri- and di-methylations of lysine 4 of histone H3 - modifications that occur at the start site of transcription in actively transcribed genes. However, the importance of the histone demethylase activity of KDM5 proteins for cancer cells has not been resolved so far. The currently available approaches suppress or remove the targeted proteins and thereby affect their putative functions as structural components and recruitment factors for other chromatin-associated proteins. Therefore, the development of specific enzymatic inhibitors for KDM5 will promote our understanding of the biological role of their catalytic activity and yield potential novel anticancer therapeutics.
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An in vivo requirement for the mediator subunit med14 in the maintenance of stem cell populations. Stem Cell Reports 2015; 4:670-84. [PMID: 25772472 PMCID: PMC4400641 DOI: 10.1016/j.stemcr.2015.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 12/24/2022] Open
Abstract
The Mediator complex has recently been shown to be a key player in the maintenance of embryonic and induced pluripotent stem cells. However, the in vivo consequences of loss of many Mediator subunits are unknown. We identified med14 as the gene affected in the zebrafish logelei (log) mutant, which displayed a morphological arrest by 2 days of development. Surprisingly, microarray analysis showed that transcription was not broadly affected in log mutants. Indeed, log cells transplanted into a wild-type environment were able to survive into adulthood. In planarians, RNAi knockdown demonstrated a requirement for med14 and many other Mediator components in adult stem cell maintenance and regeneration. Multiple stem/progenitor cell populations were observed to be reduced or absent in zebrafish med14 mutant embryos. Taken together, our results show a critical, evolutionarily conserved, in vivo function for Med14 (and Mediator) in stem cell maintenance, distinct from a general role in transcription. med14 mutant zebrafish embryos do not have global defects in transcription Mediator components are required in planaria for adult stem cell maintenance Zebrafish med14 mutant embryos have an apparent defect in stem cell maintenance Mediator has a specialized in vivo function in stem cell lineages
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Kawakami E, Tokunaga A, Ozawa M, Sakamoto R, Yoshida N. The histone demethylase Fbxl11/Kdm2a plays an essential role in embryonic development by repressing cell-cycle regulators. Mech Dev 2014; 135:31-42. [PMID: 25463925 DOI: 10.1016/j.mod.2014.10.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/02/2014] [Accepted: 10/13/2014] [Indexed: 10/24/2022]
Abstract
Methylation and de-methylation of histone lysine residues play pivotal roles in mammalian early development; these modifications influence chromatin architecture and regulate gene transcription. Fbxl11 (F-box and leucine-rich repeat 11)/Kdm2a is a histone demethylase that selectively removes mono- and di-methylation from histone H3K36. Previously, two other histone H3K36 demethylases (Jmjd5 or Fbxl10) were analyzed based on the phenotypes of the corresponding knockout (KO) mice; the results of those studies implicated H3K36 demethylases in cell proliferation, apoptosis, and senescence (Fukuda et al., 2011; Ishimura et al., 2012). To elucidate the physiological role of Fbxl11, we generated and examined Fbxl11 KO mice. Fbxl11 was expressed throughout the body during embryogenesis, and the Fbxl11 KO mice exhibited embryonic lethality at E10.5-12.5, accompanied with severe growth defects leading to reduced body size. Furthermore, knockout of Fbxl11 decreased cell proliferation and increased apoptosis. The lack of Fbxl11 resulted in downregulation of the Polycomb group protein (PcG) Ezh2, PcG mediated H2A ubiquitination and upregulation of the cyclin-dependent kinase inhibitor p21Cip1. Taken together, our findings suggest that Fbxl11 plays an essential role in embryonic development and homeostasis by regulating cell proliferation and survival.
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Affiliation(s)
- Eri Kawakami
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; The Tokunaga Laboratory, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasamamachi, Yufu-shi, Oita 879-5593, Japan
| | - Akinori Tokunaga
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; The Tokunaga Laboratory, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasamamachi, Yufu-shi, Oita 879-5593, Japan.
| | - Manabu Ozawa
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Reiko Sakamoto
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Nobuaki Yoshida
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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Shmakova A, Batie M, Druker J, Rocha S. Chromatin and oxygen sensing in the context of JmjC histone demethylases. Biochem J 2014; 462:385-95. [PMID: 25145438 PMCID: PMC4147966 DOI: 10.1042/bj20140754] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/07/2014] [Accepted: 07/09/2014] [Indexed: 01/22/2023]
Abstract
Responding appropriately to changes in oxygen availability is essential for multicellular organism survival. Molecularly, cells have evolved intricate gene expression programmes to handle this stressful condition. Although it is appreciated that gene expression is co-ordinated by changes in transcription and translation in hypoxia, much less is known about how chromatin changes allow for transcription to take place. The missing link between co-ordinating chromatin structure and the hypoxia-induced transcriptional programme could be in the form of a class of dioxygenases called JmjC (Jumonji C) enzymes, the majority of which are histone demethylases. In the present review, we will focus on the function of JmjC histone demethylases, and how these could act as oxygen sensors for chromatin in hypoxia. The current knowledge concerning the role of JmjC histone demethylases in the process of organism development and human disease will also be reviewed.
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Key Words
- chromatin
- chromatin remodeller
- histone methylation
- hypoxia
- hypoxia-inducible factor (hif)
- jumonji c (jmjc)
- transcription
- cd, chromodomain
- chd, chromodomain helicase dna binding
- crc, chromatin-remodelling complex
- fih, factor inhibiting hif
- hif, hypoxia-inducible factor
- iswi, imitation-swi protein
- jmjc, jumonji c
- kdm, lysine-specific demethylase
- lsd, lysine-specific demethylase
- nurd, nucleosome-remodelling deacetylase
- phd, plant homeodomain
- phf, phd finger protein
- rest, repressor element 1-silencing transcription factor
- vhl, von hippel–lindau protein
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Affiliation(s)
- Alena Shmakova
- *Centre for Gene Regulation and Expression, MSI/WTB/JBC Complex, Dow Street, University of Dundee, Dundee DD1 5EH, Scotland, U.K
| | - Michael Batie
- *Centre for Gene Regulation and Expression, MSI/WTB/JBC Complex, Dow Street, University of Dundee, Dundee DD1 5EH, Scotland, U.K
| | - Jimena Druker
- *Centre for Gene Regulation and Expression, MSI/WTB/JBC Complex, Dow Street, University of Dundee, Dundee DD1 5EH, Scotland, U.K
| | - Sonia Rocha
- *Centre for Gene Regulation and Expression, MSI/WTB/JBC Complex, Dow Street, University of Dundee, Dundee DD1 5EH, Scotland, U.K
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Momb J, Appling DR. Mitochondrial one-carbon metabolism and neural tube defects. ACTA ACUST UNITED AC 2014; 100:576-83. [PMID: 24985542 DOI: 10.1002/bdra.23268] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/02/2014] [Accepted: 05/19/2014] [Indexed: 11/08/2022]
Abstract
BACKGROUND Neural tube defects (NTDs) are one of the most common birth defects in humans. Maternal intake of folic acid was linked to prevention of NTDs in the 1970s. This realization led to the establishment of mandatory and/or voluntary food folic acid fortification programs in many countries that have reduced the incidence of NTDs by up to 70% in humans. Despite 40 years of intensive research, the biochemical mechanisms underlying the protective effects of folic acid remain unknown. RESULTS Recent research reveals a role for mitochondrial folate-dependent one-carbon metabolism in neural tube closure. CONCLUSION In this article, we review the evidence linking NTDs to aberrant mitochondrial one-carbon metabolism in humans and mouse models. The potential of formate, a product of mitochondrial one-carbon metabolism, to prevent NTDs is also discussed.
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Affiliation(s)
- Jessica Momb
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas
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Fueyo R, García MA, Martínez-Balbás MA. Jumonji family histone demethylases in neural development. Cell Tissue Res 2014; 359:87-98. [PMID: 24950624 DOI: 10.1007/s00441-014-1924-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 05/15/2014] [Indexed: 10/25/2022]
Abstract
Central nervous system (CNS) development is driven by coordinated actions of developmental signals and chromatin regulators that precisely regulate gene expression patterns. Histone methylation is a regulatory mechanism that controls transcriptional programs. In the last 10 years, several histone demethylases (HDM) have been identified as important players in neural development, and their implication in cell fate decisions is beginning to be recognized. Identification of the physiological roles of these enzymes and their molecular mechanisms of action will be necessary for completely understanding the process that ultimately generates different neural cells in the CNS. In this review, we provide an overview of the Jumonji family of HDMs involved in neurodevelopment, and we discuss their roles during neural fate establishment and neuronal differentiation.
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Affiliation(s)
- Raquel Fueyo
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Parc Científic de Barcelona (PCB), Barcelona, 08028, Spain
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Abstract
It has recently been demonstrated that the genes controlling the epigenetic programmes that are required for maintaining chromatin structure and cell identity include genes that drive human cancer. This observation has led to an increased awareness of chromatin-associated proteins as potentially interesting drug targets. The successful introduction of DNA methylation and histone deacetylase (HDAC) inhibitors for the treatment of specific subtypes of cancer has paved the way for the use of epigenetic therapy. Here, we highlight key biological findings demonstrating the roles of members of the histone lysine demethylase class of enzymes in the development of cancers, discuss the potential and challenges of therapeutically targeting them, and highlight emerging small-molecule inhibitors of these enzymes.
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Biechele S, Cockburn K, Lanner F, Cox BJ, Rossant J. Porcn-dependent Wnt signaling is not required prior to mouse gastrulation. Development 2013; 140:2961-71. [PMID: 23760955 DOI: 10.1242/dev.094458] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In mice and humans the X-chromosomal porcupine homolog (Porcn) gene is required for the acylation and secretion of all 19 Wnt ligands and thus represents a bottleneck for all Wnt signaling. We have generated a mouse line carrying a floxed allele for Porcn and used zygotic, oocyte-specific and visceral endoderm-specific deletions to investigate embryonic and extra-embryonic requirements for Wnt ligand secretion. We show that there is no requirement for Porcn-dependent secretion of Wnt ligands during preimplantation development of the mouse embryo. Porcn-dependent Wnts are first required for the initiation of gastrulation, where Porcn function is required in the epiblast but not the visceral endoderm. Heterozygous female embryos, which are mutant in both trophoblast and visceral endoderm due to imprinted X chromosome inactivation, complete gastrulation but display chorio-allantoic fusion defects similar to Wnt7b mutants. Our studies highlight the importance of Wnt3 and Wnt7b for embryonic and placental development but suggest that endogenous Porcn-dependent Wnt secretion does not play an essential role in either implantation or blastocyst lineage specification.
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Affiliation(s)
- Steffen Biechele
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada
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Adams D, Baldock R, Bhattacharya S, Copp AJ, Dickinson M, Greene NDE, Henkelman M, Justice M, Mohun T, Murray SA, Pauws E, Raess M, Rossant J, Weaver T, West D. Bloomsbury report on mouse embryo phenotyping: recommendations from the IMPC workshop on embryonic lethal screening. Dis Model Mech 2013; 6:571-9. [PMID: 23519032 PMCID: PMC3634642 DOI: 10.1242/dmm.011833] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Identifying genes that are important for embryo development is a crucial first step towards understanding their many functions in driving the ordered growth, differentiation and organogenesis of embryos. It can also shed light on the origins of developmental disease and congenital abnormalities. Current international efforts to examine gene function in the mouse provide a unique opportunity to pinpoint genes that are involved in embryogenesis, owing to the emergence of embryonic lethal knockout mutants. Through internationally coordinated efforts, the International Knockout Mouse Consortium (IKMC) has generated a public resource of mouse knockout strains and, in April 2012, the International Mouse Phenotyping Consortium (IMPC), supported by the EU InfraCoMP programme, convened a workshop to discuss developing a phenotyping pipeline for the investigation of embryonic lethal knockout lines. This workshop brought together over 100 scientists, from 13 countries, who are working in the academic and commercial research sectors, including experts and opinion leaders in the fields of embryology, animal imaging, data capture, quality control and annotation, high-throughput mouse production, phenotyping, and reporter gene analysis. This article summarises the outcome of the workshop, including (1) the vital scientific importance of phenotyping embryonic lethal mouse strains for basic and translational research; (2) a common framework to harmonise international efforts within this context; (3) the types of phenotyping that are likely to be most appropriate for systematic use, with a focus on 3D embryo imaging; (4) the importance of centralising data in a standardised form to facilitate data mining; and (5) the development of online tools to allow open access to and dissemination of the phenotyping data.
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Affiliation(s)
- David Adams
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | | | | | - Andrew J. Copp
- UCL Institute of Child Health, Gower Street, London, WC1E 6BT, UK
| | | | | | | | | | - Timothy Mohun
- MRC National Institute for Medical Research, London, NW7 1AA, UK
| | | | - Erwin Pauws
- UCL Institute of Child Health, Gower Street, London, WC1E 6BT, UK
| | - Michael Raess
- Helmholtz Zentrum Munich and Infrafrontier, Ingolstädter Landstraße 1 85764 Neuherberg, Munich, Germany
| | | | - Tom Weaver
- MRC Harwell, Harwell Science and Innovation Campus, Oxford, OX11 0RD, UK
| | - David West
- CHORI, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA
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The histone demethylase Jarid1b ensures faithful mouse development by protecting developmental genes from aberrant H3K4me3. PLoS Genet 2013; 9:e1003461. [PMID: 23637629 PMCID: PMC3630093 DOI: 10.1371/journal.pgen.1003461] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 03/04/2013] [Indexed: 12/12/2022] Open
Abstract
Embryonic development is tightly regulated by transcription factors and chromatin-associated proteins. H3K4me3 is associated with active transcription and H3K27me3 with gene repression, while the combination of both keeps genes required for development in a plastic state. Here we show that deletion of the H3K4me2/3 histone demethylase Jarid1b (Kdm5b/Plu1) results in major neonatal lethality due to respiratory failure. Jarid1b knockout embryos have several neural defects including disorganized cranial nerves, defects in eye development, and increased incidences of exencephaly. Moreover, in line with an overlap of Jarid1b and Polycomb target genes, Jarid1b knockout embryos display homeotic skeletal transformations typical for Polycomb mutants, supporting a functional interplay between Polycomb proteins and Jarid1b. To understand how Jarid1b regulates mouse development, we performed a genome-wide analysis of histone modifications, which demonstrated that normally inactive genes encoding developmental regulators acquire aberrant H3K4me3 during early embryogenesis in Jarid1b knockout embryos. H3K4me3 accumulates as embryonic development proceeds, leading to increased expression of neural master regulators like Pax6 and Otx2 in Jarid1b knockout brains. Taken together, these results suggest that Jarid1b regulates mouse development by protecting developmental genes from inappropriate acquisition of active histone modifications.
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Abstract
Regulated migration of hematopoietic stem cells is fundamental for hematopoiesis. The molecular mechanisms underlying stem cell trafficking are poorly defined. Based on a short hairpin RNA library and stromal cell-derived factor-1 (SDF-1) migration screening assay, we identified the histone 3 lysine 27 demethylase UTX (Kdm6a) as a novel regulator for hematopoietic cell migration. Using hematopoietic stem and progenitor cells from our conditional UTX knockout (KO) mice, we were able to confirm the regulatory function of UTX on cell migration. Moreover, adult female conditional UTX KO mice displayed myelodysplasia and splenic erythropoiesis, whereas UTX KO males showed no phenotype. During development, all UTX KO female and a portion of UTX KO male embryos developed a cardiac defect, cranioschisis, and died in utero. Therefore, UTY, the male homolog of UTX, can compensate for UTX in adults and partially during development. Additionally, we found that UTX knockdown in zebrafish significantly impairs SDF-1/CXCR4-dependent migration of primordial germ cells. Our data suggest that UTX is a critical regulator for stem cell migration and hematopoiesis.
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He F, Lu D, Jiang B, Wang Y, Liu Q, Liu Q, Shao C, Li X, Gong Y. X-linked intellectual disability gene CUL4B targets Jab1/CSN5 for degradation and regulates bone morphogenetic protein signaling. Biochim Biophys Acta Mol Basis Dis 2013; 1832:595-605. [PMID: 23357576 DOI: 10.1016/j.bbadis.2013.01.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 12/31/2012] [Accepted: 01/18/2013] [Indexed: 01/29/2023]
Abstract
Cullin 4B (CUL4B) is a scaffold protein involved in the assembly of cullin-RING ubiquitin ligase (E3) complexes. Contemporary reports have identified multiple mutations of CUL4B gene as being causally associated with X-linked intellectual disability (XLID). Identifying the specific protein substrates will help to better understand the physiological functions of CUL4B. The current study identified Jun activation domain-binding protein (Jab1/CSN5) in the COP9 signalosome (CSN) complex as a novel proteolytic target for the CUL4B ubiquitin ligase complex. The impaired degradation of Jab1 was observed in cells after RNAi-mediated CUL4B depletion. Integrity of DDB1-CUL4B-ROC1 was further demonstrated to be indispensable for the degradation of Jab1. In addition, the degradation of Jab1 is independent of CUL4A, a cullin family member closely related to CUL4B. In vitro and in vivo ubiquitination assays revealed that CUL4B promoted the polyubiquitination of Jab1. Interestingly, CUL4B-silenced cells were shown to exhibit abnormal upregulation of bone morphogenetic protein (BMP) signaling. Furthermore, in vivo studies of embryonic fibroblasts in Cul4b-deficient mice demonstrated Jab1 accumulation and increased activation of the BMP signaling pathway. Together, the current findings demonstrate the CUL4B E3 ubiquitin ligase plays a key role in targeting Jab1 for degradation, potentially revealing a previously undocumented mechanism for regulation of the BMP signaling pathway involved with the CUL4B-based E3 complex. This observation may provide novel insights into the molecular mechanisms underlying CUL4B-associated XLID pathogenesis.
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Affiliation(s)
- Fengjuan He
- Institute of Medical Genetics, Shandong University School of Medicine, Jinan, Shandong, China
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Lickert H, Van Campenhout CA. Evolution of the Discs large gene family provides new insights into the establishment of apical epithelial polarity and the etiology of mental retardation. Commun Integr Biol 2012; 5:287-90. [PMID: 22896795 PMCID: PMC3419117 DOI: 10.4161/cib.19792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cell polarity is essential to the function of many cell types, such as epithelial cells and neurons. The Discs large (Dlg) scaffolding protein was identified in Drosophila as a major regulator of basolateral epithelial identity. Four Dlg orthologs (Dlg1 through 4) are found in vertebrates, and mutations in the human Dlg3 gene are associated with X-linked mental retardation. We recently found that Dlg3 controls apical epithelial polarity and tight junction formation and contributes to neural induction in mouse development.1 During evolution, Dlg3 acquired specific PPxY motifs, which bind to the WW domains of the E3 ubiquitin ligases, Nedd4 and Nedd4-2. This interaction results in monoubiquitination of Dlg3, leading to directed microtubule-dependent protein trafficking, via the exocyst complex, in different polarized cell types. Directed trafficking of Dlg3 plays an important role, during both mammalian development and in adulthood, in the establishment and maintenance of specialized apical cell junctions, such as tight junctions in epithelial cells and synapses in neurons.
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Liu HC, Enikolopov G, Chen Y. Cul4B regulates neural progenitor cell growth. BMC Neurosci 2012; 13:112. [PMID: 22992378 PMCID: PMC3506489 DOI: 10.1186/1471-2202-13-112] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 09/10/2012] [Indexed: 12/28/2022] Open
Abstract
Background Cullin ubiquitin ligases are activated via the covalent modification of Cullins by the small ubiquitin-like protein nedd8 in a process called neddylation. Genetic mutations of cullin-4b (cul4b) cause a prevalent type of X-linked intellectual disability (XLID) in males, but the physiological function of Cul4B in neuronal cells remains unclear. Results There are three major isoforms of Cul4B (1, 2, and 3) in human and rodent tissues. By examining the endogenous Cul4B isoforms in the brain, this study demonstrates that Cul4B-1 and Cul4B-2 isoforms are unneddylated and more abundant in the brain whereas the lesser species Cul4B-3 that misses the N-terminus present in the other two isoforms is neddylated. The data suggest that the N-terminus of Cul4B inhibits neddylation in the larger isoforms. Immunostaining of human NT-2 cells also shows that most Cul4B is unneddylated, especially when it is localized in the process in G0-synchronized cells. This study demonstrates that Cul4B accumulates during mitosis and downregulation of Cul4B arrests NPCs and NT-2 cells in the G2/M phase of the cell cycle. In both human and rodent brain tissues, Cul4B-positive cells accumulate β-catenin in the dentate subgranular zone and the subventricular zone. These Cul4B-positive cells also co-express the MPM-2 mitotic epitope, suggesting that Cul4B is also necessary for mitosis progression in vivo. Conclusions This study provides first evidence that unneddylated Cul4B isoforms exist in the brain and are necessary for mitosis progression in NPCs. The data suggest that unneddylated Cul4B isoforms specifically inhibits β-catenin degradation during mitosis. Furthermore, unneddylated Cul4B may play a role in addition to cell cycle since it is exclusively localized to the processes in starved NT-2 cells. Further analyses of the different isoforms of Cul4B will help understand the cognitive deficits in Cul4B-linked XLID and give insights into drug and biomarker discoveries.
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Affiliation(s)
- Helio C Liu
- Department of Geriatrics, University of Arkansas for Medical Sciences, Slot 807, Little Rock, AR 72205, USA
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UTX regulates mesoderm differentiation of embryonic stem cells independent of H3K27 demethylase activity. Proc Natl Acad Sci U S A 2012; 109:15324-9. [PMID: 22949634 DOI: 10.1073/pnas.1204166109] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
To investigate the role of histone H3K27 demethylase UTX in embryonic stem (ES) cell differentiation, we have generated UTX knockout (KO) and enzyme-dead knock-in male ES cells. Deletion of the X-chromosome-encoded UTX gene in male ES cells markedly decreases expression of the paralogous UTY gene encoded by Y chromosome, but has no effect on global H3K27me3 level, Hox gene expression, or ES cell self-renewal. However, UTX KO cells show severe defects in mesoderm differentiation and induction of Brachyury, a transcription factor essential for mesoderm development. Surprisingly, UTX regulates mesoderm differentiation and Brachyury expression independent of its enzymatic activity. UTY, which lacks detectable demethylase activity, compensates for the loss of UTX in regulating Brachyury expression. UTX and UTY bind directly to Brachyury promoter and are required for Wnt/β-catenin signaling-induced Brachyury expression in ES cells. Interestingly, male UTX KO embryos express normal levels of UTY and survive until birth. In contrast, female UTX KO mice, which lack the UTY gene, show embryonic lethality before embryonic day 11.5. Female UTX KO embryos show severe defects in both Brachyury expression and embryonic development of mesoderm-derived posterior notochord, cardiac, and hematopoietic tissues. These results indicate that UTX controls mesoderm differentiation and Brachyury expression independent of H3K27 demethylase activity, and suggest that UTX and UTY are functionally redundant in ES cell differentiation and early embryonic development.
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Ramírez-Solis R, Ryder E, Houghton R, White JK, Bottomley J. Large-scale mouse knockouts and phenotypes. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2012; 4:547-63. [PMID: 22899600 DOI: 10.1002/wsbm.1183] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Standardized phenotypic analysis of mutant forms of every gene in the mouse genome will provide fundamental insights into mammalian gene function and advance human and animal health. The availability of the human and mouse genome sequences, the development of embryonic stem cell mutagenesis technology, the standardization of phenotypic analysis pipelines, and the paradigm-shifting industrialization of these processes have made this a realistic and achievable goal. The size of this enterprise will require global coordination to ensure economies of scale in both the generation and primary phenotypic analysis of the mutant strains, and to minimize unnecessary duplication of effort. To provide more depth to the functional annotation of the genome, effective mechanisms will also need to be developed to disseminate the information and resources produced to the wider community. Better models of disease, potential new drug targets with novel mechanisms of action, and completely unsuspected genotype-phenotype relationships covering broad aspects of biology will become apparent. To reach these goals, solutions to challenges in mouse production and distribution, as well as development of novel, ever more powerful phenotypic analysis modalities will be necessary. It is a challenging and exciting time to work in mouse genetics.
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Wang G, Fulkerson CM, Malek R, Ghassemifar S, Snyder PW, Mendrysa SM. Mutations in Lyar and p53 are synergistically lethal in female mice. ACTA ACUST UNITED AC 2012; 94:729-37. [PMID: 22815056 DOI: 10.1002/bdra.23048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Revised: 05/30/2012] [Accepted: 05/31/2012] [Indexed: 11/08/2022]
Abstract
BACKGROUND Ly-1 antibody reactive clone (LYAR) is a nucleolar zinc finger protein that has been implicated in cell growth, self-renewal of embryonic stem cells, and medulloblastoma. To test whether LYAR is critical for cell growth and development, we generated Lyar mutant mice. METHODS Mice carrying the mutant Lyar(gt) allele were generated from embryonic stem cells that contained a gene-trap insertion in the Lyar gene. Phenotypic analyses were performed on Lyar mutant mice and mouse embryonic fibroblasts. Lyar(gt/gt) mice were crossed to mice lacking the p53 tumor suppressor protein and Lyar/p53 compound mutants scored for external abnormalities. RESULTS Lyar(gt/gt) homozygotes are viable, fertile, and indistinguishable from wild type littermates. However, the growth of Lyar(+/gt) and Lyar(gt/gt) mouse embryonic fibroblasts (MEFs) was impaired, coincident with an increase in the steady-state level of p53 and a key p53 effector of growth arrest, p21, suggesting that a cellular stress response is triggered in the absence of a wild type level of LYAR. Remarkably, the majority of Lyar(+/gt) and Lyar(gt/gt) female mice lacking p53 mice failed to survive. The neural tube defect (NTD) exencephaly was observed in ≈26% and ≈61% of female Lyar(+/gt;) p53(-/-) and Lyar(gt/gt;) p53(-/-) embryos, respectively. CONCLUSIONS Lyar/p53 mutant mice represent a new digenic model of NTDs. Furthermore, these studies identify Lyar as a novel candidate gene for a role in human NTDs. These results provide new data to support the idea that loss of a p53-mediated developmental checkpoint may increase the risk of NTDs owing to some germline mutations.
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Affiliation(s)
- Guan Wang
- Department of Basic Medical Sciences, School of Veterinary Medicine, Purdue University, West Lafayette, Indiana 47907, USA
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Chen CY, Tsai MS, Lin CY, Yu IS, Chen YT, Lin SR, Juan LW, Chen YT, Hsu HM, Lee LJ, Lin SW. Rescue of the genetically engineered Cul4b mutant mouse as a potential model for human X-linked mental retardation. Hum Mol Genet 2012; 21:4270-85. [PMID: 22763239 DOI: 10.1093/hmg/dds261] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mutation in CUL4B, which encodes a scaffold protein of the E3 ubiquitin ligase complex, has been found in patients with X-linked mental retardation (XLMR). However, early deletion of Cul4b in mice causes prenatal lethality, which has frustrated attempts to characterize the phenotypes in vivo. In this report, we successfully rescued Cul4b mutant mice by crossing female mice in which exons 4-5 of Cul4b were flanked by loxP sequences with Sox2-Cre male mice. In Cul4b-deficient (Cul4b(Δ)/Y) mice, no CUL4B protein was detected in any of the major organs, including the brain. In the hippocampus, the levels of CUL4A, CUL4B substrates (TOP1, β-catenin, cyclin E and WDR5) and neuronal markers (MAP2, tau-1, GAP-43, PSD95 and syn-1) were not sensitive to Cul4b deletion, whereas the number of parvalbumin (PV)-positive GABAergic interneurons was decreased in Cul4b(Δ)/Y mice, especially in the dentate gyrus (DG). Some dendritic features, including the complexity, diameter and spine density in the CA1 and DG hippocampal neurons, were also affected by Cul4b deletion. Together, the decrease in the number of PV-positive neurons and altered dendritic properties in Cul4b(Δ)/Y mice imply a reduction in inhibitory regulation and dendritic integration in the hippocampal neural circuit, which lead to increased epileptic susceptibility and spatial learning deficits. Our results identify Cul4b(Δ)/Y mice as a potential model for the non-syndromic model of XLMR that replicates the CUL4B-associated MR and is valuable for the development of a therapeutic strategy for treating MR.
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Affiliation(s)
- Chun-Yu Chen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei 100, Taiwan
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Zhao Y, Sun Y. CUL4B ubiquitin ligase in mouse development: a model for human X-linked mental retardation syndrome? Cell Res 2012; 22:1224-6. [PMID: 22584258 DOI: 10.1038/cr.2012.79] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
CUL4B, a member of the cullin-RING ubiquitin ligase family, is frequently mutated in X-linked mental retardation (XLMR) patients. The study by Liu et al. showed that Cul4b plays an essential developmental role in the extra-embryonic tissues, while it is dispensable in the embryo proper during mouse embryogenesis. Viable Cul4b-null mice provide the first animal model to study neuronal and behavioral deficiencies seen in human CUL4B XLMR patients.
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Affiliation(s)
- Yongchao Zhao
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, University of Michigan, 4424B MS-1, 1301 Catherine Street, Ann Arbor, MI 48109, USA
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