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Abramowicz I, Carpenter G, Alfieri M, Colnaghi R, Outwin E, Parent P, Thauvin-Robinet C, Iaconis D, Franco B, O'Driscoll M. Oral-facial-digital syndrome type I cells exhibit impaired DNA repair; unanticipated consequences of defective OFD1 outside of the cilia network. Hum Mol Genet 2017; 26:19-32. [PMID: 27798113 DOI: 10.1093/hmg/ddw364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/18/2016] [Indexed: 02/11/2024] Open
Abstract
Defects in OFD1 underlie the clinically complex ciliopathy, Oral-Facial-Digital syndrome Type I (OFD Type I). Our understanding of the molecular, cellular and clinical consequences of impaired OFD1 originates from its characterised roles at the centrosome/basal body/cilia network. Nonetheless, the first described OFD1 interactors were components of the TIP60 histone acetyltransferase complex. We find that OFD1 can also localise to chromatin and its reduced expression is associated with mis-localization of TIP60 in patient-derived cell lines. TIP60 plays important roles in controlling DNA repair. OFD Type I cells exhibit reduced histone acetylation and altered chromatin dynamics in response to DNA double strand breaks (DSBs). Furthermore, reduced OFD1 impaired DSB repair via homologous recombination repair (HRR). OFD1 loss also adversely impacted upon the DSB-induced G2-M checkpoint, inducing a hypersensitive and prolonged arrest. Our findings show that OFD Type I patient cells have pronounced defects in the DSB-induced histone modification, chromatin remodelling and DSB-repair via HRR; effectively phenocopying loss of TIP60. These data extend our knowledge of the molecular and cellular consequences of impaired OFD1, demonstrating that loss of OFD1 can negatively impact upon important nuclear events; chromatin plasticity and DNA repair.
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Affiliation(s)
- Iga Abramowicz
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Gillian Carpenter
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | | | - Rita Colnaghi
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Emily Outwin
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Philippe Parent
- Service de Génétique, Centre Hospitalier Universitaire de Brest, France
| | | | | | - Brunella Franco
- Telethon Institute of Genetics and Medicine, Naples, Italy
- Department of Medical Translational Sciences, Federico II University, Naples, Italy
| | - Mark O'Driscoll
- Human DNA damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
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102
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Pozo PN, Cook JG. Regulation and Function of Cdt1; A Key Factor in Cell Proliferation and Genome Stability. Genes (Basel) 2016; 8:genes8010002. [PMID: 28025526 PMCID: PMC5294997 DOI: 10.3390/genes8010002] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 12/30/2022] Open
Abstract
Successful cell proliferation requires efficient and precise genome duplication followed by accurate chromosome segregation. The Cdc10-dependent transcript 1 protein (Cdt1) is required for the first step in DNA replication, and in human cells Cdt1 is also required during mitosis. Tight cell cycle controls over Cdt1 abundance and activity are critical to normal development and genome stability. We review here recent advances in elucidating Cdt1 molecular functions in both origin licensing and kinetochore–microtubule attachment, and we describe the current understanding of human Cdt1 regulation.
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Affiliation(s)
- Pedro N Pozo
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Jeanette Gowen Cook
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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103
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Martin CA, Murray JE, Carroll P, Leitch A, Mackenzie KJ, Halachev M, Fetit AE, Keith C, Bicknell LS, Fluteau A, Gautier P, Hall EA, Joss S, Soares G, Silva J, Bober MB, Duker A, Wise CA, Quigley AJ, Phadke SR, Wood AJ, Vagnarelli P, Jackson AP. Mutations in genes encoding condensin complex proteins cause microcephaly through decatenation failure at mitosis. Genes Dev 2016; 30:2158-2172. [PMID: 27737959 PMCID: PMC5088565 DOI: 10.1101/gad.286351.116] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/09/2016] [Indexed: 11/24/2022]
Abstract
Martin et al. report that biallelic mutations in NCAPD2, NCAPH, or NCAPD3, encoding subunits of condensin complexes, cause microcephaly. Frequent anaphase chromatin bridge formation observed in apical neural progenitors during neurogenesis are the consequence of failed sister chromatid disentanglement during chromosome compaction. Compaction of chromosomes is essential for accurate segregation of the genome during mitosis. In vertebrates, two condensin complexes ensure timely chromosome condensation, sister chromatid disentanglement, and maintenance of mitotic chromosome structure. Here, we report that biallelic mutations in NCAPD2, NCAPH, or NCAPD3, encoding subunits of these complexes, cause microcephaly. In addition, hypomorphic Ncaph2 mice have significantly reduced brain size, with frequent anaphase chromatin bridge formation observed in apical neural progenitors during neurogenesis. Such DNA bridges also arise in condensin-deficient patient cells, where they are the consequence of failed sister chromatid disentanglement during chromosome compaction. This results in chromosome segregation errors, leading to micronucleus formation and increased aneuploidy in daughter cells. These findings establish “condensinopathies” as microcephalic disorders, with decatenation failure as an additional disease mechanism for microcephaly, implicating mitotic chromosome condensation as a key process ensuring mammalian cerebral cortex size.
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Affiliation(s)
- Carol-Anne Martin
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Jennie E Murray
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Paula Carroll
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Andrea Leitch
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Karen J Mackenzie
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Mihail Halachev
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Ahmed E Fetit
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Charlotte Keith
- South East Scotland Cytogenetics Service, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Louise S Bicknell
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom.,Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Adeline Fluteau
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Philippe Gautier
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Emma A Hall
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Shelagh Joss
- West of Scotland Genetic Service, Southern General Hospital, Glasgow G51 4TF, United Kingdom
| | - Gabriela Soares
- Centro de Genética Médica Doutor Jacinto Magalhães, Centro Hospitalar do Porto, 4099-028 Porto, Portugal
| | - João Silva
- Instituto de Biologia Molecular e Celular (IBMC), 4150 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Michael B Bober
- Division of Genetics, Department of Pediatrics, A.I. duPont Hospital for Children, Wilmington, Delaware 19803, USA
| | - Angela Duker
- Division of Genetics, Department of Pediatrics, A.I. duPont Hospital for Children, Wilmington, Delaware 19803, USA
| | - Carol A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA.,Department of Orthopedic Surgery, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA.,Department of Pediatrics, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA.,McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas 75350, USA
| | - Alan J Quigley
- Department of Radiology, Royal Hospital for Sick Children, Edinburgh EH9 1LF, United Kingdom
| | - Shubha R Phadke
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh 226014, India
| | | | - Andrew J Wood
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Paola Vagnarelli
- Biosciences, Research Institute for Health and Environment, Brunel University, London UB8 3PH, United Kingdom
| | - Andrew P Jackson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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104
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Shawky RM, Gamal R. Meier–Gorlin syndrome: An additional Egyptian patient with gastroesophageal reflux, hydronephrosis, renal stones and hypoplastic labia majora and minora with clitromegaly. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2016. [DOI: 10.1016/j.ejmhg.2015.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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105
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Búa S, Sotiropoulou P, Sgarlata C, Borlado LR, Eguren M, Domínguez O, Ortega S, Malumbres M, Blanpain C, Méndez J. Deregulated expression of Cdc6 in the skin facilitates papilloma formation and affects the hair growth cycle. Cell Cycle 2016; 14:3897-907. [PMID: 26697840 DOI: 10.1080/15384101.2015.1120919] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Cdc6 encodes a key protein for DNA replication, responsible for the recruitment of the MCM helicase to replication origins during the G1 phase of the cell division cycle. The oncogenic potential of deregulated Cdc6 expression has been inferred from cellular studies, but no mouse models have been described to study its effects in mammalian tissues. Here we report the generation of K5-Cdc6, a transgenic mouse strain in which Cdc6 expression is deregulated in tissues with stratified epithelia. Higher levels of CDC6 protein enhanced the loading of MCM complexes to DNA in epidermal keratinocytes, without affecting their proliferation rate or inducing DNA damage. While Cdc6 overexpression did not promote skin tumors, it facilitated the formation of papillomas in cooperation with mutagenic agents such as DMBA. In addition, the elevated levels of CDC6 protein in the skin extended the resting stage of the hair growth cycle, leading to better fur preservation in older mice.
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Affiliation(s)
- Sabela Búa
- a DNA Replication Group; Molecular Oncology Program; Spanish National Cancer Reserch Center (CNIO) ; Madrid , Spain
| | - Peggy Sotiropoulou
- b Interdisciplinary Research Institute; Université Libre de Bruxelles ; Bruxelles , Belgium
| | - Cecilia Sgarlata
- a DNA Replication Group; Molecular Oncology Program; Spanish National Cancer Reserch Center (CNIO) ; Madrid , Spain
| | - Luis R Borlado
- a DNA Replication Group; Molecular Oncology Program; Spanish National Cancer Reserch Center (CNIO) ; Madrid , Spain
| | - Manuel Eguren
- c Cell Division and Cancer Group; Molecular Oncology Program; Spanish National Cancer Research Center (CNIO) ; Madrid , Spain
| | - Orlando Domínguez
- d Genomics Unit, Biotechnology Program; Spanish National Cancer Research Center (CNIO) ; Madrid , Spain
| | - Sagrario Ortega
- e Transgenic Mice Unit; Biotechnology Program; Spanish National Cancer Research Center (CNIO) ; Madrid , Spain
| | - Marcos Malumbres
- c Cell Division and Cancer Group; Molecular Oncology Program; Spanish National Cancer Research Center (CNIO) ; Madrid , Spain
| | - Cedric Blanpain
- b Interdisciplinary Research Institute; Université Libre de Bruxelles ; Bruxelles , Belgium
| | - Juan Méndez
- a DNA Replication Group; Molecular Oncology Program; Spanish National Cancer Reserch Center (CNIO) ; Madrid , Spain
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106
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Hossain M, Stillman B. Opposing roles for DNA replication initiator proteins ORC1 and CDC6 in control of Cyclin E gene transcription. eLife 2016; 5. [PMID: 27458800 PMCID: PMC4987141 DOI: 10.7554/elife.12785] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 07/18/2016] [Indexed: 12/28/2022] Open
Abstract
Newly born cells either continue to proliferate or exit the cell division cycle. This decision involves delaying expression of Cyclin E that promotes DNA replication. ORC1, the Origin Recognition Complex (ORC) large subunit, is inherited into newly born cells after it binds to condensing chromosomes during the preceding mitosis. We demonstrate that ORC1 represses Cyclin E gene (CCNE1) transcription, an E2F1 activated gene that is also repressed by the Retinoblastoma (RB) protein. ORC1 binds to RB, the histone methyltransferase SUV39H1 and to its repressive histone H3K9me3 mark. ORC1 cooperates with SUV39H1 and RB protein to repress E2F1-dependent CCNE1 transcription. In contrast, the ORC1-related replication protein CDC6 binds Cyclin E-CDK2 kinase and in a feedback loop removes RB from ORC1, thereby hyper-activating CCNE1 transcription. The opposing effects of ORC1 and CDC6 in controlling the level of Cyclin E ensures genome stability and a mechanism for linking directly DNA replication and cell division commitment. DOI:http://dx.doi.org/10.7554/eLife.12785.001 Living cells must replicate their DNA before they divide so that the newly formed cells can each receive an identical copy of the genetic material. Before DNA replication can begin, a number of proteins must come together to form so-called pre-replicative complexes at many locations along the DNA molecules. These protein complexes then serve as landing pads for many other DNA replication proteins. One component of the pre-replicative complex, a protein called ORC1, helps to recruit another protein called CDC6 that in turn acts with Cyclin E to promote the replication of the DNA. Cyclin E is a protein that is only expressed when cells commit to divide. Previous research has shown that a lack of ORC1 causes the levels of Cyclin E to rise in human cells, but it was not understood how cells regulate the levels of Cyclin E. Now, Hossain and Stillman show that the ORC1 protein switches off the gene that encodes Cyclin E early on in newly born cells, and therefore prevents the Cyclin E protein from being produced. The experiments show that ORC1 does this by binding near one end of the gene for Cyclin E and interacting with two other proteins to inactivate the gene. Thus, ORC1 establishes a period when Cyclin E is absent from a newly formed cell. This essentially gives the cell time to ‘decide’ (based on external cues and its own signaling) whether it will divide again or enter into a non-dividing state. When a cell does decide to divide, the levels of CDC6 rise. CDC6 is another component of the pre-replicative complex and Hossain and Stillman find that CDC6 works to counteract the effects of ORC1 and reactivate the gene for Cyclin E. This activity leads to a dramatic increase in the production of Cyclin E, which in turn allows the cells to commit to another round of DNA replication and division. The opposing effects of ORC1 and CDC6 control the levels of Cyclin E and provide a link between DNA replication and a cell’s decision to divide. Further work is now needed to see whether ORC1 inactivates other genes in addition to the one that encodes Cyclin E. DOI:http://dx.doi.org/10.7554/eLife.12785.002
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Affiliation(s)
- Manzar Hossain
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
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107
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Fenwick AL, Kliszczak M, Cooper F, Murray J, Sanchez-Pulido L, Twigg SRF, Goriely A, McGowan SJ, Miller KA, Taylor IB, Logan C, Bozdogan S, Danda S, Dixon J, Elsayed SM, Elsobky E, Gardham A, Hoffer MJV, Koopmans M, McDonald-McGinn DM, Santen GWE, Savarirayan R, de Silva D, Vanakker O, Wall SA, Wilson LC, Yuregir OO, Zackai EH, Ponting CP, Jackson AP, Wilkie AOM, Niedzwiedz W, Bicknell LS. Mutations in CDC45, Encoding an Essential Component of the Pre-initiation Complex, Cause Meier-Gorlin Syndrome and Craniosynostosis. Am J Hum Genet 2016; 99:125-38. [PMID: 27374770 PMCID: PMC5005452 DOI: 10.1016/j.ajhg.2016.05.019] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/09/2016] [Indexed: 11/19/2022] Open
Abstract
DNA replication precisely duplicates the genome to ensure stable inheritance of genetic information. Impaired licensing of origins of replication during the G1 phase of the cell cycle has been implicated in Meier-Gorlin syndrome (MGS), a disorder defined by the triad of short stature, microtia, and a/hypoplastic patellae. Biallelic partial loss-of-function mutations in multiple components of the pre-replication complex (preRC; ORC1, ORC4, ORC6, CDT1, or CDC6) as well as de novo stabilizing mutations in the licensing inhibitor, GMNN, cause MGS. Here we report the identification of mutations in CDC45 in 15 affected individuals from 12 families with MGS and/or craniosynostosis. CDC45 encodes a component of both the pre-initiation (preIC) and CMG helicase complexes, required for initiation of DNA replication origin firing and ongoing DNA synthesis during S-phase itself, respectively, and hence is functionally distinct from previously identified MGS-associated genes. The phenotypes of affected individuals range from syndromic coronal craniosynostosis to severe growth restriction, fulfilling diagnostic criteria for Meier-Gorlin syndrome. All mutations identified were biallelic and included synonymous mutations altering splicing of physiological CDC45 transcripts, as well as amino acid substitutions expected to result in partial loss of function. Functionally, mutations reduce levels of full-length transcripts and protein in subject cells, consistent with partial loss of CDC45 function and a predicted limited rate of DNA replication and cell proliferation. Our findings therefore implicate the preIC as an additional protein complex involved in the etiology of MGS and connect the core cellular machinery of genome replication with growth, chondrogenesis, and cranial suture homeostasis.
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Affiliation(s)
- Aimee L Fenwick
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Maciej Kliszczak
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Fay Cooper
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jennie Murray
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Luis Sanchez-Pulido
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Anne Goriely
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Simon J McGowan
- Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Kerry A Miller
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Indira B Taylor
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Clare Logan
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sevcan Bozdogan
- Department of Medical Genetics, Mersin University, Mersin, 33343 Cukurova, Turkey
| | - Sumita Danda
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, Tamil Nadu 632004, India
| | - Joanne Dixon
- Genetic Health Service NZ-South Island Hub, Christchurch Hospital, Christchurch, Canterbury 8140, New Zealand
| | - Solaf M Elsayed
- Children's Hospital, Ain Shams University, Cairo 11566, Egypt
| | - Ezzat Elsobky
- Children's Hospital, Ain Shams University, Cairo 11566, Egypt
| | - Alice Gardham
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Mariette J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Marije Koopmans
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Donna M McDonald-McGinn
- Clinical Genetics, The Children's Hospital of Philadelphia, 34th & Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Ravi Savarirayan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Deepthi de Silva
- Department of Physiology, Faculty of Medicine, University of Kelaniya, Ragama, Gampaha GQ 11010, Sri Lanka
| | - Olivier Vanakker
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Steven A Wall
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Louise C Wilson
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Ozge Ozalp Yuregir
- Genetic Diagnosis Center, Adana Numune Training and Research Hospital, Cukurova, Adana, 01170, Turkey
| | - Elaine H Zackai
- Clinical Genetics, The Children's Hospital of Philadelphia, 34th & Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Chris P Ponting
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Andrew P Jackson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Wojciech Niedzwiedz
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Louise S Bicknell
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK; Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, Otago 9016, New Zealand.
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108
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The Histone Variant H3.3 Is Enriched at Drosophila Amplicon Origins but Does Not Mark Them for Activation. G3-GENES GENOMES GENETICS 2016; 6:1661-71. [PMID: 27172191 PMCID: PMC4889662 DOI: 10.1534/g3.116.028068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Eukaryotic DNA replication begins from multiple origins. The origin recognition complex (ORC) binds origin DNA and scaffolds assembly of a prereplicative complex (pre-RC), which is subsequently activated to initiate DNA replication. In multicellular eukaryotes, origins do not share a strict DNA consensus sequence, and their activity changes in concert with chromatin status during development, but mechanisms are ill-defined. Previous genome-wide analyses in Drosophila and other organisms have revealed a correlation between ORC binding sites and the histone variant H3.3. This correlation suggests that H3.3 may designate origin sites, but this idea has remained untested. To address this question, we examined the enrichment and function of H3.3 at the origins responsible for developmental gene amplification in the somatic follicle cells of the Drosophila ovary. We found that H3.3 is abundant at these amplicon origins. H3.3 levels remained high when replication initiation was blocked, indicating that H3.3 is abundant at the origins before activation of the pre-RC. H3.3 was also enriched at the origins during early oogenesis, raising the possibility that H3.3 bookmarks sites for later amplification. However, flies null mutant for both of the H3.3 genes in Drosophila did not have overt defects in developmental gene amplification or genomic replication, suggesting that H3.3 is not essential for the assembly or activation of the pre-RC at origins. Instead, our results imply that the correlation between H3.3 and ORC sites reflects other chromatin attributes that are important for origin function.
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109
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Petrakis TG, Komseli ES, Papaioannou M, Vougas K, Polyzos A, Myrianthopoulos V, Mikros E, Trougakos IP, Thanos D, Branzei D, Townsend P, Gorgoulis VG. Exploring and exploiting the systemic effects of deregulated replication licensing. Semin Cancer Biol 2016; 37-38:3-15. [PMID: 26707000 DOI: 10.1016/j.semcancer.2015.12.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/10/2015] [Accepted: 12/15/2015] [Indexed: 02/07/2023]
Abstract
Maintenance and accurate propagation of the genetic material are key features for physiological development and wellbeing. The replication licensing machinery is crucial for replication precision as it ensures that replication takes place once per cell cycle. Thus, the expression status of the components comprising the replication licensing apparatus is tightly regulated to avoid re-replication; a form of replication stress that leads to genomic instability, a hallmark of cancer. In the present review we discuss the mechanistic basis of replication licensing deregulation, which leads to systemic effects, exemplified by its role in carcinogenesis and a variety of genetic syndromes. In addition, new insights demonstrate that above a particular threshold, the replication licensing factor Cdc6 acts as global transcriptional regulator, outlining new lines of exploration. The role of the putative replication licensing factor ChlR1/DDX11, mutated in the Warsaw Breakage Syndrome, in cancer is also considered. Finally, future perspectives focused on the potential therapeutic advantage by targeting replication licensing factors, and particularly Cdc6, are discussed.
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Affiliation(s)
- Theodoros G Petrakis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece
| | - Eirini-Stavroula Komseli
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece
| | - Marilena Papaioannou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece
| | - Kostas Vougas
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | | | - Emmanuel Mikros
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Athens, Athens, Greece
| | - Ioannis P Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens, Greece
| | - Dimitris Thanos
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Dana Branzei
- FIRC (Fondazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology (IFOM), Milan, Italy
| | - Paul Townsend
- Faculty Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece; Biomedical Research Foundation of the Academy of Athens, Athens, Greece; Faculty Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
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110
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Shalev SA, Khayat M, Etty DS, Elpeleg O. Further insight into the phenotype associated with a mutation in the ORC6 gene, causing Meier-Gorlin syndrome 3. Am J Med Genet A 2016; 167A:607-11. [PMID: 25691413 DOI: 10.1002/ajmg.a.36906] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 11/14/2014] [Indexed: 12/18/2022]
Abstract
Mutations in genes encoding the origin recognition complex subunits cause Meier-Gorlin syndrome. The disease manifests a triad of short stature, small ears, and small and/or absent patellae with variable expressivity. We report on the identification of a homozygous deleterious mutation in the ORC6 gene in previously described fetuses at the severe end of the Meier-Gorlin spectrum. The phenotype included severe intrauterine growth retardation, dislocation of knees, gracile bones, clubfeet, and small mandible and chest. To date, the clinical presentation of ORC6-associated Meier-Gorlin syndrome has been mild compared to other the phenotype associated with other loci. The present report expands the clinical phenotype associated with ORC6 mutations to include severely abnormal embryological development suggesting a possible genotype-phenotype correlation.
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Affiliation(s)
- Stavit Allon Shalev
- Genetics Institute, Ha'Emek Medical center, Afula, Israel; Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
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111
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Wit JM, Oostdijk W, Losekoot M, van Duyvenvoorde HA, Ruivenkamp CAL, Kant SG. MECHANISMS IN ENDOCRINOLOGY: Novel genetic causes of short stature. Eur J Endocrinol 2016; 174:R145-73. [PMID: 26578640 DOI: 10.1530/eje-15-0937] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/16/2015] [Indexed: 12/17/2022]
Abstract
The fast technological development, particularly single nucleotide polymorphism array, array-comparative genomic hybridization, and whole exome sequencing, has led to the discovery of many novel genetic causes of growth failure. In this review we discuss a selection of these, according to a diagnostic classification centred on the epiphyseal growth plate. We successively discuss disorders in hormone signalling, paracrine factors, matrix molecules, intracellular pathways, and fundamental cellular processes, followed by chromosomal aberrations including copy number variants (CNVs) and imprinting disorders associated with short stature. Many novel causes of GH deficiency (GHD) as part of combined pituitary hormone deficiency have been uncovered. The most frequent genetic causes of isolated GHD are GH1 and GHRHR defects, but several novel causes have recently been found, such as GHSR, RNPC3, and IFT172 mutations. Besides well-defined causes of GH insensitivity (GHR, STAT5B, IGFALS, IGF1 defects), disorders of NFκB signalling, STAT3 and IGF2 have recently been discovered. Heterozygous IGF1R defects are a relatively frequent cause of prenatal and postnatal growth retardation. TRHA mutations cause a syndromic form of short stature with elevated T3/T4 ratio. Disorders of signalling of various paracrine factors (FGFs, BMPs, WNTs, PTHrP/IHH, and CNP/NPR2) or genetic defects affecting cartilage extracellular matrix usually cause disproportionate short stature. Heterozygous NPR2 or SHOX defects may be found in ∼3% of short children, and also rasopathies (e.g., Noonan syndrome) can be found in children without clear syndromic appearance. Numerous other syndromes associated with short stature are caused by genetic defects in fundamental cellular processes, chromosomal abnormalities, CNVs, and imprinting disorders.
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Affiliation(s)
- Jan M Wit
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Wilma Oostdijk
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Monique Losekoot
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Hermine A van Duyvenvoorde
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Sarina G Kant
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
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112
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Li S, Yang Z, Du X, Liu R, Wilkinson AW, Gozani O, Jacobsen SE, Patel DJ, Du J. Structural Basis for the Unique Multivalent Readout of Unmodified H3 Tail by Arabidopsis ORC1b BAH-PHD Cassette. Structure 2016; 24:486-94. [PMID: 26876097 DOI: 10.1016/j.str.2016.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/28/2015] [Accepted: 01/09/2016] [Indexed: 01/22/2023]
Abstract
DNA replication initiation relies on the formation of the origin recognition complex (ORC). The plant ORC subunit 1 (ORC1) protein possesses a conserved N-terminal BAH domain with an embedded plant-specific PHD finger, whose function may be potentially regulated by an epigenetic mechanism. Here, we report structural and biochemical studies on the Arabidopsis thaliana ORC1b BAH-PHD cassette which specifically recognizes the unmodified H3 tail. The crystal structure of ORC1b BAH-PHD cassette in complex with an H3(1-15) peptide reveals a strict requirement for the unmodified state of R2, T3, and K4 on the H3 tail and a novel multivalent BAH and PHD readout mode for H3 peptide recognition. Such recognition may contribute to epigenetic regulation of the initiation of DNA replication.
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Affiliation(s)
- Sisi Li
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Zhenlin Yang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Du
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Liu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Alex W Wilkinson
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Jiamu Du
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China.
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113
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Muñoz S, Méndez J. DNA replication stress: from molecular mechanisms to human disease. Chromosoma 2016; 126:1-15. [PMID: 26797216 DOI: 10.1007/s00412-016-0573-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 12/29/2022]
Abstract
The genome of proliferating cells must be precisely duplicated in each cell division cycle. Chromosomal replication entails risks such as the possibility of introducing breaks and/or mutations in the genome. Hence, DNA replication requires the coordinated action of multiple proteins and regulatory factors, whose deregulation causes severe developmental diseases and predisposes to cancer. In recent years, the concept of "replicative stress" (RS) has attracted much attention as it impinges directly on genomic stability and offers a promising new avenue to design anticancer therapies. In this review, we summarize recent progress in three areas: (1) endogenous and exogenous factors that contribute to RS, (2) molecular mechanisms that mediate the cellular responses to RS, and (3) the large list of diseases that are directly or indirectly linked to RS.
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Affiliation(s)
- Sergio Muñoz
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain
| | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain.
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114
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Harley ME, Murina O, Leitch A, Higgs MR, Bicknell LS, Yigit G, Blackford AN, Zlatanou A, Mackenzie KJ, Reddy K, Halachev M, McGlasson S, Reijns MAM, Fluteau A, Martin CA, Sabbioneda S, Elcioglu NH, Altmüller J, Thiele H, Greenhalgh L, Chessa L, Maghnie M, Salim M, Bober MB, Nürnberg P, Jackson SP, Hurles ME, Wollnik B, Stewart GS, Jackson AP. TRAIP promotes DNA damage response during genome replication and is mutated in primordial dwarfism. Nat Genet 2016; 48:36-43. [PMID: 26595769 PMCID: PMC4697364 DOI: 10.1038/ng.3451] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/26/2015] [Indexed: 12/11/2022]
Abstract
DNA lesions encountered by replicative polymerases threaten genome stability and cell cycle progression. Here we report the identification of mutations in TRAIP, encoding an E3 RING ubiquitin ligase, in patients with microcephalic primordial dwarfism. We establish that TRAIP relocalizes to sites of DNA damage, where it is required for optimal phosphorylation of H2AX and RPA2 during S-phase in response to ultraviolet (UV) irradiation, as well as fork progression through UV-induced DNA lesions. TRAIP is necessary for efficient cell cycle progression and mutations in TRAIP therefore limit cellular proliferation, providing a potential mechanism for microcephaly and dwarfism phenotypes. Human genetics thus identifies TRAIP as a component of the DNA damage response to replication-blocking DNA lesions.
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Affiliation(s)
- Margaret E Harley
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Olga Murina
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrea Leitch
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Louise S Bicknell
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Gökhan Yigit
- Institute of Human Genetics, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | | | - Anastasia Zlatanou
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Karen J Mackenzie
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Kaalak Reddy
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Mihail Halachev
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Sarah McGlasson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Martin A M Reijns
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Adeline Fluteau
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Carol-Anne Martin
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | | | - Nursel H Elcioglu
- Department of Pediatric Genetics, Marmara University Pendik Hospital, Istanbul, Turkey
| | - Janine Altmüller
- Institute of Human Genetics, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Lynn Greenhalgh
- Cheshire and Merseyside Clinical Genetics Service, Liverpool Women's Hospital, Liverpool, L12 2AP, UK
| | - Luciana Chessa
- Department of Clinical and Molecular Medicine, University Sapienza, A.O.S. Andrea, I-00189 Roma, Italy
| | - Mohamad Maghnie
- Department of Pediatrics, IRCCS, Giannina Gaslini, University of Genova, 16147 Genova, Italy
| | - Mahmoud Salim
- Department of Pediatric Genetics, Marmara University Pendik Hospital, Istanbul, Turkey
| | - Michael B Bober
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware 19803, USA
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Stephen P Jackson
- The Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | | | - Bernd Wollnik
- Institute of Human Genetics, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
- Institute of Human Genetics, University Medical Centre Göttingen, 37073 Göttingen, Germany
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Andrew P Jackson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
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115
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Hutchins JRA, Aze A, Coulombe P, Méchali M. Characteristics of Metazoan DNA Replication Origins. DNA REPLICATION, RECOMBINATION, AND REPAIR 2016. [PMCID: PMC7120227 DOI: 10.1007/978-4-431-55873-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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116
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Burrage LC, Charng WL, Eldomery MK, Willer JR, Davis EE, Lugtenberg D, Zhu W, Leduc MS, Akdemir ZC, Azamian M, Zapata G, Hernandez PP, Schoots J, de Munnik SA, Roepman R, Pearring JN, Jhangiani S, Katsanis N, Vissers LELM, Brunner HG, Beaudet AL, Rosenfeld JA, Muzny DM, Gibbs RA, Eng CM, Xia F, Lalani SR, Lupski JR, Bongers EMHF, Yang Y. De Novo GMNN Mutations Cause Autosomal-Dominant Primordial Dwarfism Associated with Meier-Gorlin Syndrome. Am J Hum Genet 2015; 97:904-13. [PMID: 26637980 PMCID: PMC4678788 DOI: 10.1016/j.ajhg.2015.11.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 11/05/2015] [Indexed: 12/21/2022] Open
Abstract
Meier-Gorlin syndrome (MGS) is a genetically heterogeneous primordial dwarfism syndrome known to be caused by biallelic loss-of-function mutations in one of five genes encoding pre-replication complex proteins: ORC1, ORC4, ORC6, CDT1, and CDC6. Mutations in these genes cause disruption of the origin of DNA replication initiation. To date, only an autosomal-recessive inheritance pattern has been described in individuals with this disorder, with a molecular etiology established in about three-fourths of cases. Here, we report three subjects with MGS and de novo heterozygous mutations in the 5' end of GMNN, encoding the DNA replication inhibitor geminin. We identified two truncating mutations in exon 2 (the 1(st) coding exon), c.16A>T (p.Lys6(∗)) and c.35_38delTCAA (p.Ile12Lysfs(∗)4), and one missense mutation, c.50A>G (p.Lys17Arg), affecting the second-to-last nucleotide of exon 2 and possibly RNA splicing. Geminin is present during the S, G2, and M phases of the cell cycle and is degraded during the metaphase-anaphase transition by the anaphase-promoting complex (APC), which recognizes the destruction box sequence near the 5' end of the geminin protein. All three GMNN mutations identified alter sites 5' to residue Met28 of the protein, which is located within the destruction box. We present data supporting a gain-of-function mechanism, in which the GMNN mutations result in proteins lacking the destruction box and hence increased protein stability and prolonged inhibition of replication leading to autosomal-dominant MGS.
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Affiliation(s)
- Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Texas Children's Hospital, Houston, TX 77030, USA
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jason R Willer
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA
| | - Dorien Lugtenberg
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Wenmiao Zhu
- Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX 77030, USA
| | - Magalie S Leduc
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mahshid Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gladys Zapata
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Patricia P Hernandez
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeroen Schoots
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Sonja A de Munnik
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Ronald Roepman
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Jillian N Pearring
- Department of Ophthalmology, Duke University Medical Center, Durham, NC 27701, USA
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX 77030, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Texas Children's Hospital, Houston, TX 77030, USA
| | - Ernie M H F Bongers
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands.
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX 77030, USA.
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Baron J, Sävendahl L, De Luca F, Dauber A, Phillip M, Wit JM, Nilsson O. Short and tall stature: a new paradigm emerges. Nat Rev Endocrinol 2015; 11:735-46. [PMID: 26437621 PMCID: PMC5002943 DOI: 10.1038/nrendo.2015.165] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In the past, the growth hormone (GH)-insulin-like growth factor 1 (IGF-1) axis was often considered to be the main system that regulated childhood growth and, therefore, determined short stature and tall stature. However, findings have now revealed that the GH-IGF-1 axis is just one of many regulatory systems that control chondrogenesis in the growth plate, which is the biological process that drives height gain. Consequently, normal growth in children depends not only on GH and IGF-1 but also on multiple hormones, paracrine factors, extracellular matrix molecules and intracellular proteins that regulate the activity of growth plate chondrocytes. Mutations in the genes that encode many of these local proteins cause short stature or tall stature. Similarly, genome-wide association studies have revealed that the normal variation in height seems to be largely due to genes outside the GH-IGF-1 axis that affect growth at the growth plate through a wide variety of mechanisms. These findings point to a new conceptual framework for understanding short and tall stature that is centred not on two particular hormones but rather on the growth plate, which is the structure responsible for height gain.
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Affiliation(s)
- Jeffrey Baron
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Lars Sävendahl
- Division of Pediatric Endocrinology, Department of Women’s and Children’s Health, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Francesco De Luca
- St. Christopher’s Hospital for Children, Section of Endocrinology and Diabetes; Drexel University College of Medicine, Department of Pediatrics, Philadelphia, PA, U.S.A
| | - Andrew Dauber
- Cincinnati Center for Growth Disorders, Cincinnati Children’s Hospital Medical Center, Division of Endocrinology, Cincinnati, Ohio, USA
| | - Moshe Phillip
- The Jesse Z and Sara Lea Shafer Institute for Endocrinology and Diabetes, National Center for Children’s Diabetes, Schneider Children’s Medical Center of Israel, Petah Tikva, Israel
| | - Jan M. Wit
- Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Ola Nilsson
- Division of Pediatric Endocrinology, Department of Women’s and Children’s Health, Karolinska Institutet, SE-171 76 Stockholm, Sweden
- Center for Molecular Medicine, Department of Women’s and Children’s Health, Karolinska Institutet, SE-171 76 Stockholm, Sweden
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118
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van Nuland R, Gozani O. Histone H4 Lysine 20 (H4K20) Methylation, Expanding the Signaling Potential of the Proteome One Methyl Moiety at a Time. Mol Cell Proteomics 2015; 15:755-64. [PMID: 26598646 DOI: 10.1074/mcp.r115.054742] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Indexed: 12/13/2022] Open
Abstract
Covalent post-translational modifications (PTMs) of proteins can regulate the structural and functional state of a protein in the absence of primary changes in the underlying sequence. Common PTMs include phosphorylation, acetylation, and methylation. Histone proteins are critical regulators of the genome and are subject to a highly abundant and diverse array of PTMs. To highlight the functional complexity added to the proteome by lysine methylation signaling, here we will focus on lysine methylation of histone proteins, an important modification in the regulation of chromatin and epigenetic processes. We review the signaling pathways and functions associated with a single residue, H4K20, as a model chromatin and clinically important mark that regulates biological processes ranging from the DNA damage response and DNA replication to gene expression and silencing.
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Affiliation(s)
- Rick van Nuland
- From the Department of Biology, Stanford University, Stanford, California 94305
| | - Or Gozani
- From the Department of Biology, Stanford University, Stanford, California 94305
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119
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Menolfi D, Delamarre A, Lengronne A, Pasero P, Branzei D. Essential Roles of the Smc5/6 Complex in Replication through Natural Pausing Sites and Endogenous DNA Damage Tolerance. Mol Cell 2015; 60:835-46. [PMID: 26698660 PMCID: PMC4691243 DOI: 10.1016/j.molcel.2015.10.023] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/02/2015] [Accepted: 10/09/2015] [Indexed: 02/07/2023]
Abstract
The essential functions of the conserved Smc5/6 complex remain elusive. To uncover its roles in genome maintenance, we established Saccharomyces cerevisiae cell-cycle-regulated alleles that enable restriction of Smc5/6 components to S or G2/M. Unexpectedly, the essential functions of Smc5/6 segregated fully and selectively to G2/M. Genetic screens that became possible with generated alleles identified processes that crucially rely on Smc5/6 specifically in G2/M: metabolism of DNA recombination structures triggered by endogenous replication stress, and replication through natural pausing sites located in late-replicating regions. In the first process, Smc5/6 modulates remodeling of recombination intermediates, cooperating with dissolution activities. In the second, Smc5/6 prevents chromosome fragility and toxic recombination instigated by prolonged pausing and the fork protection complex, Tof1-Csm3. Our results thus dissect Smc5/6 essential roles and reveal that combined defects in DNA damage tolerance and pausing site-replication cause recombination-mediated DNA lesions, which we propose to drive developmental and cancer-prone disorders. Cell-cycle-regulated alleles reveal Smc5/6-essential functions to segregate in G2/M Genetic screen with new hypomorphic allele identifies processes relying on Smc5/6 Smc5/6 acts on recombination structures triggered by endogenous replication stress Smc5/6 prevents fragility and mediates replication through natural pausing sites
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Affiliation(s)
- Demis Menolfi
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Axel Delamarre
- IGH, Institute of Human Genetics CNRS UPR 1142, 141 rue de la Cardonille F-34396 Cedex 5, Montpellier, France
| | - Armelle Lengronne
- IGH, Institute of Human Genetics CNRS UPR 1142, 141 rue de la Cardonille F-34396 Cedex 5, Montpellier, France
| | - Philippe Pasero
- IGH, Institute of Human Genetics CNRS UPR 1142, 141 rue de la Cardonille F-34396 Cedex 5, Montpellier, France
| | - Dana Branzei
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy.
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120
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Liu F, Ren C, Li H, Zhou P, Bo X, Shu W. De novo identification of replication-timing domains in the human genome by deep learning. Bioinformatics 2015; 32:641-9. [PMID: 26545821 PMCID: PMC4795613 DOI: 10.1093/bioinformatics/btv643] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/27/2015] [Indexed: 12/31/2022] Open
Abstract
Motivation: The de novo identification of the initiation and termination zones—regions that replicate earlier or later than their upstream and downstream neighbours, respectively—remains a key challenge in DNA replication. Results: Building on advances in deep learning, we developed a novel hybrid architecture combining a pre-trained, deep neural network and a hidden Markov model (DNN-HMM) for the de novo identification of replication domains using replication timing profiles. Our results demonstrate that DNN-HMM can significantly outperform strong, discriminatively trained Gaussian mixture model–HMM (GMM-HMM) systems and other six reported methods that can be applied to this challenge. We applied our trained DNN-HMM to identify distinct replication domain types, namely the early replication domain (ERD), the down transition zone (DTZ), the late replication domain (LRD) and the up transition zone (UTZ), using newly replicated DNA sequencing (Repli-Seq) data across 15 human cells. A subsequent integrative analysis revealed that these replication domains harbour unique genomic and epigenetic patterns, transcriptional activity and higher-order chromosomal structure. Our findings support the ‘replication-domain’ model, which states (1) that ERDs and LRDs, connected by UTZs and DTZs, are spatially compartmentalized structural and functional units of higher-order chromosomal structure, (2) that the adjacent DTZ-UTZ pairs form chromatin loops and (3) that intra-interactions within ERDs and LRDs tend to be short-range and long-range, respectively. Our model reveals an important chromatin organizational principle of the human genome and represents a critical step towards understanding the mechanisms regulating replication timing. Availability and implementation: Our DNN-HMM method and three additional algorithms can be freely accessed at https://github.com/wenjiegroup/DNN-HMM. The replication domain regions identified in this study are available in GEO under the accession ID GSE53984. Contact:shuwj@bmi.ac.cn or boxc@bmi.ac.cn Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Feng Liu
- Department of Biotechnology, Beijing Institute of Radiation Medicine and
| | - Chao Ren
- Department of Biotechnology, Beijing Institute of Radiation Medicine and
| | - Hao Li
- Department of Biotechnology, Beijing Institute of Radiation Medicine and
| | - Pingkun Zhou
- Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Department of Biotechnology, Beijing Institute of Radiation Medicine and
| | - Wenjie Shu
- Department of Biotechnology, Beijing Institute of Radiation Medicine and
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121
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Geister KA, Brinkmeier ML, Cheung LY, Wendt J, Oatley MJ, Burgess DL, Kozloff KM, Cavalcoli JD, Oatley JM, Camper SA. LINE-1 Mediated Insertion into Poc1a (Protein of Centriole 1 A) Causes Growth Insufficiency and Male Infertility in Mice. PLoS Genet 2015; 11:e1005569. [PMID: 26496357 PMCID: PMC4619696 DOI: 10.1371/journal.pgen.1005569] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 09/15/2015] [Indexed: 11/19/2022] Open
Abstract
Skeletal dysplasias are a common, genetically heterogeneous cause of short stature that can result from disruptions in many cellular processes. We report the identification of the lesion responsible for skeletal dysplasia and male infertility in the spontaneous, recessive mouse mutant chagun. We determined that Poc1a, encoding protein of the centriole 1a, is disrupted by the insertion of a processed Cenpw cDNA, which is flanked by target site duplications, suggestive of a LINE-1 retrotransposon-mediated event. Mutant fibroblasts have impaired cilia formation and multipolar spindles. Male infertility is caused by defective spermatogenesis early in meiosis and progressive germ cell loss. Spermatogonial stem cell transplantation studies revealed that Poc1a is essential for normal function of both Sertoli cells and germ cells. The proliferative zone of the growth plate is small and disorganized because chondrocytes fail to re-align after cell division and undergo increased apoptosis. Poc1a and several other genes associated with centrosome function can affect the skeleton and lead to skeletal dysplasias and primordial dwarfisms. This mouse mutant reveals how centrosome dysfunction contributes to defects in skeletal growth and male infertility.
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Affiliation(s)
- Krista A. Geister
- Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Michelle L. Brinkmeier
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Leonard Y. Cheung
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jennifer Wendt
- Roche NimbleGen, Inc., Research and Development, Madison, Wisconsin, United States of America
| | - Melissa J. Oatley
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Daniel L. Burgess
- Roche NimbleGen, Inc., Research and Development, Madison, Wisconsin, United States of America
| | - Kenneth M. Kozloff
- Department of Orthopedic Surgery, University of Michigan, Ann Arbor, Michigan, United States of America
| | - James D. Cavalcoli
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jon M. Oatley
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Sally A. Camper
- Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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122
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Alvarez S, Díaz M, Flach J, Rodriguez-Acebes S, López-Contreras AJ, Martínez D, Cañamero M, Fernández-Capetillo O, Isern J, Passegué E, Méndez J. Replication stress caused by low MCM expression limits fetal erythropoiesis and hematopoietic stem cell functionality. Nat Commun 2015; 6:8548. [PMID: 26456157 PMCID: PMC4608254 DOI: 10.1038/ncomms9548] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 09/04/2015] [Indexed: 01/04/2023] Open
Abstract
Replicative stress during embryonic development influences ageing and predisposition to disease in adults. A protective mechanism against replicative stress is provided by the licensing of thousands of origins in G1 that are not necessarily activated in the subsequent S-phase. These ‘dormant' origins provide a backup in the presence of stalled forks and may confer flexibility to the replication program in specific cell types during differentiation, a role that has remained unexplored. Here we show, using a mouse strain with hypomorphic expression of the origin licensing factor mini-chromosome maintenance (MCM)3 that limiting origin licensing in vivo affects the functionality of hematopoietic stem cells and the differentiation of rapidly-dividing erythrocyte precursors. Mcm3-deficient erythroblasts display aberrant DNA replication patterns and fail to complete maturation, causing lethal anemia. Our results indicate that hematopoietic progenitors are particularly sensitive to replication stress, and full origin licensing ensures their correct differentiation and functionality. What causes hematopoietic stem cell loss of functionality? Here, Alvarez et al. show that loss of origin licensing factor MCM3 induces replicative stress (RS), causing aberrant erythrocyte maturation, but mice strains with higher tolerance to RS can overcome this defect.
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Affiliation(s)
- Silvia Alvarez
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Marcos Díaz
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Johanna Flach
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, 94143 California, USA
| | - Sara Rodriguez-Acebes
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Andrés J López-Contreras
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Dolores Martínez
- Flow Cytometry Unit, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Marta Cañamero
- Compared Pathology Unit, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Oscar Fernández-Capetillo
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Joan Isern
- Spanish National Cardiovascular Research Center (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Emmanuelle Passegué
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, 94143 California, USA
| | - Juan Méndez
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
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123
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Abdel-Salam GMH, Emam BA, Khalil YM, Abdel-Hamid MS. Long-term survival in microcephalic osteodysplastic primordial dwarfism type I: Evaluation of an 18-year-old male with g.55G>A homozygous mutation in RNU4ATAC. Am J Med Genet A 2015; 170A:277-82. [PMID: 26419500 DOI: 10.1002/ajmg.a.37409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/16/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Ghada M H Abdel-Salam
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Bayoumi A Emam
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Yasmin M Khalil
- Department of Orodental Genetics, Orodental Research Division, National Research Centre, Cairo, Egypt
| | - Mohamed S Abdel-Hamid
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
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124
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Shaheen R, Abdel-Salam GMH, Guy MP, Alomar R, Abdel-Hamid MS, Afifi HH, Ismail SI, Emam BA, Phizicky EM, Alkuraya FS. Mutation in WDR4 impairs tRNA m(7)G46 methylation and causes a distinct form of microcephalic primordial dwarfism. Genome Biol 2015; 16:210. [PMID: 26416026 PMCID: PMC4587777 DOI: 10.1186/s13059-015-0779-x] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/14/2015] [Indexed: 04/13/2023] Open
Abstract
Background Primordial dwarfism is a state of extreme prenatal and postnatal growth deficiency, and is characterized by marked clinical and genetic heterogeneity. Results Two presumably unrelated consanguineous families presented with an apparently novel form of primordial dwarfism in which severe growth deficiency is accompanied by distinct facial dysmorphism, brain malformation (microcephaly, agenesis of corpus callosum, and simplified gyration), and severe encephalopathy with seizures. Combined autozygome/exome analysis revealed a novel missense mutation in WDR4 as the likely causal variant. WDR4 is the human ortholog of the yeast Trm82, an essential component of the Trm8/Trm82 holoenzyme that effects a highly conserved and specific (m7G46) methylation of tRNA. The human mutation and the corresponding yeast mutation result in a significant reduction of m7G46 methylation of specific tRNA species, which provides a potential mechanism for primordial dwarfism associated with this lesion, since reduced m7G46 modification causes a growth deficiency phenotype in yeast. Conclusion Our study expands the number of biological pathways underlying primordial dwarfism and adds to a growing list of human diseases linked to abnormal tRNA modification. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0779-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ghada M H Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Michael P Guy
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Current address: Department of Chemistry, Northern Kentucky University, Highland Heights, KY, USA
| | - Rana Alomar
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohamed S Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Hanan H Afifi
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Samira I Ismail
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Bayoumi A Emam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
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125
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de Munnik SA, Hoefsloot EH, Roukema J, Schoots J, Knoers NVAM, Brunner HG, Jackson AP, Bongers EMHF. Meier-Gorlin syndrome. Orphanet J Rare Dis 2015; 10:114. [PMID: 26381604 PMCID: PMC4574002 DOI: 10.1186/s13023-015-0322-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 08/18/2015] [Indexed: 11/12/2022] Open
Abstract
Meier-Gorlin syndrome (MGS) is a rare autosomal recessive primordial dwarfism disorder, characterized by microtia, patellar applasia/hypoplasia, and a proportionate short stature. Associated clinical features encompass feeding problems, congenital pulmonary emphysema, mammary hypoplasia in females and urogenital anomalies, such as cryptorchidism and hypoplastic labia minora and majora. Typical facial characteristics during childhood comprise a small mouth with full lips and micro-retrognathia. During ageing, a narrow, convex nose becomes more prominent. The diagnosis MGS should be considered in patients with at least two of the three features of the clinical triad of microtia, patellar anomalies, and pre- and postnatal growth retardation. In patients with short stature and/or microtia, the patellae should be assessed with care by ultrasonography before age 6 or radiography thereafter. Mutations in one of five genes (ORC1, ORC4, ORC6, CDT1, and CDC6) of the pre-replication complex, involved in DNA-replication, are detected in approximately 67-78 % of patients with MGS. Patients with ORC1 and ORC4 mutations appear to have the most severe short stature and microcephaly. Management should be directed towards in-depth investigation, treatment and prevention of associated problems, such as growth retardation, feeding problems, hearing loss, luxating patellae, knee pain, gonarthrosis, and possible pulmonary complications due to congenital pulmonary emphysema with or without broncho- or laryngomalacia. Growth hormone treatment is ineffective in most patients with MGS, but may be effective in patients in whom growth continues to decrease after the first year of life (usually growth velocity normalizes after the first year) and with low levels of IGF1. At present, few data is available about reproduction of females with MGS, but the risk of premature labor might be increased. Here, we propose experience-based guidelines for the regular care and treatment of MGS patients.
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Affiliation(s)
- Sonja A de Munnik
- Department of Human Genetics 836, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
| | - Elisabeth H Hoefsloot
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Jolt Roukema
- Department of Pediatrics, Division of Respiratory Medicine, Radboud University Medical Center, Amalia Children's Hospital, Nijmegen, The Netherlands.
| | - Jeroen Schoots
- Department of Human Genetics 836, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
| | - Nine V A M Knoers
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Han G Brunner
- Department of Human Genetics 836, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
| | - Andrew P Jackson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK.
| | - Ernie M H F Bongers
- Department of Human Genetics 836, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
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126
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Primordial dwarfism: overview of clinical and genetic aspects. Mol Genet Genomics 2015; 291:1-15. [PMID: 26323792 DOI: 10.1007/s00438-015-1110-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 08/21/2015] [Indexed: 01/16/2023]
Abstract
Primordial dwarfism is a group of genetic disorders which include Seckel Syndrome, Silver-Russell Syndrome, Microcephalic Osteodysplastic Primordial Dwarfism types I/III, II and Meier-Gorlin Syndrome. This genetic disorder group is characterized by intra-uterine growth retardation and post-natal growth abnormalities which occur as a result of disorganized molecular and genomic changes in embryonic stage and, thus, it represents a unique area to study growth and developmental abnormalities. Lot of research has been carried out on different aspects; however, a consolidated review that discusses an overall spectrum of this disorder is not accessible. Recent research in this area points toward important molecular and cellular mechanisms in human body that regulate the complexity of growth process. Studies have emerged that have clearly associated with a number of abnormal chromosomal, genetic and epigenetic alterations that can predispose an embryo to develop PD-associated developmental defects. Finding and associating such fundamental changes to its subtypes will help in re-examination of alleged functions at both cellular and developmental levels and thus reveal the intrinsic mechanism that leads to a balanced growth. Although such findings have unraveled a subtle understanding of growth process, we further require active research in terms of identification of reliable biomarkers for different subtypes as an immediate requirement for clinical utilization. It is hoped that further study will advance the understanding of basic mechanisms regulating growth relevant to human health. Therefore, this review has been written with an aim to present an overview of chromosomal, molecular and epigenetic modifications reported to be associated with different subtypes of this heterogenous disorder. Further, latest findings with respect to clinical and molecular genetics research have been summarized to aid the medical fraternity in their clinical utility, for diagnosing disorders where there are overlapping physical attributes and simultaneously inform about the latest developments in PD biology.
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127
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Liu J, Zimmer K, Rusch DB, Paranjape N, Podicheti R, Tang H, Calvi BR. DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila. Nucleic Acids Res 2015; 43:8746-61. [PMID: 26227968 PMCID: PMC4605296 DOI: 10.1093/nar/gkv766] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/16/2015] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic origins of DNA replication are bound by the origin recognition complex (ORC), which scaffolds assembly of a pre-replicative complex (pre-RC) that is then activated to initiate replication. Both pre-RC assembly and activation are strongly influenced by developmental changes to the epigenome, but molecular mechanisms remain incompletely defined. We have been examining the activation of origins responsible for developmental gene amplification in Drosophila. At a specific time in oogenesis, somatic follicle cells transition from genomic replication to a locus-specific replication from six amplicon origins. Previous evidence indicated that these amplicon origins are activated by nucleosome acetylation, but how this affects origin chromatin is unknown. Here, we examine nucleosome position in follicle cells using micrococcal nuclease digestion with Ilumina sequencing. The results indicate that ORC binding sites and other essential origin sequences are nucleosome-depleted regions (NDRs). Nucleosome position at the amplicons was highly similar among developmental stages during which ORC is or is not bound, indicating that being an NDR is not sufficient to specify ORC binding. Importantly, the data suggest that nucleosomes and ORC have opposite preferences for DNA sequence and structure. We propose that nucleosome hyperacetylation promotes pre-RC assembly onto adjacent DNA sequences that are disfavored by nucleosomes but favored by ORC.
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Affiliation(s)
- Jun Liu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Kurt Zimmer
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Neha Paranjape
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Ram Podicheti
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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128
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Ge XQ, Han J, Cheng EC, Yamaguchi S, Shima N, Thomas JL, Lin H. Embryonic Stem Cells License a High Level of Dormant Origins to Protect the Genome against Replication Stress. Stem Cell Reports 2015; 5:185-94. [PMID: 26190528 PMCID: PMC4618655 DOI: 10.1016/j.stemcr.2015.06.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 06/12/2015] [Accepted: 06/13/2015] [Indexed: 12/27/2022] Open
Abstract
Maintaining genomic integrity during DNA replication is essential for stem cells. DNA replication origins are licensed by the MCM2–7 complexes, with most of them remaining dormant. Dormant origins (DOs) rescue replication fork stalling in S phase and ensure genome integrity. However, it is not known whether DOs exist and play important roles in any stem cell type. Here, we show that embryonic stem cells (ESCs) contain more DOs than tissue stem/progenitor cells such as neural stem/progenitor cells (NSPCs). Partial depletion of DOs does not affect ESC self-renewal but impairs their differentiation, including toward the neural lineage. However, reduction of DOs in NSPCs impairs their self-renewal due to accumulation of DNA damage and apoptosis. Furthermore, mice with reduced DOs show abnormal neurogenesis and semi-embryonic lethality. Our results reveal that ESCs are equipped with more DOs to better protect against replicative stress than tissue-specific stem/progenitor cells. ESCs possess more dormant origins than tissue stem/progenitor cells The greater number of dormant origins in ESCs effectively protects genome integrity Reduction of dormant origins impairs ESC differentiation, but not self-renewal Reduction of dormant origins severely affects neurogenesis and embryonic viability
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Affiliation(s)
- Xin Quan Ge
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jinah Han
- Yale Cardiovascular Research Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ee-Chun Cheng
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Satoru Yamaguchi
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Naoko Shima
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jean-Leon Thomas
- Yale Cardiovascular Research Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA; SIAIS and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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129
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Balasov M, Akhmetova K, Chesnokov I. Drosophila model of Meier-Gorlin syndrome based on the mutation in a conserved C-Terminal domain of Orc6. Am J Med Genet A 2015; 167A:2533-40. [PMID: 26139588 DOI: 10.1002/ajmg.a.37214] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/05/2015] [Indexed: 11/09/2022]
Abstract
Meier-Gorlin syndrome (MGS) is an autosomal recessive disorder characterized by microtia, primordial dwarfism, small ears, and skeletal abnormalities. Patients with MGS often carry mutations in the genes encoding the components of the pre-replicative complex such as Origin Recognition Complex (ORC) subunits Orc1, Orc4, Orc6, and helicase loaders Cdt1 and Cdc6. Orc6 is an important component of ORC and has functions in both DNA replication and cytokinesis. Mutation in conserved C-terminal motif of Orc6 associated with MGS impedes the interaction of Orc6 with core ORC. In order to study the effects of MGS mutation in an animal model system we introduced MGS mutation in Orc6 and established Drosophila model of MGS. Mutant flies die at third instar larval stage with abnormal chromosomes and DNA replication defects. The lethality can be rescued by elevated expression of mutant Orc6 protein. Rescued MGS flies are unable to fly and display multiple planar cell polarity defects. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Maxim Balasov
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama
| | - Katarina Akhmetova
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama.,The Federal Research Center Institute of Cytology and Genetics, Prospekt Lavrentyeva 10, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Igor Chesnokov
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama
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130
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Morris-Rosendahl DJ, Kaindl AM. What next-generation sequencing (NGS) technology has enabled us to learn about primary autosomal recessive microcephaly (MCPH). Mol Cell Probes 2015; 29:271-81. [PMID: 26050940 DOI: 10.1016/j.mcp.2015.05.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 11/27/2022]
Abstract
The impact that next-generation sequencing technology (NGS) is having on many aspects of molecular and cell biology, is becoming increasingly apparent. One of the most noticeable outcomes of the new technology in human genetics, has been the accelerated rate of identification of disease-causing genes. Especially for rare, heterogeneous disorders, such as autosomal recessive primary microcephaly (MCPH), the handful of genes previously known to harbour disease-causing mutations, has grown at an unprecedented rate within a few years. Knowledge of new genes mutated in MCPH over the last four years has contributed to our understanding of the disorder at both the clinical and cellular levels. The functions of proteins such as WDR62, CASC5, PHC1, CDK6, CENP-E, CENP-F, CEP63, ZNF335, PLK4 and TUBGPC, have been added to the complex network of critical cellular processes known to be involved in brain growth and size. In addition to the importance of mitotic spindle assembly and structure, centrosome and centriole function and DNA repair and damage response, new mechanisms involving kinetochore-associated proteins and chromatin remodelling complexes have been elucidated. Two of the major contributions to our clinical knowledge are the realisation that primary microcephaly caused by mutations in genes at the MCPH loci is seldom an isolated clinical feature and is often accompanied either by additional cortical malformations or primordial dwarfism. Gene-phenotype correlations are being revisited, with a new dimension of locus heterogeneity and phenotypic variability being revealed.
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Affiliation(s)
- Deborah J Morris-Rosendahl
- Clinical Genetics and Genomics, Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom; National Heart and Lung Institute, Imperial College London, London, United Kingdom.
| | - Angela M Kaindl
- Department of Pediatric Neurology, Charité University Medicine, Berlin, Germany; Institute of Cell Biology and Neurobiology, Charité University Medicine, Berlin, Germany
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131
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Bravo-Oro A, Lurie IW, Elizondo-Cárdenas G, Peña-Zepeda C, Salazar-Martínez A, Correa-González C, Castrillo JL, Avila S, Esmer C. A novel interstitial deletion of 2q22.3 q23.3 in a patient with dysmorphic features, epilepsy, aganglionosis, pure red cell aplasia, and skeletal malformations. Am J Med Genet A 2015; 167A:1865-71. [PMID: 25988649 DOI: 10.1002/ajmg.a.36806] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 09/08/2014] [Indexed: 12/24/2022]
Abstract
Many chromosomal deletions encompassing the 2q23.1 region have been described ranging from small deletions of 38 kb up to >19 Mb. Most phenotypic features of the 2q23.1 deletion syndrome are due to a MBD5 gene loss independent of the size of the deletion. Here, we describe a male patient harboring a novel interstitial deletion encompassing the 2q22.3 q23.3 chromosomal region. Array-CGH revealed a 7.1 Mb deletion causing haploinsufficiency of several genes including MBD5, ACVR2, KIF5C, and EPC2. This patient presents with additional findings to those already described in individuals who have deletions of MBD5 including toes absence of halluces, pure red cell aplasia, and intestinal aganglionosis. Interestingly, in the deleted region there are previously identified regulatory sequences which are located upstream to ZEB2, which is associated with Hirschsprung disease (HSCR). Several genes have been associated with pure red cell aplasia, but to our knowledge, this is the first time that 2q deletion is associated with this phenotype. These additional findings should be added to the list of manifestations associated with 2q deletion, and provide support for the hypothesis that this individual has a true contiguous gene deletion syndrome.
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Affiliation(s)
- Antonio Bravo-Oro
- Hospital Central "Dr. Ignacio Morones Prieto", San Luis Potosí, Mexico
| | - Iosif W Lurie
- Chromosome Disorder Outreach, Boca Raton, Florida, USA
| | | | | | | | | | | | | | - Carmen Esmer
- Hospital Central "Dr. Ignacio Morones Prieto", San Luis Potosí, Mexico
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132
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Zhang W, Sankaran S, Gozani O, Song J. A Meier-Gorlin syndrome mutation impairs the ORC1-nucleosome association. ACS Chem Biol 2015; 10:1176-80. [PMID: 25689043 DOI: 10.1021/cb5009684] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent studies have identified several genetic mutations within the BAH domain of human Origin Recognition Complex subunit 1 (hORC1BAH), including the R105Q mutation, implicated in Meier-Gorlin Syndrome (MGS). However, the pathological role of the hORC1 R105Q mutation remains unclear. In this study, we have investigated the interactions of the hORC1BAH domain with histone H4K20me2, DNA, and the nucleosome core particle labeled with H4Kc20me2, a chemical analog of H4K20me2. Our study revealed a nucleosomal DNA binding site for hORC1BAH. The R105Q mutation reduces the hORC1BAH-DNA binding affinity, leading to impaired hORC1BAH-nucleosome interaction, which likely influences DNA replication initiation and MGS pathogenesis. This study provides an etiologic link between the hORC1 R105Q mutation and MGS.
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Affiliation(s)
- Wei Zhang
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
| | - Saumya Sankaran
- Department
of Biology, Stanford University, Stanford, California 94305, United States
| | - Or Gozani
- Department
of Biology, Stanford University, Stanford, California 94305, United States
| | - Jikui Song
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
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133
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Barkovich AJ, Dobyns WB, Guerrini R. Malformations of cortical development and epilepsy. Cold Spring Harb Perspect Med 2015; 5:a022392. [PMID: 25934463 DOI: 10.1101/cshperspect.a022392] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Malformations of cortical development (MCDs) are an important cause of epilepsy and an extremely interesting group of disorders from the perspective of brain development and its perturbations. Many new MCDs have been described in recent years as a result of improvements in imaging, genetic testing, and understanding of the effects of mutations on the ability of their protein products to correctly function within the molecular pathways by which the brain functions. In this review, most of the major MCDs are reviewed from a clinical, embryological, and genetic perspective. The most recent literature regarding clinical diagnosis, mechanisms of development, and future paths of research are discussed.
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Affiliation(s)
- A James Barkovich
- Department of Radiology and Biomedical Imaging, Neurology, Pediatrics, and Neurosurgery, University of California, San Francisco, San Francisco, California 94143-0628
| | - William B Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington 98101
| | - Renzo Guerrini
- Pediatric Neurology Unit and Laboratories, Children's Hospital A. Meyer, University of Florence, Florence 50139, Italy
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134
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de Bruin C, Mericq V, Andrew SF, van Duyvenvoorde HA, Verkaik NS, Losekoot M, Porollo A, Garcia H, Kuang Y, Hanson D, Clayton P, van Gent DC, Wit JM, Hwa V, Dauber A. An XRCC4 splice mutation associated with severe short stature, gonadal failure, and early-onset metabolic syndrome. J Clin Endocrinol Metab 2015; 100:E789-98. [PMID: 25742519 PMCID: PMC4422886 DOI: 10.1210/jc.2015-1098] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CONTEXT Severe short stature can be caused by defects in numerous biological processes including defects in IGF-1 signaling, centromere function, cell cycle control, and DNA damage repair. Many syndromic causes of short stature are associated with medical comorbidities including hypogonadism and microcephaly. OBJECTIVE To identify an underlying genetic etiology in two siblings with severe short stature and gonadal failure. DESIGN Clinical phenotyping, genetic analysis, complemented by in vitro functional studies of the candidate gene. SETTING An academic pediatric endocrinology clinic. PATIENTS OR OTHER PARTICIPANTS Two adult siblings (male patient [P1] and female patient 2 [P2]) presented with a history of severe postnatal growth failure (adult heights: P1, -6.8 SD score; P2, -4 SD score), microcephaly, primary gonadal failure, and early-onset metabolic syndrome in late adolescence. In addition, P2 developed a malignant gastrointestinal stromal tumor at age 28. INTERVENTION(S) Single nucleotide polymorphism microarray and exome sequencing. RESULTS Combined microarray analysis and whole exome sequencing of the two affected siblings and one unaffected sister identified a homozygous variant in XRCC4 as the probable candidate variant. Sanger sequencing and mRNA studies revealed a splice variant resulting in an in-frame deletion of 23 amino acids. Primary fibroblasts (P1) showed a DNA damage repair defect. CONCLUSIONS In this study we have identified a novel pathogenic variant in XRCC4, a gene that plays a critical role in non-homologous end-joining DNA repair. This finding expands the spectrum of DNA damage repair syndromes to include XRCC4 deficiency causing severe postnatal growth failure, microcephaly, gonadal failure, metabolic syndrome, and possibly tumor predisposition.
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Affiliation(s)
- Christiaan de Bruin
- Cincinnati Center for Growth Disorders (C.d.B., S.F.A., V.H., A.D.), Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229; Institute of Maternal and Child Research (V.M.), Faculty of Medicine, University of Chile, 226-3 Santiago, Chile; Laboratory for Diagnostic Genome Analysis (H.A.v.D., M.L.), Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; Department of Genetics (N.S.V., D.C.v.G.), Erasmus MC, 3015 CE Rotterdam, The Netherlands; Center for Autoimmune Genomics and Etiology (A.P.), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229; Pediatrics Division (H.G.), Faculty of Medicine, Pontificia Universidad Catolica de Chile Santiago, 340 Santiago, Chile; Division of Developmental Biology (Y.K.), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229; Institute of Human Development (D.H., P.C.), University of Manchester and Manchester Academic Health Sciences Centre, Manchester M13 9PL, United Kingdom; and Department of Pediatrics (J.M.W.), Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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135
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Abstract
Skeletal dysplasias result from disruptions in normal skeletal growth and development and are a major contributor to severe short stature. They occur in approximately 1/5,000 births, and some are lethal. Since the most recent publication of the Nosology and Classification of Genetic Skeletal Disorders, genetic causes of 56 skeletal disorders have been uncovered. This remarkable rate of discovery is largely due to the expanded use of high-throughput genomic technologies. In this review, we discuss these recent discoveries and our understanding of the molecular mechanisms behind these skeletal dysplasia phenotypes. We also cover potential therapies, unusual genetic mechanisms, and novel skeletal syndromes both with and without known genetic causes. The acceleration of skeletal dysplasia genetics is truly spectacular, and these advances hold great promise for diagnostics, risk prediction, and therapeutic design.
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136
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Wilson BT, Omer M, Hellens SW, Zwolinski SA, Yates LM, Lynch SA. Microdeletion 1p35.2: a recognizable facial phenotype with developmental delay. Am J Med Genet A 2015; 167A:1916-20. [PMID: 25900906 DOI: 10.1002/ajmg.a.37114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/02/2015] [Indexed: 11/08/2022]
Abstract
We describe two patients with microdeletion 1p35.2, intrauterine growth retardation, small stature, hypermetropia, hearing impairment and developmental delay. Both patients have long, myopathic facies, with fine eyebrows, small mouths and micrognathia. We postulate a role for the histone deacetylase HDAC1 in the facial phenotype and suggest that deletion of KPNA6 may prevent transmission of the 1p35.2 deletion from affected girls to any offspring through impaired zygotic genome activation.
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Affiliation(s)
- Brian T Wilson
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK.,Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, International Centre for Life, Newcastle upon Tyne, UK
| | - Murwan Omer
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - Stephen W Hellens
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, International Centre for Life, Newcastle upon Tyne, UK
| | - Simon A Zwolinski
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, International Centre for Life, Newcastle upon Tyne, UK
| | - Laura M Yates
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK.,Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, International Centre for Life, Newcastle upon Tyne, UK
| | - Sally Ann Lynch
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
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137
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Qiao R, He Y, Pan B, Xiao S, Zhang X, Li J, Zhang Z, Hong Y, Xing Y, Ren J. Understanding the molecular mechanisms of human microtia via a pig model of HOXA1 syndrome. Dis Model Mech 2015; 8:611-22. [PMID: 26035869 PMCID: PMC4457031 DOI: 10.1242/dmm.018291] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 04/01/2015] [Indexed: 01/27/2023] Open
Abstract
Microtia is a congenital malformation of the outer ears. Although both genetic and environmental components have been implicated in microtia, the genetic causes of this innate disorder are poorly understood. Pigs have naturally occurring diseases comparable to those in humans, providing exceptional opportunity to dissect the molecular mechanism of human inherited diseases. Here we first demonstrated that a truncating mutation in HOXA1 causes a monogenic disorder of microtia in pigs. We further performed RNA sequencing (RNA-Seq) analysis on affected and healthy pig embryos (day 14.25). We identified a list of 337 differentially expressed genes (DEGs) between the normal and mutant samples, shedding light on the transcriptional network involving HOXA1. The DEGs are enriched in biological processes related to cardiovascular system and embryonic development, and neurological, renal and urological diseases. Aberrant expressions of many DEGs have been implicated in human innate deformities corresponding to microtia-associated syndromes. After applying three prioritizing algorithms, we highlighted appealing candidate genes for human microtia from the 337 DEGs. We searched for coding variants of functional significance within six candidate genes in 147 microtia-affected individuals. Of note, we identified one EVC2 non-synonymous mutation (p.Asp1174Asn) as a potential disease-implicating variant for a human microtia-associated syndrome. The findings advance our understanding of the molecular mechanisms underlying human microtia, and provide an interesting example of the characterization of human disease-predisposing variants using pig models. Summary: A pig model of HOXA1 syndrome provides novel insight into the molecular mechanisms of human microtia.
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Affiliation(s)
- Ruimin Qiao
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, People's Republic of China College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, People's Republic of China
| | - Yuyong He
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, People's Republic of China
| | - Bo Pan
- Plastic Surgery Hospital, Peking Union Medical College, Beijing 100144, People's Republic of China
| | - Shijun Xiao
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, People's Republic of China
| | - Xufei Zhang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, People's Republic of China
| | - Jing Li
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, People's Republic of China
| | - Zhiyan Zhang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, People's Republic of China
| | - Yuan Hong
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, People's Republic of China
| | - Yuyun Xing
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, People's Republic of China
| | - Jun Ren
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, People's Republic of China
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138
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Affiliation(s)
- Manuel M. Müller
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
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139
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Mutations in the NHEJ component XRCC4 cause primordial dwarfism. Am J Hum Genet 2015; 96:412-24. [PMID: 25728776 DOI: 10.1016/j.ajhg.2015.01.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 01/16/2015] [Indexed: 11/20/2022] Open
Abstract
Non-homologous end joining (NHEJ) is a key cellular process ensuring genome integrity. Mutations in several components of the NHEJ pathway have been identified, often associated with severe combined immunodeficiency (SCID), consistent with the requirement for NHEJ during V(D)J recombination to ensure diversity of the adaptive immune system. In contrast, we have recently found that biallelic mutations in LIG4 are a common cause of microcephalic primordial dwarfism (MPD), a phenotype characterized by prenatal-onset extreme global growth failure. Here we provide definitive molecular genetic evidence supported by biochemical, cellular, and immunological data for mutations in XRCC4, encoding the obligate binding partner of LIG4, causing MPD. We report the identification of biallelic mutations in XRCC4 in five families. Biochemical and cellular studies demonstrate that these alterations substantially decrease XRCC4 protein levels leading to reduced cellular ligase IV activity. Consequently, NHEJ-dependent repair of ionizing-radiation-induced DNA double-strand breaks is compromised in XRCC4 cells. Similarly, immunoglobulin junctional diversification is impaired in cells. However, immunoglobulin levels are normal, and individuals lack overt signs of immunodeficiency. Additionally, in contrast to individuals with LIG4 mutations, pancytopenia leading to bone marrow failure has not been observed. Hence, alterations that alter different NHEJ proteins give rise to a phenotypic spectrum, from SCID to extreme growth failure, with deficiencies in certain key components of this repair pathway predominantly exhibiting growth deficits, reflecting differential developmental requirements for NHEJ proteins to support growth and immune maturation.
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140
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Abstract
PURPOSE OF REVIEW To review the recent advances in the clinical and molecular characterization of primordial dwarfism, an extreme growth deficiency disorder that has its onset during embryonic development and persists throughout life. RECENT FINDINGS The last decade has witnessed an unprecedented acceleration in the discovery of genes mutated in primordial dwarfism, from one gene to more than a dozen genes. These genetic discoveries have confirmed the notion that primordial dwarfism is caused by defects in basic cellular processes, most notably centriolar biology and DNA damage response. Fortunately, the increasing number of reported clinical primordial dwarfism subtypes has been accompanied by more accurate molecular classification. SUMMARY Qualitative defects of centrioles with resulting abnormal mitosis dynamics, reduced proliferation, and increased apoptosis represent the predominant molecular pathogenic mechanism in primordial dwarfism. Impaired DNA damage response is another important mechanism, which we now know is not mutually exclusive to abnormal centrioles. Molecular characterization of primordial dwarfism is helping families by enabling more reproductive choices and may pave the way for the future development of therapeutics.
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Affiliation(s)
- Fowzan S Alkuraya
- aDepartment of Genetics, King Faisal Specialist Hospital and Research Center bDepartment of Anatomy and Cell Biology, College of Medicine, Alfasial University, Riyadh, Saudi Arabia
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141
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Molecular Genetic Methods to Study DNA Replication Protein Function in Haloferax volcanii, A Model Archaeal Organism. Methods Mol Biol 2015; 1300:187-218. [PMID: 25916714 DOI: 10.1007/978-1-4939-2596-4_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Successful high-fidelity chromosomal DNA replication is fundamental to all forms of cellular life and requires the complex interplay of a variety of essential and nonessential protein factors in a spatially and temporally coordinated manner. Much of what is known about the enzymes and mechanisms of chromosome replication has come from analysis of simple microbial model systems, such as yeast and archaea. Archaea possess a highly simplified eukaryotic-like replication apparatus, making them an excellent model for gaining novel insights into conserved aspects of protein function at the heart of the replisome. Amongst the thermophilic archaea, a number of species have proved useful for biochemical analysis of protein function, but few of these organisms are suited to genetic analysis. One archaeal organism that is genetically tractable is the mesophilic euryarchaeon Haloferax volcanii, a halophile that grows aerobically in high salt medium at an optimum temperature of 40-45 °C and with a doubling time of 2-3 h. The Hfx. volcanii genome has been sequenced and a range of methods have been developed to allow reverse genetic analysis of protein function in vivo, including techniques for gene replacement and gene deletion, transcriptional regulation, point mutation and gene tagging. Here we briefly summarize current knowledge of the chromosomal DNA replication machinery in the haloarchaea before describing in detail the molecular methods available to probe protein structure and function within the Hfx. volcanii replication apparatus.
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142
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Mazouzi A, Velimezi G, Loizou JI. DNA replication stress: causes, resolution and disease. Exp Cell Res 2014; 329:85-93. [PMID: 25281304 DOI: 10.1016/j.yexcr.2014.09.030] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/20/2014] [Accepted: 09/22/2014] [Indexed: 12/17/2022]
Abstract
DNA replication is a fundamental process of the cell that ensures accurate duplication of the genetic information and subsequent transfer to daughter cells. Various pertubations, originating from endogenous or exogenous sources, can interfere with proper progression and completion of the replication process, thus threatening genome integrity. Coordinated regulation of replication and the DNA damage response is therefore fundamental to counteract these challenges and ensure accurate synthesis of the genetic material under conditions of replication stress. In this review, we summarize the main sources of replication stress and the DNA damage signaling pathways that are activated in order to preserve genome integrity during DNA replication. We also discuss the association of replication stress and DNA damage in human disease and future perspectives in the field.
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Affiliation(s)
- Abdelghani Mazouzi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Georgia Velimezi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria.
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143
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Abstract
CONTEXT Genetics plays a major role in determining an individual's height. Although there are many monogenic disorders that lead to perturbations in growth and result in short stature, there is still no consensus as to the role that genetic diagnostics should play in the evaluation of a child with short stature. EVIDENCE ACQUISITION A search of PubMed was performed, focusing on the genetic diagnosis of short stature as well as on specific diagnostic subgroups included in this article. Consensus guidelines were reviewed. EVIDENCE SYNTHESIS There are a multitude of rare genetic causes of severe short stature. There is no high-quality evidence to define the optimal approach to the genetic evaluation of short stature. We review genetic etiologies of a number of diagnostic subgroups and propose an algorithm for genetic testing based on these subgroups. CONCLUSION Advances in genomic technologies are revolutionizing the diagnostic approach to short stature. Endocrinologists must become facile with the use of genetic testing in order to identify the various monogenic disorders that present with short stature.
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Affiliation(s)
- Andrew Dauber
- Division of Endocrinology (A.D., J.N.H.), Boston Children's Hospital, Boston, Massachusetts 02115; Broad Institute (A.D., J.N.H.), Cambridge, Massachusetts 02142; Department of Pediatrics (R.G.R.), Oregon Health & Science University, Portland, Oregon 97239; Division of Genetics (J.N.H.), Boston Children's Hospital, Boston, Massachusetts 02115; and Departments of Genetics and Pediatrics (J.N.H.), Harvard Medical School, Boston, Massachusetts 02115
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144
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Mirzaa GM, Vitre B, Carpenter G, Abramowicz I, Gleeson JG, Paciorkowski AR, Cleveland DW, Dobyns WB, O’Driscoll M. Mutations in CENPE define a novel kinetochore-centromeric mechanism for microcephalic primordial dwarfism. Hum Genet 2014; 133:1023-39. [PMID: 24748105 PMCID: PMC4415612 DOI: 10.1007/s00439-014-1443-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 03/31/2014] [Indexed: 11/30/2022]
Abstract
Defects in centrosome, centrosomal-associated and spindle-associated proteins are the most frequent cause of primary microcephaly (PM) and microcephalic primordial dwarfism (MPD) syndromes in humans. Mitotic progression and segregation defects, microtubule spindle abnormalities and impaired DNA damage-induced G2-M cell cycle checkpoint proficiency have been documented in cell lines from these patients. This suggests that impaired mitotic entry, progression and exit strongly contribute to PM and MPD. Considering the vast protein networks involved in coordinating this cell cycle stage, the list of potential target genes that could underlie novel developmental disorders is large. One such complex network, with a direct microtubule-mediated physical connection to the centrosome, is the kinetochore. This centromeric-associated structure nucleates microtubule attachments onto mitotic chromosomes. Here, we described novel compound heterozygous variants in CENPE in two siblings who exhibit a profound MPD associated with developmental delay, simplified gyri and other isolated abnormalities. CENPE encodes centromere-associated protein E (CENP-E), a core kinetochore component functioning to mediate chromosome congression initially of misaligned chromosomes and in subsequent spindle microtubule capture during mitosis. Firstly, we present a comprehensive clinical description of these patients. Then, using patient cells we document abnormalities in spindle microtubule organization, mitotic progression and segregation, before modeling the cellular pathogenicity of these variants in an independent cell system. Our cellular analysis shows that a pathogenic defect in CENP-E, a kinetochore-core protein, largely phenocopies PCNT-mutated microcephalic osteodysplastic primordial dwarfism-type II patient cells. PCNT encodes a centrosome-associated protein. These results highlight a common underlying pathomechanism. Our findings provide the first evidence for a kinetochore-based route to MPD in humans.
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Affiliation(s)
- Ghayda M. Mirzaa
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Benjamin Vitre
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gillian Carpenter
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, United Kingdom
| | - Iga Abramowicz
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, United Kingdom
| | - Joseph G. Gleeson
- Department of Neurosciences and Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Alex R. Paciorkowski
- Departments of Neurology, Pediatrics & Biomedical Genetics, Center for Neural Development & Disease, University of Rochester Medical Center, Rochester, NY, USA
| | - Don W. Cleveland
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - William B. Dobyns
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Mark O’Driscoll
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, United Kingdom
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145
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Alver RC, Chadha GS, Blow JJ. The contribution of dormant origins to genome stability: from cell biology to human genetics. DNA Repair (Amst) 2014; 19:182-9. [PMID: 24767947 PMCID: PMC4065331 DOI: 10.1016/j.dnarep.2014.03.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The ability of a eukaryotic cell to precisely and accurately replicate its DNA is crucial to maintain genome stability. Here we describe our current understanding of the process by which origins are licensed for DNA replication and review recent work suggesting that fork stalling has exerted a strong selective pressure on the positioning of licensed origins. In light of this, we discuss the complex and disparate phenotypes observed in mouse models and humans patients that arise due to defects in replication licensing proteins.
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Affiliation(s)
- Robert C Alver
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Gaganmeet Singh Chadha
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - J Julian Blow
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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146
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Alcantara D, O'Driscoll M. Congenital microcephaly. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2014; 166C:124-39. [PMID: 24816482 DOI: 10.1002/ajmg.c.31397] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The underlying etiologies of genetic congenital microcephaly are complex and multifactorial. Recently, with the exponential growth in the identification and characterization of novel genetic causes of congenital microcephaly, there has been a consolidation and emergence of certain themes concerning underlying pathomechanisms. These include abnormal mitotic microtubule spindle structure, numerical and structural abnormalities of the centrosome, altered cilia function, impaired DNA repair, DNA Damage Response signaling and DNA replication, along with attenuated cell cycle checkpoint proficiency. Many of these processes are highly interconnected. Interestingly, a defect in a gene whose encoded protein has a canonical function in one of these processes can often have multiple impacts at the cellular level involving several of these pathways. Here, we overview the key pathomechanistic themes underlying profound congenital microcephaly, and emphasize their interconnected nature.
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147
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Liang L, Haug JS, Seidel CW, Gibson MC. Functional genomic analysis of the periodic transcriptome in the developing Drosophila wing. Dev Cell 2014; 29:112-27. [PMID: 24684830 DOI: 10.1016/j.devcel.2014.02.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 11/27/2013] [Accepted: 02/25/2014] [Indexed: 12/26/2022]
Abstract
The eukaryotic cell cycle, driven by both transcriptional and posttranslational mechanisms, is the central molecular oscillator underlying tissue growth throughout animals. Although genome-wide studies have investigated cell-cycle-associated transcription in unicellular systems, global patterns of periodic transcription in multicellular tissues remain largely unexplored. Here we define the cell-cycle-associated transcriptome of the developing Drosophila wing epithelium and compare it with that of cultured Drosophila S2 cells, revealing a core set of periodic genes and a surprising degree of context specificity in periodic transcription. We further employ RNAi-mediated phenotypic profiling to define functional requirements for more than 300 periodic genes, with a focus on those required for cell proliferation in vivo. Finally, we investigate uncharacterized genes required for interkinetic nuclear migration. Combined, these findings provide a global perspective on cell-cycle control in vivo, and they highlight a critical need to understand the context-specific regulation of cell proliferation.
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Affiliation(s)
- Liang Liang
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Jeffrey S Haug
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Chris W Seidel
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Matthew C Gibson
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA; Department of Anatomy and Cell Biology, Kansas University Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA.
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148
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Champeris Tsaniras S, Kanellakis N, Symeonidou IE, Nikolopoulou P, Lygerou Z, Taraviras S. Licensing of DNA replication, cancer, pluripotency and differentiation: an interlinked world? Semin Cell Dev Biol 2014; 30:174-80. [PMID: 24641889 DOI: 10.1016/j.semcdb.2014.03.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 03/10/2014] [Indexed: 01/06/2023]
Abstract
Recent findings provide evidence for a functional interplay between DNA replication and the seemingly distinct areas of cancer, development and pluripotency. Protein complexes participating in DNA replication origin licensing are now known to have roles in development, while their deregulation can lead to cancer. Moreover, transcription factors implicated in the maintenance of or reversal to the pluripotent state have links to the pre-replicative machinery. Several studies have shown that overexpression of these factors is associated to cancer.
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Affiliation(s)
- S Champeris Tsaniras
- Department of Physiology, Medical School, University of Patras, Rio, 26504 Patras, Greece.
| | - N Kanellakis
- Department of Physiology, Medical School, University of Patras, Rio, 26504 Patras, Greece.
| | - I E Symeonidou
- Department of Biology, Medical School, University of Patras, Rio, 26504 Patras, Greece.
| | - P Nikolopoulou
- Department of Physiology, Medical School, University of Patras, Rio, 26504 Patras, Greece.
| | - Z Lygerou
- Department of Biology, Medical School, University of Patras, Rio, 26504 Patras, Greece.
| | - S Taraviras
- Department of Physiology, Medical School, University of Patras, Rio, 26504 Patras, Greece.
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149
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Shaheen R, Faqeih E, Ansari S, Abdel-Salam G, Al-Hassnan ZN, Al-Shidi T, Alomar R, Sogaty S, Alkuraya FS. Genomic analysis of primordial dwarfism reveals novel disease genes. Genome Res 2014; 24:291-9. [PMID: 24389050 PMCID: PMC3912419 DOI: 10.1101/gr.160572.113] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in defining clinical subgroups. In this study, we present the results of clinical and genomic characterization of 16 new patients in whom a broad definition of PD was used (e.g., 3M syndrome was included). We report a novel PD syndrome with distinct facies in two unrelated patients, each with a different homozygous truncating mutation in CRIPT. Our analysis also reveals, in addition to mutations in known PD disease genes, the first instance of biallelic truncating BRCA2 mutation causing PD with normal bone marrow analysis. In addition, we have identified a novel locus for Seckel syndrome based on a consanguineous multiplex family and identified a homozygous truncating mutation in DNA2 as the likely cause. An additional novel PD disease candidate gene XRCC4 was identified by autozygome/exome analysis, and the knockout mouse phenotype is highly compatible with PD. Thus, we add a number of novel genes to the growing list of PD-linked genes, including one which we show to be linked to a novel PD syndrome with a distinct facial appearance. PD is extremely heterogeneous genetically and clinically, and genomic tools are often required to reach a molecular diagnosis.
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Affiliation(s)
- Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
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150
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Jackson AP, Laskey RA, Coleman N. Replication proteins and human disease. Cold Spring Harb Perspect Biol 2014; 6:cshperspect.a013060. [PMID: 23881941 DOI: 10.1101/cshperspect.a013060] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this article, we discuss the significance of DNA replication proteins in human disease. There is a broad range of mutations in genes encoding replication proteins, which result in several distinct clinical disorders that share common themes. One group of replication proteins, the MCMs, has emerged as effective biomarkers for early detection of a range of common cancers. They offer practical and theoretical advantages over other replication proteins and have been developed for widespread clinical use.
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Affiliation(s)
- Andrew P Jackson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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