1
|
Przanowska RK, Chen Y, Uchida TO, Shibata E, Hao X, Rueda IS, Jensen K, Przanowski P, Trimboli A, Shibata Y, Leone G, Dutta A. Endo-reduplication in mouse liver after conditional mutation of ORC2 and combined mutation of ORC1 and ORC2. bioRxiv 2024:2024.04.04.588006. [PMID: 38617300 PMCID: PMC11014565 DOI: 10.1101/2024.04.04.588006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The six subunit Origin Recognition Complex (ORC) is essential for loading MCM2-7 at origins of DNA replication to promote initiation of DNA replication in organisms ranging from S. cerevisiae to humans. In rare instances, as in cancer cell-lines in culture with mutations in ORC1 , ORC2 or ORC5 , or in endo-reduplicating mouse hepatocytes in vivo without ORC1 , DNA replication has been observed in the virtual absence of individual ORC subunits. Although ORC1 is dispensable in the mouse liver for endo-reduplication, because of the homology of ORC1 with CDC6, it could be argued that CDC6 was substituting for ORC1 to restore functional ORC. Here, we have created mice with a conditional deletion of ORC2 , to demonstrate that mouse embryo fibroblasts require ORC2 for proliferation, but that the mouse hepatocytes can carry out DNA synthesis in vitro and endo-reduplicate in vivo , despite the deletion of ORC2 . Combining the conditional mutation of ORC1 and ORC2 revealed that the mouse liver can still carry out endo-reduplication despite the deletion of the two genes, both during normal development and after partial hepatectomy. Since endo-reduplication, like normal S phase replication, requires the presence of MCM2-7 on the chromatin, these results suggest that in primary hepatocytes there is a mechanism to load sufficient MCM2-7 to carry out effective DNA replication despite the virtual absence of two subunits of ORC.
Collapse
|
2
|
Abok JI, Garver WS, Edwards JS. Bioinformatic analysis of human ZPR1 gene pathogenic exome mutations. bioRxiv 2024:2024.02.27.582196. [PMID: 38464185 PMCID: PMC10925172 DOI: 10.1101/2024.02.27.582196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Advanced sequencing technologies enable rapid detection of sequence variants, aiming to uncover the molecular foundations of human genetic disorders. The challenge lies in interpreting the influence of new exome variants that lead to diverse phenotypes. Our study introduces a detailed, multi-tiered method for assessing the impact of novel variants, particularly focusing on the zinc finger protein 1 (ZPR1) gene. Herein, we employed a combination of variant effect predictors, protein stability analyses, and the American College of Medical Genetics and Association of Molecular Pathology (ACMG/AMP) guidelines. Our structural analysis pinpoints specific amino acid residues in the ZPR1 zinc finger domains that are sensitive to changes, distinguishing between benign and disease-causing coding variants using rigorous in silico tools. We examined 223 germline ZPR1 exome variants, uncovering significant ethnic disparities in the frequency of heterozygous harmful ZPR1 variants, ranging from 0.04% in the Ashkenazi Jewish population to 0.34% in African/African Americans. Additionally, the discovery of three homozygous carriers in European and South Asian groups suggests a higher occurrence of ZPR1 variants in these demographics, meriting further exploration. This research provides insights into the prevalence and implications of amino acid substitutions in the ZPR1 protein.
Collapse
Affiliation(s)
- Jeremiah I. Abok
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - William S. Garver
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - Jeremy S. Edwards
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| |
Collapse
|
3
|
Chien SC, Chen CP. Genetic Counseling of Fetal Microcephaly. J Med Ultrasound 2024; 32:1-7. [PMID: 38665355 PMCID: PMC11040482 DOI: 10.4103/jmu.jmu_18_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 04/28/2024] Open
Abstract
Fetal microcephaly is a small head with various losses of cerebral cortical volume. The affected cases may suffer from a wide range in severity of impaired cerebral development from slight to severe mental retardation. It can be an isolated finding or with other anomalies depending on the heterogeneous causes including genetic mutations, chromosomal abnormalities, congenital infectious diseases, maternal alcohol consumption, and metabolic disorders during pregnancy. It is often a lifelong and incurable condition. Thus, early detection of fetal microcephaly and identification of the underlying causes are important for clinical staff to provide appropriate genetic counseling to the parents and accurate management.
Collapse
Affiliation(s)
| | - Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Department of Biotechnology, Asia University, Taichung, Taiwan
- Institute of Clinical and Community Health Nursing, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Obstetrics and Gynecology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medical and Health Science, Asia University, Taichung, Taiwan
| |
Collapse
|
4
|
Lim Y, Tamayo-Orrego L, Schmid E, Tarnauskaite Z, Kochenova OV, Gruar R, Muramatsu S, Lynch L, Schlie AV, Carroll PL, Chistol G, Reijns MAM, Kanemaki MT, Jackson AP, Walter JC. In silico protein interaction screening uncovers DONSON's role in replication initiation. Science 2023; 381:eadi3448. [PMID: 37590370 PMCID: PMC10801813 DOI: 10.1126/science.adi3448] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
CDC45-MCM2-7-GINS (CMG) helicase assembly is the central event in eukaryotic replication initiation. In yeast, a multi-subunit "pre-loading complex" (pre-LC) accompanies GINS to chromatin-bound MCM2-7, leading to CMG formation. Here, we report that DONSON, a metazoan protein mutated in microcephalic primordial dwarfism, is required for CMG assembly in vertebrates. Using AlphaFold to screen for protein-protein interactions followed by experimental validation, we show that DONSON scaffolds a vertebrate pre-LC containing GINS, TOPBP1, and DNA pol ε. Our evidence suggests that DONSON docks the pre-LC onto MCM2-7, delivering GINS to its binding site in CMG. A patient-derived DONSON mutation compromises CMG assembly and recapitulates microcephalic dwarfism in mice. These results unify our understanding of eukaryotic replication initiation, implicate defective CMG assembly in microcephalic dwarfism, and illustrate how in silico protein-protein interaction screening accelerates mechanistic discovery.
Collapse
Affiliation(s)
- Yang Lim
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute; Boston, MA 02115, USA
| | - Lukas Tamayo-Orrego
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Edinburgh, EH4 2XU, UK
| | - Ernst Schmid
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute; Boston, MA 02115, USA
| | - Zygimante Tarnauskaite
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Edinburgh, EH4 2XU, UK
| | - Olga V. Kochenova
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute; Boston, MA 02115, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
| | - Rhian Gruar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute; Boston, MA 02115, USA
| | - Sachiko Muramatsu
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS); Mishima, Shizuoka 411-8540, Japan
| | - Luke Lynch
- Biochemistry Department, Stanford School of Medicine; Stanford, CA 94305, USA
| | - Aitana Verdu Schlie
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Edinburgh, EH4 2XU, UK
| | - Paula L. Carroll
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Edinburgh, EH4 2XU, UK
| | - Gheorghe Chistol
- Chemical and Systems Biology Department, Stanford School of Medicine; Stanford, CA 94305, USA
| | - Martin A. M. Reijns
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Edinburgh, EH4 2XU, UK
| | - Masato T. Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS); Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI; Mishima, Shizuoka 411-8540, Japan
- Department of Biological Science, The University of Tokyo; Tokyo 113-0033, Japan
| | - Andrew P. Jackson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Edinburgh, EH4 2XU, UK
| | - Johannes C. Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute; Boston, MA 02115, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
| |
Collapse
|
5
|
Farcy S, Hachour H, Bahi-Buisson N, Passemard S. Genetic Primary Microcephalies: When Centrosome Dysfunction Dictates Brain and Body Size. Cells 2023; 12:1807. [PMID: 37443841 PMCID: PMC10340463 DOI: 10.3390/cells12131807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/04/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
Primary microcephalies (PMs) are defects in brain growth that are detectable at or before birth and are responsible for neurodevelopmental disorders. Most are caused by biallelic or, more rarely, dominant mutations in one of the likely hundreds of genes encoding PM proteins, i.e., ubiquitous centrosome or microtubule-associated proteins required for the division of neural progenitor cells in the embryonic brain. Here, we provide an overview of the different types of PMs, i.e., isolated PMs with or without malformations of cortical development and PMs associated with short stature (microcephalic dwarfism) or sensorineural disorders. We present an overview of the genetic, developmental, neurological, and cognitive aspects characterizing the most representative PMs. The analysis of phenotypic similarities and differences among patients has led scientists to elucidate the roles of these PM proteins in humans. Phenotypic similarities indicate possible redundant functions of a few of these proteins, such as ASPM and WDR62, which play roles only in determining brain size and structure. However, the protein pericentrin (PCNT) is equally required for determining brain and body size. Other PM proteins perform both functions, albeit to different degrees. Finally, by comparing phenotypes, we considered the interrelationships among these proteins.
Collapse
Affiliation(s)
- Sarah Farcy
- UMR144, Institut Curie, 75005 Paris, France;
- Inserm UMR-S 1163, Institut Imagine, 75015 Paris, France
| | - Hassina Hachour
- Service de Neurologie Pédiatrique, DMU INOV-RDB, APHP, Hôpital Robert Debré, 75019 Paris, France;
| | - Nadia Bahi-Buisson
- Service de Neurologie Pédiatrique, DMU MICADO, APHP, Hôpital Necker Enfants Malades, 75015 Paris, France;
- Université Paris Cité, Inserm UMR-S 1163, Institut Imagine, 75015 Paris, France
| | - Sandrine Passemard
- Service de Neurologie Pédiatrique, DMU INOV-RDB, APHP, Hôpital Robert Debré, 75019 Paris, France;
- Université Paris Cité, Inserm UMR 1141, NeuroDiderot, 75019 Paris, France
| |
Collapse
|
6
|
Vetro A. Comment on: "The expanding genetic and clinical landscape associated with Meier-Gorlin syndrome" by Nielsen-Dandoroff et al. Eur J Hum Genet 2023:10.1038/s41431-023-01397-7. [PMID: 37248383 PMCID: PMC10400570 DOI: 10.1038/s41431-023-01397-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023] Open
Affiliation(s)
- Annalisa Vetro
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy.
| |
Collapse
|
7
|
Nielsen-Dandoroff E, Ruegg MSG, Bicknell LS. The expanding genetic and clinical landscape associated with Meier-Gorlin syndrome. Eur J Hum Genet 2023:10.1038/s41431-023-01359-z. [PMID: 37059840 PMCID: PMC10400559 DOI: 10.1038/s41431-023-01359-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/26/2023] [Accepted: 03/30/2023] [Indexed: 04/16/2023] Open
Abstract
High-throughput sequencing has become a standard first-tier approach for both diagnostics and research-based genetic testing. Consequently, this hypothesis-free testing manner has revealed the true breadth of clinical features for many established genetic disorders, including Meier-Gorlin syndrome (MGORS). Previously known as ear-patella short stature syndrome, MGORS is characterized by growth delay, microtia, and patella hypo/aplasia, as well as genital abnormalities, and breast agenesis in females. Following the initial identification of genetic causes in 2011, a total of 13 genes have been identified to date associated with MGORS. In this review, we summarise the genetic and clinical findings of each gene associated with MGORS and highlight molecular insights that have been made through studying patient variants. We note interesting observations arising across this group of genes as the number of patients has increased, such as the unusually high number of synonymous variants affecting splicing in CDC45 and a subgroup of genes that also cause craniosynostosis. We focus on the complicated molecular genetics for DONSON, where we examine potential genotype-phenotype patterns using the first 3D structural model of DONSON. The canonical role of all proteins associated with MGORS are involved in different stages of DNA replication and in addition to summarising how patient variants impact on this process, we discuss the potential contribution of non-canonical roles of these proteins to the pathophysiology of MGORS.
Collapse
Affiliation(s)
| | - Mischa S G Ruegg
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Louise S Bicknell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
| |
Collapse
|
8
|
Ter Brugge P, Moser SC, Bièche I, Kristel P, Ibadioune S, Eeckhoutte A, de Bruijn R, van der Burg E, Lutz C, Annunziato S, de Ruiter J, Masliah Planchon J, Vacher S, Courtois L, El-Botty R, Dahmani A, Montaudon E, Morisset L, Sourd L, Huguet L, Derrien H, Nemati F, Chateau-Joubert S, Larcher T, Salomon A, Decaudin D, Reyal F, Coussy F, Popova T, Wesseling J, Stern MH, Jonkers J, Marangoni E. Homologous recombination deficiency derived from whole-genome sequencing predicts platinum response in triple-negative breast cancers. Nat Commun 2023; 14:1958. [PMID: 37029129 PMCID: PMC10082194 DOI: 10.1038/s41467-023-37537-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 03/22/2023] [Indexed: 04/09/2023] Open
Abstract
The high frequency of homologous recombination deficiency (HRD) is the main rationale of testing platinum-based chemotherapy in triple-negative breast cancer (TNBC), however, the existing methods to identify HRD are controversial and there is a medical need for predictive biomarkers. We assess the in vivo response to platinum agents in 55 patient-derived xenografts (PDX) of TNBC to identify determinants of response. The HRD status, determined from whole genome sequencing, is highly predictive of platinum response. BRCA1 promoter methylation is not associated with response, in part due to residual BRCA1 gene expression and homologous recombination proficiency in different tumours showing mono-allelic methylation. Finally, in 2 cisplatin sensitive tumours we identify mutations in XRCC3 and ORC1 genes that are functionally validated in vitro. In conclusion, our results demonstrate that the genomic HRD is predictive of platinum response in a large cohort of TNBC PDX and identify alterations in XRCC3 and ORC1 genes driving cisplatin response.
Collapse
Affiliation(s)
- Petra Ter Brugge
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sarah C Moser
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ivan Bièche
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Petra Kristel
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sabrina Ibadioune
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Alexandre Eeckhoutte
- INSERM U830, Institut Curie, PSL University, 75005, Paris, France
- Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Roebi de Bruijn
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Eline van der Burg
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Catrin Lutz
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Stefano Annunziato
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Julian de Ruiter
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Sophie Vacher
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Laura Courtois
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Rania El-Botty
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Ahmed Dahmani
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Elodie Montaudon
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Ludivine Morisset
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Laura Sourd
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Léa Huguet
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Heloise Derrien
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Fariba Nemati
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | | | | | - Anne Salomon
- Department of Pathology, Institut Curie, PSL University, 75005, Paris, France
| | - Didier Decaudin
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Fabien Reyal
- Department of Surgery, Institut Curie, PSL University, 75005, Paris, France
| | - Florence Coussy
- Department of Medical Oncology, Institut Curie, PSL University, 75005, Paris, France
| | - Tatiana Popova
- INSERM U830, Institut Curie, PSL University, 75005, Paris, France
- Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Jelle Wesseling
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Marc-Henri Stern
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
- INSERM U830, Institut Curie, PSL University, 75005, Paris, France
- Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands.
| | - Elisabetta Marangoni
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France.
| |
Collapse
|
9
|
Willemsen M, Staels F, Gerbaux M, Neumann J, Schrijvers R, Meyts I, Humblet-Baron S, Liston A. DNA replication-associated inborn errors of immunity. J Allergy Clin Immunol 2023; 151:345-360. [PMID: 36395985 DOI: 10.1016/j.jaci.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
Abstract
Inborn errors of immunity are a heterogeneous group of monogenic immunologic disorders caused by mutations in genes with critical roles in the development, maintenance, or function of the immune system. The genetic basis is frequently a mutation in a gene with restricted expression and/or function in immune cells, leading to an immune disorder. Several classes of inborn errors of immunity, however, result from mutation in genes that are ubiquitously expressed. Despite the genes participating in cellular processes conserved between cell types, immune cells are disproportionally affected, leading to inborn errors of immunity. Mutations in DNA replication, DNA repair, or DNA damage response factors can result in monogenic human disease, some of which are classified as inborn errors of immunity. Genetic defects in the DNA repair machinery are a well-known cause of T-B-NK+ severe combined immunodeficiency. An emerging class of inborn errors of immunity is those caused by mutations in DNA replication factors. Considerable heterogeneity exists within the DNA replication-associated inborn errors of immunity, with diverse immunologic defects and clinical manifestations observed. These differences are suggestive for differential sensitivity of certain leukocyte subsets to deficiencies in specific DNA replication factors. Here, we provide an overview of DNA replication-associated inborn errors of immunity and discuss the emerging mechanistic insights that can explain the observed immunologic heterogeneity.
Collapse
Affiliation(s)
- Mathijs Willemsen
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.
| | - Frederik Staels
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Margaux Gerbaux
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; Pediatric Department, Academic Children Hospital Queen Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Julika Neumann
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Rik Schrijvers
- Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium; Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Isabelle Meyts
- Department of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium; Department of Pediatrics, Division of Primary Immunodeficiencies, University Hospitals Leuven, Leuven, Belgium; ERN-RITA Core Center Member, Leuven, Belgium
| | - Stephanie Humblet-Baron
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium.
| | - Adrian Liston
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium; Immunology Program, The Babraham Institute, Babraham Research Campus, Cambridge.
| |
Collapse
|
10
|
Connally NJ, Nazeen S, Lee D, Shi H, Stamatoyannopoulos J, Chun S, Cotsapas C, Cassa CA, Sunyaev SR. The missing link between genetic association and regulatory function. eLife 2022; 11:74970. [PMID: 36515579 PMCID: PMC9842386 DOI: 10.7554/elife.74970] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
The genetic basis of most traits is highly polygenic and dominated by non-coding alleles. It is widely assumed that such alleles exert small regulatory effects on the expression of cis-linked genes. However, despite the availability of gene expression and epigenomic datasets, few variant-to-gene links have emerged. It is unclear whether these sparse results are due to limitations in available data and methods, or to deficiencies in the underlying assumed model. To better distinguish between these possibilities, we identified 220 gene-trait pairs in which protein-coding variants influence a complex trait or its Mendelian cognate. Despite the presence of expression quantitative trait loci near most GWAS associations, by applying a gene-based approach we found limited evidence that the baseline expression of trait-related genes explains GWAS associations, whether using colocalization methods (8% of genes implicated), transcription-wide association (2% of genes implicated), or a combination of regulatory annotations and distance (4% of genes implicated). These results contradict the hypothesis that most complex trait-associated variants coincide with homeostatic expression QTLs, suggesting that better models are needed. The field must confront this deficit and pursue this 'missing regulation.'
Collapse
Affiliation(s)
- Noah J Connally
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Sumaiya Nazeen
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Daniel Lee
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Huwenbo Shi
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Epidemiology, Harvard T.H. Chan School of Public HealthBostonUnited States
| | | | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s HospitalBostonUnited States
| | - Chris Cotsapas
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Neurology, Yale Medical SchoolNew HavenUnited States
- Department of Genetics, Yale Medical SchoolNew HavenUnited States
| | - Christopher A Cassa
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| |
Collapse
|
11
|
Caballero M, Ge T, Rebelo AR, Seo S, Kim S, Brooks K, Zuccaro M, Kanagaraj R, Vershkov D, Kim D, Smogorzewska A, Smolka M, Benvenisty N, West SC, Egli D, Mace EM, Koren A. Comprehensive analysis of DNA replication timing across 184 cell lines suggests a role for MCM10 in replication timing regulation. Hum Mol Genet 2022; 31:2899-2917. [PMID: 35394024 PMCID: PMC9433724 DOI: 10.1093/hmg/ddac082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/18/2022] [Accepted: 04/03/2022] [Indexed: 11/14/2022] Open
Abstract
Cellular proliferation depends on the accurate and timely replication of the genome. Several genetic diseases are caused by mutations in key DNA replication genes; however, it remains unclear whether these genes influence the normal program of DNA replication timing. Similarly, the factors that regulate DNA replication dynamics are poorly understood. To systematically identify trans-acting modulators of replication timing, we profiled replication in 184 cell lines from three cell types, encompassing 60 different gene knockouts or genetic diseases. Through a rigorous approach that considers the background variability of replication timing, we concluded that most samples displayed normal replication timing. However, mutations in two genes showed consistently abnormal replication timing. The first gene was RIF1, a known modulator of replication timing. The second was MCM10, a highly conserved member of the pre-replication complex. Cells from a single patient carrying MCM10 mutations demonstrated replication timing variability comprising 46% of the genome and at different locations than RIF1 knockouts. Replication timing alterations in the mutated MCM10 cells were predominantly comprised of replication delays and initiation site gains and losses. Taken together, this study demonstrates the remarkable robustness of the human replication timing program and reveals MCM10 as a novel candidate modulator of DNA replication timing.
Collapse
Affiliation(s)
- Madison Caballero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Tiffany Ge
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ana Rita Rebelo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Seungmae Seo
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Sean Kim
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Kayla Brooks
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Michael Zuccaro
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
- Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | | | - Dan Vershkov
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Dongsung Kim
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, USA
| | - Marcus Smolka
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | | | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
- Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Emily M Mace
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
12
|
Sun F, Zhu G, He P, Wei E, Wang R, Wang Q, Tang X, Zhang Y, Shen Z. Identification, expression and subcellular localization of Orc1 in the microsporidian Nosema bombycis. Gene X 2022; 834:146607. [PMID: 35609797 DOI: 10.1016/j.gene.2022.146607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/14/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
As a typical species of microsporidium, Nosema bombycis is the pathogen causing the pébrine disease of silkworm. Rapid proliferation of N. bombycis in host cells requires replication of genetic material. As eukaryotic origin recognition protein, origin recognition complex (ORC) plays an important role in regulating DNA replication, and Orc1 is a key subunit of the origin recognition complex. In this study, we identified the Orc1 in the microsporidian N. bombycis (NbOrc1) for the first time. The NbOrc1 gene contains a complete ORF of 987 bp in length that encodes a 328 amino acid polypeptide. Indirect immunofluorescence results showed that NbOrc1 were colocalized with Nbactin and NbSAS-6 in the nuclei of N. bombycis. Subsequently, we further identified the interaction between the NbOrc1 and Nbactin by CO-IP and Western blot. These results imply that Orc1 may be involved in the proliferation of the microsporidian N. bombycis through interacting with actin.
Collapse
Affiliation(s)
- Fuzhen Sun
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Guanyu Zhu
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Ping He
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Erjun Wei
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Runpeng Wang
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China
| | - Qiang Wang
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Sericulture Research Institute of Chinese Academy of Agricultural Sciences, Zhenjiang 212018, Jiangsu Province, China
| | - Xudong Tang
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Sericulture Research Institute of Chinese Academy of Agricultural Sciences, Zhenjiang 212018, Jiangsu Province, China
| | - Yiling Zhang
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Sericulture Research Institute of Chinese Academy of Agricultural Sciences, Zhenjiang 212018, Jiangsu Province, China
| | - Zhongyuan Shen
- Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu Province, China; Sericulture Research Institute of Chinese Academy of Agricultural Sciences, Zhenjiang 212018, Jiangsu Province, China.
| |
Collapse
|
13
|
Kang TZE, Wan YCE, Zhang Z, Chan KM. Lrwd1 impacts cell proliferation and the silencing of repetitive DNA elements. Genesis 2022; 60:e23475. [PMID: 35451548 PMCID: PMC9233303 DOI: 10.1002/dvg.23475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 11/08/2022]
Abstract
LRWD1, also known as ORCA, is a nuclear protein functioning in multiple biological processes. Using its WD40 domain LRWD1 interacts with repressive histone marks and maintains the silencing of heterochromatin regions in mammalian cells. ORCA also associates with the origin recognition complex (ORC) and facilitates prereplication complex formation at late‐replicating origins. However, whether LRWD1 plays a role during development and the functional significance of LRWD1 in vivo remains largely unknown. Using gene‐trap approach we generated Lrwd1 knockout mice and examined the expression of Lrwd1 during embryonic development. We found that Lrwd1 is ubiquitously expressed in the majority of the developing mouse embryo. Depletion of LRWD1 did not affect embryonic development but the postnatal growth of the homozygous mutants is retarded. In vitro cultured mouse embryonic fibroblasts (MEFs) depleted of LRWD1 displayed a reduced proliferation compared to wild type cells. We also showed that the knockout of Lrwd1 in MEFs increased the expression of the epigenetically silenced repetitive elements but with minimal effect on the expression of protein coding genes. Together, these results suggest that LRWD1 plays an important, but not essential, role in postnatal development by regulating cell proliferation likely through modulating DNA replication.
Collapse
Affiliation(s)
- Tze Zhen Evangeline Kang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Yi Ching Esther Wan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, USA
| | - Kui Ming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| |
Collapse
|
14
|
Abstract
In this review, Phan et al. discuss the different models that have been proposed to explain how centrosome dysfunction impairs cortical development, and review the evidence supporting a unified model in which centrosome defects reduce cell proliferation in the developing cortex by prolonging mitosis and activating a mitotic surveillance pathway. Last, they also extend their discussion to centrosome-independent microcephaly mutations, such as those involved in DNA replication and repair Primary microcephaly is a brain growth disorder characterized by a severe reduction of brain size and thinning of the cerebral cortex. Many primary microcephaly mutations occur in genes that encode centrosome proteins, highlighting an important role for centrosomes in cortical development. Centrosomes are microtubule organizing centers that participate in several processes, including controlling polarity, catalyzing spindle assembly in mitosis, and building primary cilia. Understanding which of these processes are altered and how these disruptions contribute to microcephaly pathogenesis is a central unresolved question. In this review, we revisit the different models that have been proposed to explain how centrosome dysfunction impairs cortical development. We review the evidence supporting a unified model in which centrosome defects reduce cell proliferation in the developing cortex by prolonging mitosis and activating a mitotic surveillance pathway. Finally, we also extend our discussion to centrosome-independent microcephaly mutations, such as those involved in DNA replication and repair.
Collapse
|
15
|
Mei L, Cook JG. Efficiency and equity in origin licensing to ensure complete DNA replication. Biochem Soc Trans 2021; 49:2133-41. [PMID: 34545932 DOI: 10.1042/BST20210161] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/19/2021] [Accepted: 08/31/2021] [Indexed: 12/21/2022]
Abstract
The cell division cycle must be strictly regulated during both development and adult maintenance, and efficient and well-controlled DNA replication is a key event in the cell cycle. DNA replication origins are prepared in G1 phase of the cell cycle in a process known as origin licensing which is essential for DNA replication initiation in the subsequent S phase. Appropriate origin licensing includes: (1) Licensing enough origins at adequate origin licensing speed to complete licensing before G1 phase ends; (2) Licensing origins such that they are well-distributed on all chromosomes. Both aspects of licensing are critical for replication efficiency and accuracy. In this minireview, we will discuss recent advances in defining how origin licensing speed and distribution are critical to ensure DNA replication completion and genome stability.
Collapse
|
16
|
Petell CJ, Randene K, Pappas M, Sandoval D, Strahl BD, Harrison JS, Steimel JP. Mechanically transduced immunosorbent assay to measure protein-protein interactions. eLife 2021; 10:67525. [PMID: 34581668 PMCID: PMC8479797 DOI: 10.7554/elife.67525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/28/2021] [Indexed: 12/16/2022] Open
Abstract
Measuring protein-protein interaction (PPI) affinities is fundamental to biochemistry. Yet, conventional methods rely upon the law of mass action and cannot measure many PPIs due to a scarcity of reagents and limitations in the measurable affinity ranges. Here, we present a novel technique that leverages the fundamental concept of friction to produce a mechanical signal that correlates to binding potential. The mechanically transduced immunosorbent (METRIS) assay utilizes rolling magnetic probes to measure PPI interaction affinities. METRIS measures the translational displacement of protein-coated particles on a protein-functionalized substrate. The translational displacement scales with the effective friction induced by a PPI, thus producing a mechanical signal when a binding event occurs. The METRIS assay uses as little as 20 pmols of reagents to measure a wide range of affinities while exhibiting a high resolution and sensitivity. We use METRIS to measure several PPIs that were previously inaccessible using traditional methods, providing new insights into epigenetic recognition.
Collapse
Affiliation(s)
- Christopher J Petell
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, United States.,UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
| | - Kathyrn Randene
- Department of Chemistry, University of the Pacific, Stockton, United States
| | - Michael Pappas
- Department of Biological Engineering, University of the Pacific, Stockton, United States
| | - Diego Sandoval
- Department of Biological Engineering, University of the Pacific, Stockton, United States
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, United States.,UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
| | - Joseph S Harrison
- Department of Chemistry, University of the Pacific, Stockton, United States
| | - Joshua P Steimel
- Department of Mechanical Engineering, University of the Pacific, Stockton, United States
| |
Collapse
|
17
|
Padmanabhan S, Sanyal K, Dubey D. Identification and in silico analysis of the origin recognition complex in the human fungal pathogen Candida albicans. MicroPubl Biol 2021; 2021:10.17912/micropub.biology.000465. [PMID: 34568775 PMCID: PMC8456302 DOI: 10.17912/micropub.biology.000465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 11/06/2022]
Abstract
DNA replication in eukaryotes is initiated by the orchestrated assembly and association of initiator proteins (heterohexameric Origin Recognition Complex, ORC) on the replication origins. These functionally conserved proteins play significant roles in diverse cellular processes besides their central role in ignition of DNA replication at origins. Candida albicans, a major human fungal pathogen, is a diploid budding yeast that belongs to Ascomycota. However, C. albicans is significantly diverged from a well-studied model organism Saccharomyces cerevisiae, another ascomycete. The components of the DNA replication machinery in C. albicans remain largely uncharacterized. Identification of factors required for DNA replication is essential for understanding the evolution of the DNA replication machinery. We identified the putative ORC homologs in C. albicans and determined their relatedness with those of other eukaryotes including several yeast species. Our extensive in silico studies demonstrate that the domain architecture of CaORC proteins share similarities with the ORC proteins of S. cerevisiae. We dissect the domain organization of ORC (trans-acting factors) subunits that seem to associate with DNA replication origins in C. albicans. We present a model of the 3D structure of CaORC4 to gain further insights of this protein's function.
Collapse
Affiliation(s)
- Sreedevi Padmanabhan
- Molecular Biology Laboratory, Veer Bahadur Singh Purvanchal University, Jaunpur- 222003, Uttar Pradesh, India
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, JNCASR, Bangalore - 560064, India.,
Correspondence to: Kaustuv Sanyal (); Dharanidhar Dubey ()
| | - Dharanidhar Dubey
- Molecular Biology Laboratory, Veer Bahadur Singh Purvanchal University, Jaunpur- 222003, Uttar Pradesh, India.,
Correspondence to: Kaustuv Sanyal (); Dharanidhar Dubey ()
| |
Collapse
|
18
|
Zhang J, Bellani MA, Huang J, James RC, Pokharel D, Gichimu J, Gali H, Stewart G, Seidman MM. Replication of the Mammalian Genome by Replisomes Specific for Euchromatin and Heterochromatin. Front Cell Dev Biol 2021; 9:729265. [PMID: 34532320 PMCID: PMC8438199 DOI: 10.3389/fcell.2021.729265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/10/2021] [Indexed: 11/26/2022] Open
Abstract
Replisomes follow a schedule in which replication of DNA in euchromatin is early in S phase while sequences in heterochromatin replicate late. Impediments to DNA replication, referred to as replication stress, can stall replication forks triggering activation of the ATR kinase and downstream pathways. While there is substantial literature on the local consequences of replisome stalling-double strand breaks, reversed forks, or genomic rearrangements-there is limited understanding of the determinants of replisome stalling vs. continued progression. Although many proteins are recruited to stalled replisomes, current models assume a single species of "stressed" replisome, independent of genomic location. Here we describe our approach to visualizing replication fork encounters with the potent block imposed by a DNA interstrand crosslink (ICL) and our discovery of an unexpected pathway of replication restart (traverse) past an intact ICL. Additionally, we found two biochemically distinct replisomes distinguished by activity in different stages of S phase and chromatin environment. Each contains different proteins that contribute to ICL traverse.
Collapse
Affiliation(s)
- Jing Zhang
- Department of Neurosurgery, Institute for Advanced Study, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Marina A. Bellani
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Jing Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, China
| | - Ryan C. James
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Durga Pokharel
- Horizon Discovery Group plc, Lafayette, CO, United States
| | - Julia Gichimu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Himabindu Gali
- Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Grant Stewart
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, United Kingdom
| | - Michael M. Seidman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| |
Collapse
|
19
|
Nabais Sá MJ, Miller KA, McQuaid M, Koelling N, Wilkie AOM, Wurtele H, de Brouwer APM, Oliveira J. Biallelic GINS2 variant p.(Arg114Leu) causes Meier-Gorlin syndrome with craniosynostosis. J Med Genet 2021; 59:776-780. [PMID: 34353863 PMCID: PMC9340002 DOI: 10.1136/jmedgenet-2020-107572] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 07/14/2021] [Indexed: 11/04/2022]
Abstract
Introduction Replication of the nuclear genome is an essential step for cell division. Pathogenic variants in genes coding for highly conserved components of the DNA replication machinery cause Meier-Gorlin syndrome (MGORS). Objective Identification of novel genes associated with MGORS. Methods Exome sequencing was performed to investigate the genotype of an individual presenting with prenatal and postnatal growth restriction, a craniofacial gestalt of MGORS and coronal craniosynostosis. The analysis of the candidate variants employed bioinformatic tools, in silico structural protein analysis and modelling in budding yeast. Results A novel homozygous missense variant NM_016095.2:c.341G>T, p.(Arg114Leu), in GINS2 was identified. Both non-consanguineous healthy parents carried this variant. Bioinformatic analysis supports its classification as pathogenic. Functional analyses using yeast showed that this variant increases sensitivity to nicotinamide, a compound that interferes with DNA replication processes. The phylogenetically highly conserved residue p.Arg114 localises at the docking site of CDC45 and MCM5 at GINS2. Moreover, the missense change possibly disrupts the effective interaction between the GINS complex and CDC45, which is necessary for the CMG helicase complex (Cdc45/MCM2–7/GINS) to accurately operate. Interestingly, our patient’s phenotype is strikingly similar to the phenotype of patients with CDC45-related MGORS, particularly those with craniosynostosis, mild short stature and patellar hypoplasia. Conclusion GINS2 is a new disease-associated gene, expanding the genetic aetiology of MGORS.
Collapse
Affiliation(s)
- Maria J Nabais Sá
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands .,Unit for Multidisciplinary Research in Biomedicine, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Kerry A Miller
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mary McQuaid
- Maisonneuve-Rosemont Hospital Research Center, Montréal, Québec, Canada
| | - Nils Koelling
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Hugo Wurtele
- Maisonneuve-Rosemont Hospital Research Center, Montréal, Québec, Canada
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Jorge Oliveira
- Centre for Predictive and Preventive Genetics (CGPP), Institute for Molecular and Cell Biology (IBMC), Universidade do Porto, Porto, Portugal.,UnIGENe, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| |
Collapse
|
20
|
Knapp KM, Jenkins DE, Sullivan R, Harms FL, von Elsner L, Ockeloen CW, de Munnik S, Bongers EMHF, Murray J, Pachter N, Denecke J, Kutsche K, Bicknell LS. MCM complex members MCM3 and MCM7 are associated with a phenotypic spectrum from Meier-Gorlin syndrome to lipodystrophy and adrenal insufficiency. Eur J Hum Genet 2021; 29:1110-1120. [PMID: 33654309 PMCID: PMC8298597 DOI: 10.1038/s41431-021-00839-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/06/2021] [Accepted: 02/17/2021] [Indexed: 12/30/2022] Open
Abstract
The MCM2-7 helicase is a heterohexameric complex with essential roles as part of both the pre-replication and pre-initiation complexes in the early stages of DNA replication. Meier-Gorlin syndrome, a rare primordial dwarfism, is strongly associated with disruption to the pre-replication complex, including a single case described with variants in MCM5. Conversely, a biallelic pathogenic variant in MCM4 underlies immune deficiency with growth retardation, features also seen in individuals with pathogenic variants in other pre-initiation complex encoding genes such as GINS1, MCM10, and POLE. Through exome and chromium genome sequencing, supported by functional studies, we identify biallelic pathogenic variants in MCM7 and a strong candidate biallelic pathogenic variant in MCM3. We confirm variants in MCM7 are deleterious and through interfering with MCM complex formation, impact efficiency of S phase progression. The associated phenotypes are striking; one patient has typical Meier-Gorlin syndrome, whereas the second case has a multi-system disorder with neonatal progeroid appearance, lipodystrophy and adrenal insufficiency. We provide further insight into the developmental complexity of disrupted MCM function, highlighted by two patients with a similar variant profile in MCM7 but disparate clinical features. Our results build on other genetic findings linked to disruption of the pre-replication and pre-initiation complexes, and the replisome, and expand the complex clinical genetics landscape emerging due to disruption of DNA replication.
Collapse
Affiliation(s)
- Karen M Knapp
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Danielle E Jenkins
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Rosie Sullivan
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leonie von Elsner
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Charlotte W Ockeloen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sonja de Munnik
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ernie M H F Bongers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jennie Murray
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- South East Scotland Clinical Genetics Service, NHS Lothian, Western General Hospital, Edinburgh, UK
| | - Nicholas Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, Australia
- Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA, Australia
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Louise S Bicknell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
| |
Collapse
|
21
|
Alhendi ASN, Lim D, McKee S, McEntagart M, Tatton-Brown K, Temple IK, Davies JH, Mackay DJG. Whole-genome analysis as a diagnostic tool for patients referred for diagnosis of Silver-Russell syndrome: a real-world study. J Med Genet 2021; 59:613-622. [PMID: 34135092 DOI: 10.1136/jmedgenet-2021-107699] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/06/2021] [Indexed: 02/01/2023]
Abstract
BACKGROUND Silver-Russell syndrome (SRS) is an imprinting disorder characterised by prenatal and postnatal growth restriction, but its clinical features are non-specific and its differential diagnosis is broad. Known molecular causes of SRS include imprinting disturbance, single nucleotide variant (SNV), CNV or UPD affecting several genes; however, up to 40% of individuals with a clinical diagnosis of SRS currently receive no positive molecular diagnosis. METHODS To determine whether whole-genome sequencing (WGS) could uncover pathogenic variants missed by current molecular testing, we analysed data of 72 participants recruited to the 100,000 Genomes Project within the clinical category of SRS. RESULTS In 20 participants (27% of the cohort) we identified genetic variants plausibly accounting for SRS. Coding SNVs were identified in genes including CDKN1C, IGF2, IGF1R and ORC1. Maternal-effect variants were found in mothers of five participants, including two participants with imprinting disturbance and one with multilocus imprinting disorder. Two regions of homozygosity were suggestive of UPD involving imprinted regions implicated in SRS and Temple syndrome, and three plausibly pathogenic CNVs were found, including a paternal deletion of PLAGL1. In 48 participants with no plausible pathogenic variant, unbiased analysis of SNVs detected a potential association with STX4. CONCLUSION WGS analysis can detect UPD, CNV and SNV and is potentially a valuable addition to diagnosis of SRS and related growth-restricting disorders.
Collapse
Affiliation(s)
- Ahmed S N Alhendi
- Human Genetics and Genomic Medicine, Faculty of Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Derek Lim
- Department of Clinical Genetics, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - Shane McKee
- Department of Genetic Medicine, Belfast City Hospital, Belfast, UK
| | - Meriel McEntagart
- Department of Clinical Genetics, St George's Healthcare NHS Trust, London, UK
| | | | - I Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Justin H Davies
- Human Genetics and Genomic Medicine, Faculty of Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Deborah J G Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, UK .,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| |
Collapse
|
22
|
Fan H, Guo Y, Tsai YH, Storey AJ, Kim A, Gong W, Edmondson RD, Mackintosh SG, Li H, Byrum SD, Tackett AJ, Cai L, Wang GG. A conserved BAH module within mammalian BAHD1 connects H3K27me3 to Polycomb gene silencing. Nucleic Acids Res 2021; 49:4441-4455. [PMID: 33823544 PMCID: PMC8096256 DOI: 10.1093/nar/gkab210] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/28/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
Trimethylation of histone H3 lysine 27 (H3K27me3) is important for gene silencing and imprinting, (epi)genome organization and organismal development. In a prevalent model, the functional readout of H3K27me3 in mammalian cells is achieved through the H3K27me3-recognizing chromodomain harbored within the chromobox (CBX) component of canonical Polycomb repressive complex 1 (cPRC1), which induces chromatin compaction and gene repression. Here, we report that binding of H3K27me3 by a Bromo Adjacent Homology (BAH) domain harbored within BAH domain-containing protein 1 (BAHD1) is required for overall BAHD1 targeting to chromatin and for optimal repression of the H3K27me3-demarcated genes in mammalian cells. Disruption of direct interaction between BAHD1BAH and H3K27me3 by point mutagenesis leads to chromatin remodeling, notably, increased histone acetylation, at its Polycomb gene targets. Mice carrying an H3K27me3-interaction-defective mutation of Bahd1BAH causes marked embryonic lethality, showing a requirement of this pathway for normal development. Altogether, this work demonstrates an H3K27me3-initiated signaling cascade that operates through a conserved BAH ‘reader’ module within BAHD1 in mammals.
Collapse
Affiliation(s)
- Huitao Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Yiran Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Arum Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Weida Gong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Haitao Li
- Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, and Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
23
|
Ravindran E, Gutierrez de Velazco C, Ghazanfar A, Kraemer N, Zaqout S, Waheed A, Hanif M, Mughal S, Prigione A, Li N, Fang X, Hu H, Kaindl AM. Homozygous mutation in MCM7 causes autosomal recessive primary microcephaly and intellectual disability. J Med Genet 2021; 59:453-461. [PMID: 34059554 PMCID: PMC9046757 DOI: 10.1136/jmedgenet-2020-107518] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/15/2021] [Accepted: 03/02/2021] [Indexed: 11/19/2022]
Abstract
Background Minichromosomal maintenance (MCM) complex components 2, 4, 5 and 6 have been linked to human disease with phenotypes including microcephaly and intellectual disability. The MCM complex has DNA helicase activity and is thereby important for the initiation and elongation of the replication fork and highly expressed in proliferating neural stem cells. Methods Whole-exome sequencing was applied to identify the genetic cause underlying the neurodevelopmental disease of the index family. The expression pattern of Mcm7 was characterised by performing quantitative real-time PCR, in situ hybridisation and immunostaining. To prove the disease-causative nature of identified MCM7, a proof-of-principle experiment was performed. Results We reported that the homozygous missense variant c.793G>A/p.A265T (g.7:99695841C>T, NM_005916.4) in MCM7 was associated with autosomal recessive primary microcephaly (MCPH), severe intellectual disability and behavioural abnormalities in a consanguineous pedigree with three affected individuals. We found concordance between the spatiotemporal expression pattern of Mcm7 in mice and a proliferative state: Mcm7 expression was higher in early mouse developmental stages and in proliferative zones of the brain. Accordingly, Mcm7/MCM7 levels were detectable particularly in undifferentiated mouse embryonal stem cells and human induced pluripotent stem cells compared with differentiated neurons. We further demonstrate that the downregulation of Mcm7 in mouse neuroblastoma cells reduces cell viability and proliferation, and, as a proof-of-concept, that this is counterbalanced by the overexpression of wild-type but not mutant MCM7. Conclusion We report mutations of MCM7 as a novel cause of autosomal recessive MCPH and intellectual disability and highlight the crucial function of MCM7 in nervous system development.
Collapse
Affiliation(s)
- Ethiraj Ravindran
- Institute of Cell Biology and Neurobiology, Charité Universitätsmedizin Berlin, Berlin, Germany.,Department of Pediatric Neurology, Charité Universitätsmedizin Berlin, Berlin, Germany.,Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Cynthia Gutierrez de Velazco
- Institute of Cell Biology and Neurobiology, Charité Universitätsmedizin Berlin, Berlin, Germany.,Department of Pediatric Neurology, Charité Universitätsmedizin Berlin, Berlin, Germany.,Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ali Ghazanfar
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Nadine Kraemer
- Institute of Cell Biology and Neurobiology, Charité Universitätsmedizin Berlin, Berlin, Germany.,Department of Pediatric Neurology, Charité Universitätsmedizin Berlin, Berlin, Germany.,Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sami Zaqout
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar.,Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar
| | - Abdul Waheed
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Mohsan Hanif
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sadia Mughal
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Alessandro Prigione
- University Children's Hospital, Department of General Pediatrics, Heinrich-Heine-Universitat Dusseldorf, Düsseldorf, Germany
| | - Na Li
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiang Fang
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Hao Hu
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,School of Medicine, South China University of Technology, Guangzhou, China
| | - Angela M Kaindl
- Institute of Cell Biology and Neurobiology, Charité Universitätsmedizin Berlin, Berlin, Germany .,Department of Pediatric Neurology, Charité Universitätsmedizin Berlin, Berlin, Germany.,Center for Chronically Sick Children (Sozialpädiatrisches Zentrum, SPZ), Charité - Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
24
|
Bellelli R, Boulton SJ. Spotlight on the Replisome: Aetiology of DNA Replication-Associated Genetic Diseases. Trends Genet 2021; 37:317-36. [DOI: 10.1016/j.tig.2020.09.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/26/2022]
|
25
|
Hossain M, Bhalla K, Stillman B. Multiple, short protein binding motifs in ORC1 and CDC6 control the initiation of DNA replication. Mol Cell 2021; 81:1951-1969.e6. [PMID: 33761311 DOI: 10.1016/j.molcel.2021.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/18/2021] [Accepted: 02/27/2021] [Indexed: 12/18/2022]
Abstract
The initiation of DNA replication involves cell cycle-dependent assembly and disassembly of protein complexes, including the origin recognition complex (ORC) and CDC6 AAA+ ATPases. We report that multiple short linear protein motifs (SLiMs) within intrinsically disordered regions (IDRs) in ORC1 and CDC6 mediate cyclin-CDK-dependent and independent protein-protein interactions, conditional on the cell cycle phase. A domain within the ORC1 IDR is required for interaction between the ORC1 and CDC6 AAA+ domains in G1, whereas the same domain prevents CDC6-ORC1 interaction during mitosis. Then, during late G1, this domain facilitates ORC1 destruction by a SKP2-cyclin A-CDK2-dependent mechanism. During G1, the CDC6 Cy motif cooperates with cyclin E-CDK2 to promote ORC1-CDC6 interactions. The CDC6 IDR regulates self-interaction by ORC1, thereby controlling ORC1 protein levels. Protein phosphatase 1 binds directly to a SLiM in the ORC1 IDR, causing ORC1 de-phosphorylation upon mitotic exit, increasing ORC1 protein, and promoting pre-RC assembly.
Collapse
|
26
|
Chou HC, Bhalla K, Demerdesh OE, Klingbeil O, Hanington K, Aganezov S, Andrews P, Alsudani H, Chang K, Vakoc CR, Schatz MC, McCombie WR, Stillman B. The human origin recognition complex is essential for pre-RC assembly, mitosis, and maintenance of nuclear structure. eLife 2021; 10:61797. [PMID: 33522487 PMCID: PMC7877914 DOI: 10.7554/elife.61797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/30/2021] [Indexed: 12/23/2022] Open
Abstract
The origin recognition complex (ORC) cooperates with CDC6, MCM2-7, and CDT1 to form pre-RC complexes at origins of DNA replication. Here, using tiling-sgRNA CRISPR screens, we report that each subunit of ORC and CDC6 is essential in human cells. Using an auxin-inducible degradation system, we created stable cell lines capable of ablating ORC2 rapidly, revealing multiple cell division cycle phenotypes. The primary defects in the absence of ORC2 were cells encountering difficulty in initiating DNA replication or progressing through the cell division cycle due to reduced MCM2-7 loading onto chromatin in G1 phase. The nuclei of ORC2-deficient cells were also large, with decompacted heterochromatin. Some ORC2-deficient cells that completed DNA replication entered into, but never exited mitosis. ORC1 knockout cells also demonstrated extremely slow cell proliferation and abnormal cell and nuclear morphology. Thus, ORC proteins and CDC6 are indispensable for normal cellular proliferation and contribute to nuclear organization.
Collapse
Affiliation(s)
- Hsiang-Chen Chou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States.,Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, United States
| | - Kuhulika Bhalla
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | | | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | | | - Sergey Aganezov
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, United States
| | - Peter Andrews
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Habeeb Alsudani
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Kenneth Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | | | - Michael C Schatz
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, United States
| | | | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| |
Collapse
|
27
|
Schmit M, Bielinsky AK. Congenital Diseases of DNA Replication: Clinical Phenotypes and Molecular Mechanisms. Int J Mol Sci 2021; 22:E911. [PMID: 33477564 PMCID: PMC7831139 DOI: 10.3390/ijms22020911] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/19/2022] Open
Abstract
Deoxyribonucleic acid (DNA) replication can be divided into three major steps: initiation, elongation and termination. Each time a human cell divides, these steps must be reiteratively carried out. Disruption of DNA replication can lead to genomic instability, with the accumulation of point mutations or larger chromosomal anomalies such as rearrangements. While cancer is the most common class of disease associated with genomic instability, several congenital diseases with dysfunctional DNA replication give rise to similar DNA alterations. In this review, we discuss all congenital diseases that arise from pathogenic variants in essential replication genes across the spectrum of aberrant replisome assembly, origin activation and DNA synthesis. For each of these conditions, we describe their clinical phenotypes as well as molecular studies aimed at determining the functional mechanisms of disease, including the assessment of genomic stability. By comparing and contrasting these diseases, we hope to illuminate how the disruption of DNA replication at distinct steps affects human health in a surprisingly cell-type-specific manner.
Collapse
Affiliation(s)
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA;
| |
Collapse
|
28
|
Knapp KM, Murray J, Temple IK, Bicknell LS. Successful pregnancies in an adult with Meier-Gorlin syndrome harboring biallelic CDT1 variants. Am J Med Genet A 2020; 185:871-876. [PMID: 33338304 DOI: 10.1002/ajmg.a.62016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/18/2020] [Accepted: 11/27/2020] [Indexed: 01/16/2023]
Abstract
Meier-Gorlin syndrome is an autosomal recessively inherited disorder of growth retardation, accompanied by microtia and patellae a/hypoplasia and characteristic facies. Pathogenic variants in genes associated with the initiation of DNA replication underlie the condition, with biallelic variants in CDT1 the most common cause. Using 10× Chromium genome sequencing, we report CDT1 variants in an adult female, with an inframe amino acid deletion inherited in trans with a deep intronic variant which likely serves as the branchpoint site in Intron 8. Splicing defects arising from this variant were confirmed through in vitro analysis. At 49 years, she represents the oldest patient with a molecular diagnosis described in the literature and is the first reported patient with Meier-Gorlin syndrome to have carried a successful pregnancy to term. Both of her pregnancies were complicated by postpartum hemorrhage and upon subsequent necessary hysterectomy, revealed uterine abnormalities. There is scant knowledge on reproductive ability and success in patients with Meier-Gorlin syndrome. Successful pregnancies among other clinically recognizable forms of primordial dwarfism have also not been described previously. This case is therefore of clinical interest for many forms of inherited growth retardation, and will assist in providing more information and clinical guidance for females of reproductive age.
Collapse
Affiliation(s)
- Karen M Knapp
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Jennie Murray
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,South East Scotland Clinical Genetics Service, NHS Lothian, Western General Hospital, Edinburgh, UK
| | - I Karen Temple
- Human Development and Health, Faculty of Medicine University of Southampton, Southampton, UK.,Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Louise S Bicknell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| |
Collapse
|
29
|
Balasov M, Akhmetova K, Chesnokov I. Humanized Drosophila Model of the Meier-Gorlin Syndrome Reveals Conserved and Divergent Features of the Orc6 Protein. Genetics 2020; 216:995-1007. [PMID: 33037049 PMCID: PMC7768257 DOI: 10.1534/genetics.120.303698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/06/2020] [Indexed: 11/18/2022] Open
Abstract
Meier-Gorlin syndrome (MGS) is a rare, autosomal recessive disorder characterized by microtia, primordial dwarfism, small ears, and skeletal abnormalities. Patients with MGS often carry mutations in genes encoding the subunits of the Origin Recognition Complex (ORC), components of the prereplicative complex and replication machinery. Orc6 is an important component of ORC and has functions in both DNA replication and cytokinesis. A mutation in the conserved C-terminal motif of Orc6 associated with MGS impedes the interaction of Orc6 with core ORC. Recently, a new mutation in Orc6 was also identified; however, it is localized in the N-terminal domain of the protein. To study the functions of Orc6, we used the human gene to rescue the orc6 deletion in Drosophila Using this "humanized" Orc6-based Drosophila model of MGS, we discovered that unlike the previous Y225S MGS mutation in Orc6, the K23E substitution in the N-terminal TFIIB-like domain of Orc6 disrupts the protein ability to bind DNA. Our studies revealed the importance of evolutionarily conserved and variable domains of Orc6 protein, and allowed the studies of human protein functions and the analysis of the critical amino acids in live animal heterologous system, as well as provided novel insights into the mechanisms underlying MGS pathology.
Collapse
Affiliation(s)
- Maxim Balasov
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Alabama 35294
| | - Katarina Akhmetova
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Alabama 35294
| | - Igor Chesnokov
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Alabama 35294
| |
Collapse
|
30
|
McRae HM, Eccles S, Whitehead L, Alexander WS, Gécz J, Thomas T, Voss AK. Downregulation of the GHRH/GH/IGF1 axis in a mouse model of Börjeson-Forssman-Lehman syndrome. Development 2020; 147:dev.187021. [PMID: 32994169 DOI: 10.1242/dev.187021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 09/09/2020] [Indexed: 12/28/2022]
Abstract
Börjeson-Forssman-Lehmann syndrome (BFLS) is an intellectual disability and endocrine disorder caused by plant homeodomain finger 6 (PHF6) mutations. Individuals with BFLS present with short stature. We report a mouse model of BFLS, in which deletion of Phf6 causes a proportional reduction in body size compared with control mice. Growth hormone (GH) levels were reduced in the absence of PHF6. Phf6 - /Y animals displayed a reduction in the expression of the genes encoding GH-releasing hormone (GHRH) in the brain, GH in the pituitary gland and insulin-like growth factor 1 (IGF1) in the liver. Phf6 deletion specifically in the nervous system caused a proportional growth defect, indicating a neuroendocrine contribution to the phenotype. Loss of suppressor of cytokine signaling 2 (SOCS2), a negative regulator of growth hormone signaling partially rescued body size, supporting a reversible deficiency in GH signaling. These results demonstrate that PHF6 regulates the GHRH/GH/IGF1 axis.
Collapse
Affiliation(s)
- Helen M McRae
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3052, Australia.,Department of Medical Biology, The University of Melbourne, Victoria 3052, Australia
| | - Samantha Eccles
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3052, Australia
| | - Lachlan Whitehead
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3052, Australia.,Department of Medical Biology, The University of Melbourne, Victoria 3052, Australia
| | - Warren S Alexander
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3052, Australia.,Department of Medical Biology, The University of Melbourne, Victoria 3052, Australia
| | - Jozef Gécz
- Adelaide Medical School and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Tim Thomas
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3052, Australia .,Department of Medical Biology, The University of Melbourne, Victoria 3052, Australia
| | - Anne K Voss
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3052, Australia .,Department of Medical Biology, The University of Melbourne, Victoria 3052, Australia
| |
Collapse
|
31
|
Li S, Zhu A, Ren K, Li S, Chen L. DEFA1B inhibits ZIKV replication and retards cell cycle progression through interaction with ORC1. Life Sci 2020; 263:118564. [PMID: 33075374 PMCID: PMC7567675 DOI: 10.1016/j.lfs.2020.118564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/22/2020] [Accepted: 10/01/2020] [Indexed: 12/19/2022]
Abstract
Aims Zika virus (ZIKV) infection causes a public health concern because of its potential association with the development of microcephaly. During viral infections, the host innate immune response is mounted quickly to produce some endogenous functional molecules to limit virus replication and spread. Exosomes contain molecules from their cell of origin following virus infection and can enter recipient cells for intercellular communication. Here, we aim to clarify whether ZIKV-induced exosomes can regulate viral pathogenicity by transferring specific RNAs. Main methods In this study, exosomes were isolated from the supernatants of A549 cells with or without ZIKV infection. Human transcriptome array (HTA) was performed to analyze the profiling of RNAs wrapped in exosomes. Then qPCR, western blotting and ELISA were used to determine ZIKV replication. CCK-8 and flow cytometry were used to test the cell proliferation and cell cycles. Co-culture assay was used to analyze the effect of exosomes on the cell cycles of recipient cells. Key findings Through human transcriptome array (HTA) we found the defensin alpha 1B (DEFA1B) expression was significantly increased within exosomes isolated from ZIKV infected A549 cells. Additionally, we found that the extracellular DEFA1B exerts significant anti-ZIKV activity, mainly before ZIKV entering host cells. Interestingly, up-regulated DEFA1B retards the cell cycle of host cells. Further studies demonstrated that DEFA1B interacted with the origin recognition complex 1 (ORC1) which is required to initiate DNA replication during the cell cycle and increased DEFA1B expression decreased the ORC1 level in the cell nuclei. Accordingly, DEFA1B-containing exosomes can be internalized by the recipient cells to retard their cell cycles. Significance Together, our results demonstrated that the anti-ZIKV activity of DEFA1B can be mediated by exosomes, and DEFA1B interacts with ORC1 to retard cell cycles. Our study provides a novel concept that DEFA1B not only acts as an antiviral molecule during ZIKV infection but also may correlate with cell proliferation by retarding the progression of cell cycles.
Collapse
Affiliation(s)
- Shuang Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan 610052, China.
| | - Anjing Zhu
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan 610052, China
| | - Kai Ren
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan 610052, China
| | - Shilin Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan 610052, China
| | - Limin Chen
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan 610052, China; Toronto General Research Institute, University of Toronto, ON M5G 1L6, Canada.
| |
Collapse
|
32
|
Parry DA, Tamayo-Orrego L, Carroll P, Marsh JA, Greene P, Murina O, Uggenti C, Leitch A, Káposzta R, Merő G, Nagy A, Orlik B, Kovács-Pászthy B, Quigley AJ, Riszter M, Rankin J, Reijns MAM, Szakszon K, Jackson AP. PRIM1 deficiency causes a distinctive primordial dwarfism syndrome. Genes Dev 2020; 34:1520-1533. [PMID: 33060134 PMCID: PMC7608753 DOI: 10.1101/gad.340190.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 09/18/2020] [Indexed: 12/26/2022]
Abstract
DNA replication is fundamental for cell proliferation in all organisms. Nonetheless, components of the replisome have been implicated in human disease, and here we report PRIM1 encoding the catalytic subunit of DNA primase as a novel disease gene. Using a variant classification agnostic approach, biallelic mutations in PRIM1 were identified in five individuals. PRIM1 protein levels were markedly reduced in patient cells, accompanied by replication fork asymmetry, increased interorigin distances, replication stress, and prolonged S-phase duration. Consequently, cell proliferation was markedly impaired, explaining the patients' extreme growth failure. Notably, phenotypic features distinct from those previously reported with DNA polymerase genes were evident, highlighting differing developmental requirements for this core replisome component that warrant future investigation.
Collapse
Affiliation(s)
- David A Parry
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Lukas Tamayo-Orrego
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Paula Carroll
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Joseph A Marsh
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Philip Greene
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Olga Murina
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Carolina Uggenti
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Andrea Leitch
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | | | - Rita Káposzta
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Gabriella Merő
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Andrea Nagy
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Brigitta Orlik
- Institute of Pathology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Balázs Kovács-Pászthy
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Alan J Quigley
- Department of Radiology, Royal Hospital for Sick Children, Edinburgh EH9 1LF, United Kingdom
| | - Magdolna Riszter
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Julia Rankin
- Department Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter EX1 2ED, United Kingdom
| | - Martin A M Reijns
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Katalin Szakszon
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Andrew P Jackson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, the University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | | |
Collapse
|
33
|
Jaremko MJ, On KF, Thomas DR, Stillman B, Joshua-Tor L. The dynamic nature of the human origin recognition complex revealed through five cryoEM structures. eLife 2020; 9:e58622. [PMID: 32808929 PMCID: PMC7467728 DOI: 10.7554/elife.58622] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022] Open
Abstract
Genome replication is initiated from specific origin sites established by dynamic events. The Origin Recognition Complex (ORC) is necessary for orchestrating the initiation process by binding to origin DNA, recruiting CDC6, and assembling the MCM replicative helicase on DNA. Here we report five cryoEM structures of the human ORC (HsORC) that illustrate the native flexibility of the complex. The absence of ORC1 revealed a compact, stable complex of ORC2-5. Introduction of ORC1 opens the complex into several dynamic conformations. Two structures revealed dynamic movements of the ORC1 AAA+ and ORC2 winged-helix domains that likely impact DNA incorporation into the ORC core. Additional twist and pinch motions were observed in an open ORC conformation revealing a hinge at the ORC5·ORC3 interface that may facilitate ORC binding to DNA. Finally, a structure of ORC was determined with endogenous DNA bound in the core revealing important differences between human and yeast origin recognition.
Collapse
Affiliation(s)
- Matt J Jaremko
- W. M. Keck Structural Biology LaboratoryNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
- Cold Spring Harbor LaboratoryNew YorkUnited States
| | - Kin Fan On
- W. M. Keck Structural Biology LaboratoryNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
- Cold Spring Harbor LaboratoryNew YorkUnited States
| | - Dennis R Thomas
- W. M. Keck Structural Biology LaboratoryNew YorkUnited States
- Cold Spring Harbor LaboratoryNew YorkUnited States
| | | | - Leemor Joshua-Tor
- W. M. Keck Structural Biology LaboratoryNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
- Cold Spring Harbor LaboratoryNew YorkUnited States
| |
Collapse
|
34
|
Berti M, Cortez D, Lopes M. The plasticity of DNA replication forks in response to clinically relevant genotoxic stress. Nat Rev Mol Cell Biol 2020; 21:633-651. [PMID: 32612242 DOI: 10.1038/s41580-020-0257-5] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2020] [Indexed: 12/28/2022]
Abstract
Complete and accurate DNA replication requires the progression of replication forks through DNA damage, actively transcribed regions, structured DNA and compact chromatin. Recent studies have revealed a remarkable plasticity of the replication process in dealing with these obstacles, which includes modulation of replication origin firing, of the architecture of replication forks, and of the functional organization of the replication machinery in response to replication stress. However, these specialized mechanisms also expose cells to potentially dangerous transactions while replicating DNA. In this Review, we discuss how replication forks are actively stalled, remodelled, processed, protected and restarted in response to specific types of stress. We also discuss adaptations of the replication machinery and the role of chromatin modifications during these transactions. Finally, we discuss interesting recent data on the relevance of replication fork plasticity to human health, covering its role in tumorigenesis, its crosstalk with innate immunity responses and its potential as an effective cancer therapy target.
Collapse
Affiliation(s)
- Matteo Berti
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
35
|
Petr MA, Tulika T, Carmona-Marin LM, Scheibye-Knudsen M. Protecting the Aging Genome. Trends Cell Biol 2020; 30:117-132. [DOI: 10.1016/j.tcb.2019.12.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 12/15/2022]
|
36
|
McDaniel SL, Hollatz AJ, Branstad AM, Gaskill MM, Fox CA, Harrison MM. Tissue-Specific DNA Replication Defects in Drosophila melanogaster Caused by a Meier-Gorlin Syndrome Mutation in Orc4. Genetics 2020; 214:355-367. [PMID: 31818869 PMCID: PMC7017028 DOI: 10.1534/genetics.119.302938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Meier-Gorlin syndrome is a rare recessive disorder characterized by a number of distinct tissue-specific developmental defects. Genes encoding members of the origin recognition complex (ORC) and additional proteins essential for DNA replication (CDC6, CDT1, GMNN, CDC45, MCM5, and DONSON) are mutated in individuals diagnosed with MGS. The essential role of ORC is to license origins during the G1 phase of the cell cycle, but ORC has also been implicated in several nonreplicative functions. Because of its essential role in DNA replication, ORC is required for every cell division during development. Thus, it is unclear how the Meier-Gorlin syndrome mutations in genes encoding ORC lead to the tissue-specific defects associated with the disease. To begin to address these issues, we used Cas9-mediated genome engineering to generate a Drosophila melanogaster model of individuals carrying a specific Meier-Gorlin syndrome mutation in ORC4 along with control strains. Together these strains provide the first metazoan model for an MGS mutation in which the mutation was engineered at the endogenous locus along with precisely defined control strains. Flies homozygous for the engineered MGS allele reach adulthood, but with several tissue-specific defects. Genetic analysis revealed that this Orc4 allele was a hypomorph. Mutant females were sterile, and phenotypic analyses suggested that defects in DNA replication was an underlying cause. By leveraging the well-studied Drosophila system, we provide evidence that a disease-causing mutation in Orc4 disrupts DNA replication, and we propose that in individuals with MGS defects arise preferentially in tissues with a high-replication demand.
Collapse
Affiliation(s)
- Stephen L McDaniel
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Allison J Hollatz
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Anna M Branstad
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Marissa M Gaskill
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Catherine A Fox
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| |
Collapse
|
37
|
Masai H. For 60th birthday of BBRC: DNA replication factors outside S phase. Biochem Biophys Res Commun 2019; 520:685-686. [PMID: 31761077 DOI: 10.1016/j.bbrc.2019.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/01/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Hisao Masai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan.
| |
Collapse
|
38
|
Knapp KM, Sullivan R, Murray J, Gimenez G, Arn P, D'Souza P, Gezdirici A, Wilson WG, Jackson AP, Ferreira C, Bicknell LS. Linked-read genome sequencing identifies biallelic pathogenic variants in DONSON as a novel cause of Meier-Gorlin syndrome. J Med Genet 2019; 57:195-202. [PMID: 31784481 PMCID: PMC7042968 DOI: 10.1136/jmedgenet-2019-106396] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/16/2019] [Accepted: 09/20/2019] [Indexed: 11/20/2022]
Abstract
Material Linked-read whole genome sequencing (WGS) presents a new opportunity for cost-efficient singleton sequencing in place of traditional trio-based designs while generating informative-phased variants, effective for recessive disorders when parental DNA is unavailable. Methods We have applied linked-read WGS to identify novel causes of Meier-Gorlin syndrome (MGORS), a condition recognised by short stature, microtia and patella hypo/aplasia. There are eight genes associated with MGORS to date, all encoding essential components involved in establishing and initiating DNA replication. Results Our successful phasing of linked-read data led to the identification of biallelic rare variants in four individuals (24% of our cohort) in DONSON, a recently established DNA replication fork surveillance factor. The variants include five novel missense and one deep intronic variant. All were demonstrated to be deleterious to function; the missense variants all disrupted the nuclear localisation of DONSON, while the intronic variant created a novel splice site that generated an out-of-frame transcript with no residual canonical transcript produced. Conclusion Variants in DONSON have previously been associated with extreme microcephaly, short stature and limb anomalies and perinatal lethal microcephaly-micromelia syndrome. Our novel genetic findings extend the complicated spectrum of phenotypes associated with DONSON variants and promote novel hypotheses for the role of DONSON in DNA replication. While our findings reiterate that MGORS is a disorder of DNA replication, the pathophysiology is obviously complex. This successful identification of a novel disease gene for MGORS highlights the utility of linked-read WGS as a successful technology to be considered in the genetic studies of recessive conditions.
Collapse
Affiliation(s)
- Karen M Knapp
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Rosie Sullivan
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Jennie Murray
- MRC HGU, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, UK
| | - Gregory Gimenez
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Pamela Arn
- Nemours Children's Clinic, Jacksonville, Florida, USA
| | - Precilla D'Souza
- Office of the Clinical Director, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - William G Wilson
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Andrew P Jackson
- MRC HGU, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, UK
| | - Carlos Ferreira
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Louise S Bicknell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| |
Collapse
|
39
|
Casar Tena T, Maerz LD, Szafranski K, Groth M, Blätte TJ, Donow C, Matysik S, Walther P, Jeggo PA, Burkhalter MD, Philipp M. Resting cells rely on the DNA helicase component MCM2 to build cilia. Nucleic Acids Res 2019; 47:134-151. [PMID: 30329080 PMCID: PMC6326816 DOI: 10.1093/nar/gky945] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 10/04/2018] [Indexed: 12/24/2022] Open
Abstract
Minichromosome maintenance (MCM) proteins facilitate replication by licensing origins and unwinding the DNA double strand. Interestingly, the number of MCM hexamers greatly exceeds the number of firing origins suggesting additional roles of MCMs. Here we show a hitherto unanticipated function of MCM2 in cilia formation in human cells and zebrafish that is uncoupled from replication. Zebrafish depleted of MCM2 develop ciliopathy-phenotypes including microcephaly and aberrant heart looping due to malformed cilia. In non-cycling human fibroblasts, loss of MCM2 promotes transcription of a subset of genes, which cause cilia shortening and centriole overduplication. Chromatin immunoprecipitation experiments show that MCM2 binds to transcription start sites of cilia inhibiting genes. We propose that such binding may block RNA polymerase II-mediated transcription. Depletion of a second MCM (MCM7), which functions in complex with MCM2 during its canonical functions, reveals an overlapping cilia-deficiency phenotype likely unconnected to replication, although MCM7 appears to regulate a distinct subset of genes and pathways. Our data suggests that MCM2 and 7 exert a role in ciliogenesis in post-mitotic tissues.
Collapse
Affiliation(s)
- Teresa Casar Tena
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Lars D Maerz
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Karol Szafranski
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Marco Groth
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Tamara J Blätte
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Cornelia Donow
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Sabrina Matysik
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, 89081 Ulm, Germany
| | - Penelope A Jeggo
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Martin D Burkhalter
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Melanie Philipp
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| |
Collapse
|
40
|
Tarnauskaitė Ž, Bicknell LS, Marsh JA, Murray JE, Parry DA, Logan CV, Bober MB, de Silva DC, Duker AL, Sillence D, Wise C, Jackson AP, Murina O, Reijns MAM. Biallelic variants in DNA2 cause microcephalic primordial dwarfism. Hum Mutat 2019; 40:1063-1070. [PMID: 31045292 PMCID: PMC6773220 DOI: 10.1002/humu.23776] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/15/2019] [Accepted: 04/28/2019] [Indexed: 11/11/2022]
Abstract
Microcephalic primordial dwarfism (MPD) is a group of rare single-gene disorders characterized by the extreme reduction in brain and body size from early development onwards. Proteins encoded by MPD-associated genes play important roles in fundamental cellular processes, notably genome replication and repair. Here we report the identification of four MPD individuals with biallelic variants in DNA2, which encodes an adenosine triphosphate (ATP)-dependent helicase/nuclease involved in DNA replication and repair. We demonstrate that the two intronic variants (c.1764-38_1764-37ins(53) and c.74+4A>C) found in these individuals substantially impair DNA2 transcript splicing. Additionally, we identify a missense variant (c.1963A>G), affecting a residue of the ATP-dependent helicase domain that is highly conserved between humans and yeast, with the resulting substitution (p.Thr655Ala) predicted to directly impact ATP/ADP (adenosine diphosphate) binding by DNA2. Our findings support the pathogenicity of these variants as biallelic hypomorphic mutations, establishing DNA2 as an MPD disease gene.
Collapse
Affiliation(s)
- Žygimantė Tarnauskaitė
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Louise S. Bicknell
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Joseph A. Marsh
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Jennie E. Murray
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - David A. Parry
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Clare V. Logan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Michael B. Bober
- Division of Genetics, Department of PediatricsNemours/Alfred I. duPont Hospital for ChildrenWilmingtonDelaware
| | - Deepthi C. de Silva
- Department of Physiology, Faculty of MedicineUniversity of KelaniyaColomboSri Lanka
| | - Angela L. Duker
- Division of Genetics, Department of PediatricsNemours/Alfred I. duPont Hospital for ChildrenWilmingtonDelaware
| | - David Sillence
- Discipline of Genomic Medicine, Faculty of Medicine and HealthUniversity of SydneySydneyAustralia
- Western Sydney Genetics ProgramSydney Children's Hospitals NetworkWestmeadAustralia
| | - Carol Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal ResearchTexas Scottish, Rite Hospital for ChildrenDallasTexas
- McDermott Center for Human Growth and DevelopmentUniversity of Texas, Southwestern Medical CenterDallasTexas
- Department of Orthopaedic SurgeryUniversity of Texas Southwestern Medical CenterDallasTexas
- Department of PediatricsUniversity of Texas Southwestern Medical CenterDallasTexas
| | - Andrew P. Jackson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Olga Murina
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Martin A. M. Reijns
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| |
Collapse
|
41
|
Belaid R, Zouaoui H, Yazidi M, Oueslati I, Grira W, Chaker F, Chihaoui M. Meier-Gorlin syndrome: an additional case report in an adult woman. Clin Dysmorphol 2019; 28:86-90. [PMID: 30451704 DOI: 10.1097/MCD.0000000000000253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
42
|
Graber-Feesl CL, Pederson KD, Aney KJ, Shima N. Mitotic DNA Synthesis Is Differentially Regulated between Cancer and Noncancerous Cells. Mol Cancer Res 2019; 17:1687-1698. [PMID: 31113828 DOI: 10.1158/1541-7786.mcr-19-0057] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/12/2019] [Accepted: 05/16/2019] [Indexed: 11/16/2022]
Abstract
Mitotic DNA synthesis is a recently discovered mechanism that resolves late replication intermediates, thereby supporting cell proliferation under replication stress. This unusual form of DNA synthesis occurs in the absence of RAD51 or BRCA2, which led to the identification of RAD52 as a key player in this process. Notably, mitotic DNA synthesis is predominantly observed at chromosome loci that colocalize with FANCD2 foci. However, the role of this protein in mitotic DNA synthesis remains largely unknown. In this study, we investigated the role of FANCD2 and its interplay with RAD52 in mitotic DNA synthesis using aphidicolin as a universal inducer of this process. After examining eight human cell lines, we provide evidence for FANCD2 rather than RAD52 as a fundamental supporter of mitotic DNA synthesis. In cancer cell lines, FANCD2 exerts this role independently of RAD52. Surprisingly, RAD52 is dispensable for mitotic DNA synthesis in noncancerous cell lines, but these cells strongly depend on FANCD2 for this process. Therefore, RAD52 functions selectively in cancer cells as a secondary regulator in addition to FANCD2 to facilitate mitotic DNA synthesis. As an alternative to aphidicolin, we found partial inhibition of origin licensing as an effective way to induce mitotic DNA synthesis preferentially in cancer cells. Importantly, cancer cells still perform mitotic DNA synthesis by dual regulation of FANCD2 and RAD52 under such conditions. IMPLICATIONS: These key differences in mitotic DNA synthesis between cancer and noncancerous cells advance our understanding of this mechanism and can be exploited for cancer therapies.
Collapse
Affiliation(s)
- Cari L Graber-Feesl
- Department of Genetics, Cell Biology and Development, University of Minnesota, at Twin Cities, Masonic Cancer Center, Minneapolis, Minnesota
| | - Kayla D Pederson
- Department of Genetics, Cell Biology and Development, University of Minnesota, at Twin Cities, Masonic Cancer Center, Minneapolis, Minnesota
| | - Katherine J Aney
- Department of Genetics, Cell Biology and Development, University of Minnesota, at Twin Cities, Masonic Cancer Center, Minneapolis, Minnesota
| | - Naoko Shima
- Department of Genetics, Cell Biology and Development, University of Minnesota, at Twin Cities, Masonic Cancer Center, Minneapolis, Minnesota.
| |
Collapse
|
43
|
Nguyen H, Ward WS, James NG. Spatial and temporal resolution of mORC4 fluorescent variants reveals structural requirements for achieving higher order self-association and pronuclei entry. Methods Appl Fluoresc 2019; 7:035002. [PMID: 30865939 PMCID: PMC6636821 DOI: 10.1088/2050-6120/ab0f57] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The Origin Replication Complex (ORC), which is a multi-subunit protein complex composed of six proteins ORC1-6, is essential for initiating licensing at DNA replication origins. We have previously reported that ORC4 has an alternative function wherein it forms a cage surrounding the extruded chromatin in female meiosis and is required for polar body extrusion (PBE). As this is a highly unexpected finding for protein that normally binds DNA, we tested whether ORC4 can actually form larger, higher order structures, which would be necessary to form a cage-like structure. We generated two fluorescent constructs of mouse ORC4, mORC4-EGFP and mORC4-FlAsH, to examine its spatial dynamics during oocyte activation in live cells. We show that both constructs were primarily monomeric throughout the embryo but self-association into larger units was detected with both probes. However, mORC4-FlAsH clearly showed higher order self-association and unique spatial distribution while mORC4-EGFP failed to form large structures during Anaphase II. Interestingly, both variants were found in the pronuclei suggesting that its role in DNA licensing is still functional. Our results with both constructs support the prediction that ORC4 can form higher order structures in the cytoplasm, suggesting that it is possible to form a cage-like structure. The finding that FlAsH labeled ORC4 formed demonstrably larger higher order structures than ORC4-GFP suggests that ORC4 oligomerization is sensitive to the bulky addition of GFP at its carboxy terminus.
Collapse
Affiliation(s)
- Hieu Nguyen
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, 1960 East-West Rd., University of Hawaii, Honolulu, HI 96822, United States of America
| | | | | |
Collapse
|
44
|
Ting CY, Bhatia NS, Lim JY, Goh CYJ, Vasanwala RF, Ong CCP, Seow WT, Yeow VKL, Ting TW, Ng ISL, Jamuar SS. Further delineation of CDC45-related Meier-Gorlin syndrome with craniosynostosis and review of literature. Eur J Med Genet 2019; 63:103652. [PMID: 30986546 DOI: 10.1016/j.ejmg.2019.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 03/26/2019] [Accepted: 04/09/2019] [Indexed: 11/19/2022]
Abstract
Meier-Gorlin syndrome (MGS) is a rare autosomal recessive disorder characterized by the triad of short stature, microtia and absent or small patellae. We report on a patient with MGS secondary to biallelic mutations in CDC45 detected on whole exome sequencing (WES). Patients with MGS caused by mutations in CDC45 display a distinct phenotype characterized by craniosynostosis and anorectal malformation. Our patient had craniosynostosis, anorectal malformation and short stature, but did not have the microtia or patella hypoplasia. Our report also highlights the value of WES in aiding diagnosis of patients with rare genetic diseases. In conclusion, our case report and review of the literature illustrates the unique features of CDC45-related MGS as well as the benefits of WES in reducing the diagnostic odyssey for patients with rare genetic disorders.
Collapse
Affiliation(s)
- Chun Yi Ting
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore.
| | - Neha Singh Bhatia
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore; Division of Genetics, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Jiin Ying Lim
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore.
| | - Chew-Yin Jasmine Goh
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore; Division of Nursing, KK Women's and Children's Hospital, Singapore.
| | - Rashida Farhad Vasanwala
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore; Paediatrics Academic Clinical Programme, Duke-NUS Medical School, Singapore.
| | | | - Wan Tew Seow
- Neurosurgery Service, KK Women's and Children's Hospital, Singapore.
| | - Vincent Kok-Leng Yeow
- Department of Plastic, Reconstructive and Aesthetic Surgery, KK Women's and Children's Hospital, Singapore.
| | - Teck Wah Ting
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore; Paediatrics Academic Clinical Programme, Duke-NUS Medical School, Singapore.
| | - Ivy Swee-Lian Ng
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore; Paediatrics Academic Clinical Programme, Duke-NUS Medical School, Singapore.
| | - Saumya Shekhar Jamuar
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore; Paediatrics Academic Clinical Programme, Duke-NUS Medical School, Singapore; Institute of Precision Medicine, SingHealth Duke-NUS Medical School, Singapore.
| |
Collapse
|
45
|
Wang Y, Brady KS, Caiello BP, Ackerson SM, Stewart JA. Human CST suppresses origin licensing and promotes AND-1/Ctf4 chromatin association. Life Sci Alliance 2019; 2:2/2/e201800270. [PMID: 30979824 PMCID: PMC6464128 DOI: 10.26508/lsa.201800270] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 12/17/2022] Open
Abstract
Human CTC1-STN1-TEN1 (CST) is an RPA-like single-stranded DNA-binding protein that interacts with DNA polymerase α-primase (pol α) and functions in telomere replication. Previous studies suggest that CST also promotes replication restart after fork stalling. However, the precise role of CST in genome-wide replication remains unclear. In this study, we sought to understand whether CST alters origin licensing and activation. Replication origins are licensed by loading of the minichromosome maintenance 2-7 (MCM) complex in G1 followed by replisome assembly and origin firing in S-phase. We find that CST directly interacts with the MCM complex and disrupts binding of CDT1 to MCM, leading to decreased origin licensing. We also show that CST enhances replisome assembly by promoting AND-1/pol α chromatin association. Moreover, these interactions are not dependent on exogenous replication stress, suggesting that CST acts as a specialized replication factor during normal replication. Overall, our findings implicate CST as a novel regulator of origin licensing and replisome assembly/fork progression through interactions with MCM, AND-1, and pol α.
Collapse
Affiliation(s)
- Yilin Wang
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Kathryn S Brady
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Benjamin P Caiello
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Stephanie M Ackerson
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Jason A Stewart
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA .,Center for Colon Cancer Research, University of South Carolina, Columbia, SC, USA
| |
Collapse
|
46
|
Mahady L, Nadeem M, Malek-Ahmadi M, Chen K, Perez SE, Mufson EJ. Frontal Cortex Epigenetic Dysregulation During the Progression of Alzheimer's Disease. J Alzheimers Dis 2019; 62:115-131. [PMID: 29439356 DOI: 10.3233/jad-171032] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although the frontal cortex plays an important role in cognitive function and undergoes neuronal dysfunction in Alzheimer's disease (AD), the factors driving these cellular alterations remain unknown. Recent studies suggest that alterations in epigenetic regulation play a pivotal role in this process in AD. We evaluated frontal cortex histone deacetylase (HDAC) and sirtuin (SIRT) levels in tissue obtained from subjects with a premortem diagnosis of no-cognitive impairment (NCI), mild cognitive impairment (MCI), mild to moderate AD (mAD), and severe AD (sAD) using quantitative western blotting. Immunoblots revealed significant increases in HDAC1 and HDAC3 in MCI and mAD, followed by a decrease in sAD compared to NCI. HDAC2 levels remained stable across clinical groups. HDAC4 was significantly increased in MCI and mAD, but not in sAD compared to NCI. HDAC6 significantly increased during disease progression, while SIRT1 decreased in MCI, mAD, and sAD compared to NCI. HDAC1 levels negatively correlated with perceptual speed, while SIRT1 positively correlated with perceptual speed, episodic memory, global cognitive score, and Mini-Mental State Examination. HDAC1 positively, while SIRT1 negatively correlated with cortical neurofibrillary tangle counts. These findings suggest that dysregulation of epigenetic proteins contribute to neuronal dysfunction and cognitive decline in the early stage of AD.
Collapse
Affiliation(s)
- Laura Mahady
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA.,Arizona State University Interdisciplinary Graduate Program in Neuroscience, Tempe, AZ, USA
| | - Muhammad Nadeem
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
| | | | - Kewei Chen
- Banner Alzheimer's Institute, Phoenix, AZ, USA
| | - Sylvia E Perez
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Elliott J Mufson
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
| |
Collapse
|
47
|
Kalogeropoulou A, Lygerou Z, Taraviras S. Cortical Development and Brain Malformations: Insights From the Differential Regulation of Early Events of DNA Replication. Front Cell Dev Biol 2019; 7:29. [PMID: 30915332 PMCID: PMC6421272 DOI: 10.3389/fcell.2019.00029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/20/2019] [Indexed: 12/27/2022] Open
Abstract
During the development of the cortex distinct populations of Neural Stem Cells (NSCs) are defined by differences in their cell cycle duration, self-renewal capacity and transcriptional profile. A key difference across the distinct populations of NSCs is the length of G1 phase, where the licensing of the DNA replication origins takes place by the assembly of a pre-replicative complex. Licensing of DNA replication is a process that is adapted accordingly to the cell cycle length of NSCs to secure the timed duplication of the genome. Moreover, DNA replication should be efficiently coordinated with ongoing transcription for the prevention of conflicts that would impede the progression of both processes, compromising the normal course of development. In the present review we discuss how the differential regulation of the licensing and initiation of DNA replication in different cortical NSCs populations is integrated with the properties of these stem cells populations. Moreover, we examine the implication of the initial steps of DNA replication in the pathogenetic mechanisms of neurodevelopmental defects and Zika virus-related microcephaly, highlighting the significance of the differential regulation of DNA replication during brain development.
Collapse
Affiliation(s)
| | - Zoi Lygerou
- Department of General Biology, Medical School, University of Patras, Patras, Greece
| | - Stavros Taraviras
- Department of Physiology, Medical School, University of Patras, Patras, Greece
| |
Collapse
|
48
|
Maerz LD, Casar Tena T, Gerhards J, Donow C, Jeggo PA, Philipp M. Analysis of cilia dysfunction phenotypes in zebrafish embryos depleted of Origin recognition complex factors. Eur J Hum Genet 2019; 27:772-782. [PMID: 30696958 DOI: 10.1038/s41431-019-0338-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 12/26/2018] [Accepted: 01/04/2019] [Indexed: 12/15/2022] Open
Abstract
Meier-Gorlin syndrome (MGS) is a rare, congenital primordial microcephalic dwarfism disorder. MGS is caused by genetic variants of components of the origin recognition complex (ORC) consisting of ORC1-6 and the pre-replication complex, which together enable origin firing and hence genome replication. In addition, ORC1 has previously been shown to play a role in ciliogenesis. Here, we extend this work and investigate the function of ORC1 and two other members of the complex on cilia at an organismal level. Knockdown experiments in zebrafish confirmed the impact of ORC1 on cilia. ORC1-deficiency confers defects anticipated to arise from impaired cilia function such as formation of oedema, kidney cysts, curved bodies and left-right asymmetry defects. We found ORC1 furthermore required for cilium formation in zebrafish and demonstrate that ciliopathy phenotypes in ORC1-depleted zebrafish could not be rescued by reconstitution with ORC1 bearing a genetic variant previously identified in MGS patients. Loss-of-function of Orc4 and Orc6, respectively, conferred similar ciliopathy phenotypes and cilium shortening in zebrafish, suggesting that several, if not all, components of the ORC regulate ciliogenesis downstream to or in addition to their canonical function in replication initiation. This study presents the first in vivo evidence of an influence of the MGS genes of the ORC family on cilia, and consolidates the possibility that cilia dysfunction could contribute to the clinical manifestation of ORC-deficient MGS.
Collapse
Affiliation(s)
- Lars D Maerz
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany
| | - Teresa Casar Tena
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany
| | - Julian Gerhards
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany
| | - Cornelia Donow
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany
| | - Penelope A Jeggo
- Genome Damage and Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Melanie Philipp
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany.
| |
Collapse
|
49
|
Abstract
We review genetic diseases with identified molecular bases that include abnormal, reduced (hypoplasia), or absent (aplasia) patellae as a significant aspect of the phenotype. The known causal genes can be broadly organized according to three major developmental and cellular processes, although some genes may act in more than one of these: limb specification and pattern formation; DNA replication and chromatin structure; bone development and differentiation. There are also several genes whose phenotypes in mice indicate relevance to patellar development, for which human equivalent syndromes have not been reported. Developmental studies in mouse and chick embryos, as well as patellar involvement in human diseases with decreased mobility, document the additional importance of local environmental factors in patellar ontogenesis. Patellar anomalies found in humans can be an important clue to a clinical genetic diagnosis, and a better knowledge of the genetics of patellar anomalies will improve our understanding of limb development.
Collapse
Affiliation(s)
- Mark E Samuels
- Département de médicine, Université de Montréal, Montreal, Canada. .,Centre de Recherche du CHU Ste-Justine, Montreal, Canada.
| | - Philippe M Campeau
- Department of Pediatrics, Centre de Recherche du CHU Ste-Justine, Montreal, Canada
| |
Collapse
|
50
|
Heyn P, Logan CV, Fluteau A, Challis RC, Auchynnikava T, Martin CA, Marsh JA, Taglini F, Kilanowski F, Parry DA, Cormier-Daire V, Fong CT, Gibson K, Hwa V, Ibáñez L, Robertson SP, Sebastiani G, Rappsilber J, Allshire RC, Reijns MAM, Dauber A, Sproul D, Jackson AP. Gain-of-function DNMT3A mutations cause microcephalic dwarfism and hypermethylation of Polycomb-regulated regions. Nat Genet 2019; 51:96-105. [PMID: 30478443 PMCID: PMC6520989 DOI: 10.1038/s41588-018-0274-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 10/10/2018] [Indexed: 12/29/2022]
Abstract
DNA methylation and Polycomb are key factors in the establishment of vertebrate cellular identity and fate. Here we report de novo missense mutations in DNMT3A, which encodes the DNA methyltransferase DNMT3A. These mutations cause microcephalic dwarfism, a hypocellular disorder of extreme global growth failure. Substitutions in the PWWP domain abrogate binding to the histone modifications H3K36me2 and H3K36me3, and alter DNA methylation in patient cells. Polycomb-associated DNA methylation valleys, hypomethylated domains encompassing developmental genes, become methylated with concomitant depletion of H3K27me3 and H3K4me3 bivalent marks. Such de novo DNA methylation occurs during differentiation of Dnmt3aW326R pluripotent cells in vitro, and is also evident in Dnmt3aW326R/+ dwarf mice. We therefore propose that the interaction of the DNMT3A PWWP domain with H3K36me2 and H3K36me3 normally limits DNA methylation of Polycomb-marked regions. Our findings implicate the interplay between DNA methylation and Polycomb at key developmental regulators as a determinant of organism size in mammals.
Collapse
Affiliation(s)
- Patricia Heyn
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Clare V Logan
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Adeline Fluteau
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Rachel C Challis
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Tatsiana Auchynnikava
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Carol-Anne Martin
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Francesca Taglini
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Fiona Kilanowski
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - David A Parry
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Valerie Cormier-Daire
- Department of Medical Genetics, INSERM UMR 1163, Université Paris-Descartes-Sorbonne Paris Cité, Institut Imagine, AP-HP, Hôpital Necker-Enfants Malades, Paris, France
| | - Chin-To Fong
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Kate Gibson
- Genetic Health Service New Zealand, Christchurch Hospital, Christchurch, New Zealand
| | - Vivian Hwa
- Cincinnati Center for Growth Disorders, Division of Endocrinology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Lourdes Ibáñez
- Department of Endocrinology, Pediatric Research Institute Sant Joan de Déu, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - Stephen P Robertson
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Giorgia Sebastiani
- Neonatology Unit, Hospital Clinic-Maternitat, ICGON, BCNatal, University of Barcelona, Barcelona, Spain
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Robin C Allshire
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Martin A M Reijns
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Andrew Dauber
- Cincinnati Center for Growth Disorders, Division of Endocrinology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Endocrinology, Children's National Medical Center, Washington, DC, USA
| | - Duncan Sproul
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK.
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, UK.
| | - Andrew P Jackson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|