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Gocuk SA, Jolly JK, Edwards TL, Ayton LN. Female carriers of X-linked inherited retinal diseases - Genetics, diagnosis, and potential therapies. Prog Retin Eye Res 2023; 96:101190. [PMID: 37406879 DOI: 10.1016/j.preteyeres.2023.101190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023]
Abstract
Inherited retinal diseases (IRDs) are a group of heterogeneous conditions that cause progressive vision loss, typically due to monogenic mutations. Female carriers of X-linked IRDs have a single copy of the disease-causing gene, and therefore, may exhibit variable clinical signs that vary from near normal retina to severe disease and vision loss. The relationships between individual genetic mutations and disease severity in X-linked carriers requires further study. This review summarises the current literature surrounding the spectrum of disease seen in female carriers of choroideremia and X-linked retinitis pigmentosa. Various classification systems are contrasted to accurately grade retinal disease. Furthermore, genetic mechanisms at the early embryonic stage are explored to potentially explain the variability of disease seen in female carriers. Future research in this area will provide insight into the association between genotype and retinal phenotypes of female carriers, which will guide in the management of these patients. This review acknowledges the importance of identifying which patients may be at high risk of developing severe symptoms, and therefore should be considered for emerging treatments, such as retinal gene therapy.
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Affiliation(s)
- Sena A Gocuk
- Department of Optometry and Vision Sciences, The University of Melbourne, Melbourne, Victoria, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jasleen K Jolly
- Vision and Eye Research Institute, Anglia Ruskin University, Cambridge, UK
| | - Thomas L Edwards
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lauren N Ayton
- Department of Optometry and Vision Sciences, The University of Melbourne, Melbourne, Victoria, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, The University of Melbourne, Melbourne, Victoria, Australia.
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2
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Werner JM, Ballouz S, Hover J, Gillis J. Variability of cross-tissue X-chromosome inactivation characterizes timing of human embryonic lineage specification events. Dev Cell 2022; 57:1995-2008.e5. [PMID: 35914524 PMCID: PMC9398941 DOI: 10.1016/j.devcel.2022.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 05/11/2022] [Accepted: 07/07/2022] [Indexed: 12/14/2022]
Abstract
X-chromosome inactivation (XCI) is a random, permanent, and developmentally early epigenetic event that occurs during mammalian embryogenesis. We harness these features to investigate characteristics of early lineage specification events during human development. We initially assess the consistency of X-inactivation and establish a robust set of XCI-escape genes. By analyzing variance in XCI ratios across tissues and individuals, we find that XCI is shared across all tissues, suggesting that XCI is completed in the epiblast (in at least 6-16 cells) prior to specification of the germ layers. Additionally, we exploit tissue-specific variability to characterize the number of cells present during tissue-lineage commitment, ranging from approximately 20 cells in liver and whole blood tissues to 80 cells in brain tissues. By investigating the variability of XCI ratios using adult tissue, we characterize embryonic features of human XCI and lineage specification that are otherwise difficult to ascertain experimentally.
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Affiliation(s)
- Jonathan M Werner
- The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sara Ballouz
- The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW Australia
| | - John Hover
- The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jesse Gillis
- The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
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3
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X-chromosome regulation and sex differences in brain anatomy. Neurosci Biobehav Rev 2020; 120:28-47. [PMID: 33171144 DOI: 10.1016/j.neubiorev.2020.10.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 10/13/2020] [Accepted: 10/20/2020] [Indexed: 01/08/2023]
Abstract
Humans show reproducible sex-differences in cognition and psychopathology that may be contributed to by influences of gonadal sex-steroids and/or sex-chromosomes on regional brain development. Gonadal sex-steroids are well known to play a major role in sexual differentiation of the vertebrate brain, but far less is known regarding the role of sex-chromosomes. Our review focuses on this latter issue by bridging together two literatures that have to date been largely disconnected. We first consider "bottom-up" genetic and molecular studies focused on sex-chromosome gene content and regulation. This literature nominates specific sex-chromosome genes that could drive developmental sex-differences by virtue of their sex-biased expression and their functions within the brain. We then consider the complementary "top down" view, from magnetic resonance imaging studies that map sex- and sex chromosome effects on regional brain anatomy, and link these maps to regional gene-expression within the brain. By connecting these top-down and bottom-up approaches, we emphasize the potential role of X-linked genes in driving sex-biased brain development and outline key goals for future work in this field.
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Xiol C, Vidal S, Pascual-Alonso A, Blasco L, Brandi N, Pacheco P, Gerotina E, O'Callaghan M, Pineda M, Armstrong J. X chromosome inactivation does not necessarily determine the severity of the phenotype in Rett syndrome patients. Sci Rep 2019; 9:11983. [PMID: 31427717 PMCID: PMC6700087 DOI: 10.1038/s41598-019-48385-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/05/2019] [Indexed: 11/24/2022] Open
Abstract
Rett syndrome (RTT) is a severe neurological disorder usually caused by mutations in the MECP2 gene. Since the MECP2 gene is located on the X chromosome, X chromosome inactivation (XCI) could play a role in the wide range of phenotypic variation of RTT patients; however, classical methylation-based protocols to evaluate XCI could not determine whether the preferentially inactivated X chromosome carried the mutant or the wild-type allele. Therefore, we developed an allele-specific methylation-based assay to evaluate methylation at the loci of several recurrent MECP2 mutations. We analyzed the XCI patterns in the blood of 174 RTT patients, but we did not find a clear correlation between XCI and the clinical presentation. We also compared XCI in blood and brain cortex samples of two patients and found differences between XCI patterns in these tissues. However, RTT mainly being a neurological disease complicates the establishment of a correlation between the XCI in blood and the clinical presentation of the patients. Furthermore, we analyzed MECP2 transcript levels and found differences from the expected levels according to XCI. Many factors other than XCI could affect the RTT phenotype, which in combination could influence the clinical presentation of RTT patients to a greater extent than slight variations in the XCI pattern.
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Affiliation(s)
- Clara Xiol
- Molecular and Genetics Medicine Section, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Silvia Vidal
- Molecular and Genetics Medicine Section, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Ainhoa Pascual-Alonso
- Molecular and Genetics Medicine Section, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Laura Blasco
- Molecular and Genetics Medicine Section, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Núria Brandi
- Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Paola Pacheco
- Molecular and Genetics Medicine Section, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Edgar Gerotina
- Molecular and Genetics Medicine Section, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Mar O'Callaghan
- Neurology Service, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Mercè Pineda
- Institut de Recerca Pediàtrica, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Judith Armstrong
- Molecular and Genetics Medicine Section, Hospital Sant Joan de Déu, Barcelona, Spain. .,Institut de Recerca Pediàtrica, Hospital Sant Joan de Déu, Barcelona, Spain. .,CIBER-ER (Biomedical Network Research Center for Rare Diseases), Instituto de Salud Carlos III, Madrid, Spain.
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5
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Krishnaraj R, Ho G, Christodoulou J. RettBASE: Rett syndrome database update. Hum Mutat 2017; 38:922-931. [PMID: 28544139 DOI: 10.1002/humu.23263] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/21/2016] [Accepted: 07/27/2016] [Indexed: 12/20/2022]
Abstract
Rett syndrome (RTT) is an X-linked progressive neurodevelopmental disorder that primarily affects females. Mutations in the MECP2 gene have been attributed as the major genetic cause of RTT. Recently, mutations in CDKL5 and FOXG1 genes have also been suggested to give rise to RTT, although subsequent more extensive studies suggest that diseases resulting from mutations in these two genes should be considered as distinct clinical entities. While the genetic basis for the RTT has been recognized, so far there is no effective cure for the disease and the treatments available are mainly aimed at ameliorating clinical problems associated with the disorder. The swift identification of the mutations in children is crucial for pursuing the best therapeutic care. RettBASE was created in 2002 as a MECP2 variant database and has grown to become a comprehensive variant database for RTT and related clinical phenotypes, containing a curated collection of variants for MECP2, CDKL5, and FOXG1 genes. Here, we describe the development and growth of RettBASE after its inception in 2001. Currently, RettBASE holds a total of 4,668 variants in MECP2, 498 variants in CDKL5, and 64 variants in FOXG1.
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Affiliation(s)
- Rahul Krishnaraj
- NSW Centre for Rett Syndrome Research, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia
| | - Gladys Ho
- NSW Centre for Rett Syndrome Research, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia.,Disciplines of Child and Adolescent, Child Health, University of Sydney, Sydney, Australia
| | - John Christodoulou
- NSW Centre for Rett Syndrome Research, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia.,Disciplines of Child and Adolescent, Child Health, University of Sydney, Sydney, Australia.,Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, Australia.,Neurodevelopmental Genomics Research Group, Murdoch Childrens Research Institute and Department of Paediatrics, Melbourne Medical School, University of Melbourne, Melbourne, Australia
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6
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Walter J, Hümpel A. Introduction to Epigenetics. Epigenetics 2017. [DOI: 10.1007/978-3-658-14460-9_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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7
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Payer B. Developmental regulation of X-chromosome inactivation. Semin Cell Dev Biol 2016; 56:88-99. [PMID: 27112543 DOI: 10.1016/j.semcdb.2016.04.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/13/2016] [Accepted: 04/21/2016] [Indexed: 12/01/2022]
Abstract
With the emergence of sex-determination by sex chromosomes, which differ in composition and number between males and females, appeared the need to equalize X-chromosomal gene dosage between the sexes. Mammals have devised the strategy of X-chromosome inactivation (XCI), in which one of the two X-chromosomes is rendered transcriptionally silent in females. In the mouse, the best-studied model organism with respect to XCI, this inactivation process occurs in different forms, imprinted and random, interspersed by periods of X-chromosome reactivation (XCR), which is needed to switch between the different modes of XCI. In this review, I describe the recent advances with respect to the developmental control of XCI and XCR and in particular their link to differentiation and pluripotency. Furthermore, I review the mechanisms, which influence the timing and choice, with which one of the two X-chromosomes is chosen for inactivation during random XCI. This has an impact on how females are mosaics with regard to which X-chromosome is active in different cells, which has implications on the severity of diseases caused by X-linked mutations.
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Affiliation(s)
- Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra (UPF), Dr. Aiguader, 88, Barcelona 08003, Spain.
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8
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Vacca M, Della Ragione F, Scalabrì F, D'Esposito M. X inactivation and reactivation in X-linked diseases. Semin Cell Dev Biol 2016; 56:78-87. [PMID: 26994527 DOI: 10.1016/j.semcdb.2016.03.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 12/22/2022]
Abstract
X chromosome inactivation (XCI) is the phenomenon by which mammals compensate for dosage of X-linked genes in females (XX) versus males (XY). XCI patterns can be random or show extreme skewing, and can modify the mode of inheritance of X-driven phenotypes, which contributes to the variability of human pathologies. Recent findings have shown reversibility of the XCI process, which has opened new avenues in the approaches used for the treatment of X-linked diseases.
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Affiliation(s)
- Marcella Vacca
- Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, via Pietro Castellino, 111, 80131, Naples, Italy.
| | - Floriana Della Ragione
- Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, via Pietro Castellino, 111, 80131, Naples, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
| | | | - Maurizio D'Esposito
- Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, via Pietro Castellino, 111, 80131, Naples, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
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9
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Wang X, Clark AG. Using next-generation RNA sequencing to identify imprinted genes. Heredity (Edinb) 2014; 113:156-66. [PMID: 24619182 PMCID: PMC4105452 DOI: 10.1038/hdy.2014.18] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 12/02/2013] [Accepted: 12/19/2013] [Indexed: 12/15/2022] Open
Abstract
Genomic imprinting is manifested as differential allelic expression (DAE) depending on the parent-of-origin. The most direct way to identify imprinted genes is to directly score the DAE in a context where one can identify which parent transmitted each allele. Because many genes display DAE, simply scoring DAE in an individual is not sufficient to identify imprinted genes. In this paper, we outline many technical aspects of a scheme for identification of imprinted genes that makes use of RNA sequencing (RNA-seq) from tissues isolated from F1 offspring derived from the pair of reciprocal crosses. Ideally, the parental lines are from two inbred strains that are not closely related to each other. Aspects of tissue purity, RNA extraction, library preparation and bioinformatic inference of imprinting are all covered. These methods have already been applied in a number of organisms, and one of the most striking results is the evolutionary fluidity with which novel imprinted genes are gained and lost within genomes. The general methodology is also applicable to a wide range of other biological problems that require quantification of allele-specific expression using RNA-seq, such as cis-regulation of gene expression, X chromosome inactivation and random monoallelic expression.
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Affiliation(s)
- X Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, NY, USA
| | - A G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, NY, USA
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10
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Deng X, Berletch JB, Nguyen DK, Disteche CM. X chromosome regulation: diverse patterns in development, tissues and disease. Nat Rev Genet 2014; 15:367-78. [PMID: 24733023 PMCID: PMC4117651 DOI: 10.1038/nrg3687] [Citation(s) in RCA: 216] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genes on the mammalian X chromosome are present in one copy in males and two copies in females. The complex mechanisms that regulate the X chromosome lead to evolutionary and physiological variability in gene expression between species, the sexes, individuals, developmental stages, tissues and cell types. In early development, delayed and incomplete X chromosome inactivation (XCI) in some species causes variability in gene expression. Additional diversity stems from escape from XCI and from mosaicism or XCI skewing in females. This causes sex-specific differences that manifest as differential gene expression and associated phenotypes. Furthermore, the complexity and diversity of X dosage regulation affect the severity of diseases caused by X-linked mutations.
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Affiliation(s)
- Xinxian Deng
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Joel B Berletch
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Di K Nguyen
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Christine M Disteche
- 1] Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA. [2] Department of Medicine, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
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Abstract
Genes on the mammalian X chromosome are present in one copy in males and two copies in females. The complex mechanisms that regulate the X chromosome lead to evolutionary and physiological variability in gene expression between species, the sexes, individuals, developmental stages, tissues and cell types. In early development, delayed and incomplete X chromosome inactivation (XCI) in some species causes variability in gene expression. Additional diversity stems from escape from XCI and from mosaicism or XCI skewing in females. This causes sex-specific differences that manifest as differential gene expression and associated phenotypes. Furthermore, the complexity and diversity of X dosage regulation affect the severity of diseases caused by X-linked mutations.
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12
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Deng X, Berletch JB, Nguyen DK, Disteche CM. X chromosome regulation: diverse patterns in development, tissues and disease. Nat Rev Genet 2014. [PMID: 24733023 DOI: 10.1038/nrg3687,+10.1038/nrn3745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genes on the mammalian X chromosome are present in one copy in males and two copies in females. The complex mechanisms that regulate the X chromosome lead to evolutionary and physiological variability in gene expression between species, the sexes, individuals, developmental stages, tissues and cell types. In early development, delayed and incomplete X chromosome inactivation (XCI) in some species causes variability in gene expression. Additional diversity stems from escape from XCI and from mosaicism or XCI skewing in females. This causes sex-specific differences that manifest as differential gene expression and associated phenotypes. Furthermore, the complexity and diversity of X dosage regulation affect the severity of diseases caused by X-linked mutations.
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Affiliation(s)
- Xinxian Deng
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Joel B Berletch
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Di K Nguyen
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
| | - Christine M Disteche
- 1] Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA. [2] Department of Medicine, School of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98115, USA
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Itm2a is a Pax3 target gene, expressed at sites of skeletal muscle formation in vivo. PLoS One 2013; 8:e63143. [PMID: 23650549 PMCID: PMC3641095 DOI: 10.1371/journal.pone.0063143] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 03/30/2013] [Indexed: 11/19/2022] Open
Abstract
The paired-box homeodomain transcription factor Pax3 is a key regulator of the nervous system, neural crest and skeletal muscle development. Despite the important role of this transcription factor, very few direct target genes have been characterized. We show that Itm2a, which encodes a type 2 transmembrane protein, is a direct Pax3 target in vivo, by combining genetic approaches and in vivo chromatin immunoprecipitation assays. We have generated a conditional mutant allele for Itm2a, which is an imprinted gene, by flanking exons 2–4 with loxP sites and inserting an IRESnLacZ reporter in the 3′ UTR of the gene. The LacZ reporter reproduces the expression profile of Itm2a, and allowed us to further characterize its expression at sites of myogenesis, in the dermomyotome and myotome of somites, and in limb buds, in the mouse embryo. We further show that Itm2a is not only expressed in adult muscle fibres but also in the satellite cells responsible for regeneration. Itm2a mutant mice are viable and fertile with no overt phenotype during skeletal muscle formation or regeneration. Potential compensatory mechanisms are discussed.
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Connallon T, Clark AG. Sex-differential selection and the evolution of X inactivation strategies. PLoS Genet 2013; 9:e1003440. [PMID: 23637618 PMCID: PMC3630082 DOI: 10.1371/journal.pgen.1003440] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 02/24/2013] [Indexed: 11/25/2022] Open
Abstract
X inactivation—the transcriptional silencing of one X chromosome copy per female somatic cell—is universal among therian mammals, yet the choice of which X to silence exhibits considerable variation among species. X inactivation strategies can range from strict paternally inherited X inactivation (PXI), which renders females haploid for all maternally inherited alleles, to unbiased random X inactivation (RXI), which equalizes expression of maternally and paternally inherited alleles in each female tissue. However, the underlying evolutionary processes that might account for this observed diversity of X inactivation strategies remain unclear. We present a theoretical population genetic analysis of X inactivation evolution and specifically consider how conditions of dominance, linkage, recombination, and sex-differential selection each influence evolutionary trajectories of X inactivation. The results indicate that a single, critical interaction between allelic dominance and sex-differential selection can select for a broad and continuous range of X inactivation strategies, including unequal rates of inactivation between maternally and paternally inherited X chromosomes. RXI is favored over complete PXI as long as alleles deleterious to female fitness are sufficiently recessive, and the criteria for RXI evolution is considerably more restrictive when fitness variation is sexually antagonistic (i.e., alleles deleterious to females are beneficial to males) relative to variation that is deleterious to both sexes. Evolutionary transitions from PXI to RXI also generally increase mean relative female fitness at the expense of decreased male fitness. These results provide a theoretical framework for predicting and interpreting the evolution of chromosome-wide expression of X-linked genes and lead to several useful predictions that could motivate future studies of allele-specific gene expression variation. With the exception of its most primitive members, mammal species practice X inactivation, where one copy of each X chromosome pair is silenced in each cell of the female body. The particular copy of the X that is silenced nevertheless shows considerable variability among species, and the evolutionary causes for this variability remain unclear. Here, we show that X inactivation strategies are likely to evolve in response to the sex-differential fitness properties of X-linked genetic variation. Genetic variation with similar effects on male and female fitness will generally favor the evolution of random X inactivation, potentially including preferential inactivation of the maternally inherited X chromosome. Variation with opposing fitness effects in each sex (“sexually antagonistic” variation, which includes mutations that both decrease female fitness and enhance male fitness) selects for preferential or complete inactivation of the paternally inherited X. Paternally biased X inactivation patterns appear to be common in nature, which suggests that sexually antagonistic genetic variation might be an important factor underlying the evolution of X inactivation. The theory provides a conceptual framework for understanding the evolution of X inactivation strategies and generates several novel predictions that may soon be tested with modern genome sequencing technologies.
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Affiliation(s)
- Tim Connallon
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.
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15
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Desai V, Donsante A, Swoboda KJ, Martensen M, Thompson J, Kaler SG. Favorably skewed X-inactivation accounts for neurological sparing in female carriers of Menkes disease. Clin Genet 2011; 79:176-82. [PMID: 20497190 DOI: 10.1111/j.1399-0004.2010.01451.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Classical Menkes disease is an X-linked recessive neurodegenerative disorder caused by mutations in ATP7A, which is located at Xq13.1-q21. ATP7A encodes a copper-transporting P-type ATPase and plays a critical role in development of the central nervous system. With rare exceptions involving sex chromosome aneuploidy or X-autosome translocations, female carriers of ATP7A mutations are asymptomatic except for subtle hair and skin abnormalities, although the mechanism for this neurological sparing has not been reported. We studied a three-generation family in which a severe ATP7A mutation, a 5.5-kb genomic deletion spanning exons 13 and 14, segregated. The deletion junction fragment was amplified from the proband by long-range polymerase chain reaction and sequenced to characterize the breakpoints. We screened at-risk females in the family for this junction fragment and analyzed their X-inactivation patterns using the human androgen-receptor (HUMARA) gene methylation assay. We detected the junction fragment in the proband, two obligate heterozygotes, and four of six at-risk females. Skewed inactivation of the X chromosome harboring the deletion was noted in all female carriers of the deletion (n = 6), whereas random X-inactivation was observed in all non-carriers (n = 2). Our results formally document one mechanism for neurological sparing in female carriers of ATP7A mutations. Based on review of X-inactivation patterns in female carriers of other X-linked recessive diseases, our findings imply that substantial expression of a mutant ATP7A at the expense of the normal allele could be associated with neurologic symptoms in female carriers of Menkes disease and its allelic variants, occipital horn syndrome, and ATP7A-related distal motor neuropathy.
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Affiliation(s)
- V Desai
- Unit on Human Copper Metabolism, Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-1832, USA
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Affiliation(s)
- Céline Morey
- Département de Biologie du Développement, Unité de Génétique Moléculaire Murine, Institut Pasteur, CNRS, Paris, France
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Beutler S, Beutler B. Ernest Beutler: his life and contribution to medical science. Br J Haematol 2011; 152:543-50. [PMID: 21241280 DOI: 10.1111/j.1365-2141.2010.08542.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ernest Beutler was one of the preeminent haematologists of the last half of the 20th and the early 21st century. In a career that spanned six decades, his research interests included such diverse areas as red cell metabolism, blood preservation, glycolipid storage diseases, leukaemias and iron metabolism. Indeed, he was quite different from most of his contemporaries in that his knowledge encompassed not only haematology and not only the medical sciences, but the biological sciences as a whole. He was among the first to describe X chromosome inactivation, and he established the critical link between glucose-6-phosphate dehydrogenase deficiency and drug-induced haemolysis. He was a skilled and innovative clinician, and an early advocate of bone marrow transplantation for the treatment of acute leukaemia. He was a prolific author, with over 800 publications; a long time member of the Editorial Board of Blood; founder of the journal Blood Cells Molecules and Diseases; and an editor of Williams Haematology from the time of its inception. He bequeathed $1 million to the American Society of Haematology to recognise and reward outstanding basic research and its clinical application: a pursuit to which he had committed his life. Indeed, he became an extraordinary exemplar of the bench-to-bedside ethos, which holds that even today, an MD researcher, working with limited means and independent of pharmaceutical companies, can have a great impact on the practice of medicine.
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Lissoni S, Baronchelli S, Villa N, Lucchini V, Betri E, Cavalli P, Dalprà L. Chromosome territories, X;Y translocation and Premature Ovarian Failure: is there a relationship? Mol Cytogenet 2009; 2:19. [PMID: 19781104 PMCID: PMC2761935 DOI: 10.1186/1755-8166-2-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 09/27/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Premature ovarian failure (POF) is a secondary hypergonadotrophic amenorrhea occurring before the age of 40 and affecting 1-3% of females. Chromosome anomalies account for 6-8% of POF cases, but only few cases are associated with translocations involving X and Y chromosomes.This study shows the cytogenetic and molecular analysis of a POF patient came to our attention as she developed a left ovary choriocarcinoma at the age of 10 and at 14 years of age she presented secondary amenorrhea with elevated levels of gonadotropins. RESULTS Breakpoint position on X and Y chromosomes was investigated using Fluorescent In Situ Hybridisation (FISH) with a panel of specific BAC probes, microsatellite analysis and evaluation of copy number changes and loss of heterozigosity by Affymetrix(R) GeneChip platform (Santa Clara, CA, USA). Patient's karyotype resulted 46, X, der(Y)t(X;Y)(q13.1;q11.223). X inactivation study was assessed by RBA banding and showed preferential inactivation of derivative chromosome. The reciprocal spatial disposition of sexual chromosome territories was investigated using whole chromosome painting and centromeres probes: patient's results didn't show a significant difference in comparison to normal controls. CONCLUSION The peculiar clinical case come to our attention highlighted the complexity of POF aetiology and of the translocation event, even if our results seem to exclude any effect on nuclear organisation. POF phenotype could be partially explained by skewed X chromosome inactivation that influences gene expression.
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Affiliation(s)
- Sara Lissoni
- Department of Neuroscience and Biomedical Technologies, University of Milan-Bicocca, via Cadore 48, 20052, Monza, Italy.
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Abstract
CTCF is a ubiquitous transcription factor that is involved in numerous, seemingly unrelated functions. These functions include, but are not limited to, positive or negative regulation of transcription, enhancer-blocking activities at developmentally regulated gene clusters and at imprinted loci, and X-chromosome inactivation. Here, we review recent data acquired with state-of-the-art technologies that illuminate possible mechanisms behind the diversity of CTCF functions. CTCF interacts with numerous protein partners, including cohesin, nucleophosmin, PARP1, Yy1 and RNA polymerase II. We propose that CTCF interacts with one or two different partners according to the biological context, applying the Roman principle of governance, 'divide and rule' (divide et impera).
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Affiliation(s)
- Jordanka Zlatanova
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
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20
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Beltran WA, Acland GM, Aguirre GD. Age-dependent disease expression determines remodeling of the retinal mosaic in carriers of RPGR exon ORF15 mutations. Invest Ophthalmol Vis Sci 2009; 50:3985-95. [PMID: 19255154 DOI: 10.1167/iovs.08-3364] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To characterize the retinal histopathology in carriers of X-linked progressive retinal atrophy (XLPRA1 and XLPRA2), two canine models of X-linked retinitis pigmentosa caused, respectively, by a stop and a frameshift mutation in RPGRORF15. METHODS Retinas of XLPRA2 and XLPRA1 carriers of different ages were processed for morphologic evaluation, TUNEL assay, and immunohistochemistry. Cell-specific markers were used to examine retinal remodeling events. RESULTS A mosaic pattern composed of patches of diseased and normal retina was first detected in XLPRA2 carriers at 4.9 weeks of age. A peak of photoreceptor cell death led to focal rod loss; however, in these patches an increased density of cones was found to persist over time. Patches of disease gradually disappeared so that by 39 weeks of age the overall retinal morphology, albeit thinner, had improved lamination. In older XLPRA2 carriers (>or=8.8 years), extended regions of severe degeneration occurred in the peripheral/mid-peripheral retina. In XLPRA1 carriers, opsin mislocalization and rare events of rod death were detected by TUNEL assay at 20 weeks of age; however, only patchy degeneration was seen by 1.4 years and was still apparent at 7.8 years. CONCLUSIONS The time of onset and the progression of the disease differed between the two models. In the early-onset form (XLPRA2) the morphologic appearance of the retinal mosaic changed as a function of age, suggesting that structural plasticity persists in the early postnatal canine retina as mutant photoreceptors die. In the late-onset form (XLPRA1), patches of disease persisted until later ages.
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Affiliation(s)
- William A Beltran
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104,
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21
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Martínez R, Bonilla-Henao V, Ramos I, Sobrino F, Lucas M, Pintado E. May anomalous X chromosome methylation be responsible for the spontaneous abortion of a male foetus? J Genet 2009; 87:261-4. [PMID: 19147911 DOI: 10.1007/s12041-008-0040-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R Martínez
- Departamento de Bioquimica Médica y Biología Molecular, Facultad de Medicina, Avda. Sanchez Pizjuán, 4 E-41009, Sevilla, Spain
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22
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Bolduc V, Chagnon P, Provost S, Dubé MP, Belisle C, Gingras M, Mollica L, Busque L. No evidence that skewing of X chromosome inactivation patterns is transmitted to offspring in humans. J Clin Invest 2008; 118:333-41. [PMID: 18097474 DOI: 10.1172/jci33166] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 10/31/2007] [Indexed: 11/17/2022] Open
Abstract
Skewing of X chromosome inactivation (XCI) can occur in normal females and increases in tissues with age. The mechanisms underlying skewing in normal females, however, remain controversial. To better understand the phenomenon of XCI in nondisease states, we evaluated XCI patterns in epithelial and hematopoietic cells of over 500 healthy female mother-neonate pairs. The incidence of skewing observed in mothers was twice that observed in neonates, and in both cohorts, the incidence of XCI was lower in epithelial cells than hematopoietic cells. These results suggest that XCI incidence varies by tissue type and that age-dependent mechanisms can influence skewing in both epithelial and hematopoietic cells. In both cohorts, a correlation was identified in the direction of skewing in epithelial and hematopoietic cells, suggesting common underlying skewing mechanisms across tissues. However, there was no correlation between the XCI patterns of mothers and their respective neonates, and skewed mothers gave birth to skewed neonates at the same frequency as nonskewed mothers. Taken together, our data suggest that in humans, the XCI pattern observed at birth does not reflect a single heritable genetic locus, but rather corresponds to a complex trait determined, at least in part, by selection biases occurring after XCI.
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Affiliation(s)
- Véronique Bolduc
- Research Centre, Maisonneuve-Rosemont Hospital, University of Montreal, Montreal, Quebec, Canada
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23
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Abstract
Our knowledge of heredity has recently undergone major upheaval. Heredity transmits considerably more than just genetic elements. First, the oocyte is full of maternal cytoplasmic components that subsequently are present in each new cell. Second, maternal cells can pass to the progeny, where they remain active into adult life (microchimerism). Here, we examine the notion that the transmission of characters involves at least two processes in addition to that of mendelian heredity, long considered to be the only hereditary mechanism. These processes all involve epigenetic processes, including the transmission of macromolecules, subcellular organelles, and living cells solely from the mother to her offspring, whether female or male, during pregnancy and lactation. We postulate that cytoplasmic heredity and maternal transmission of cells leading to a long-term state of microchimerism in progeny are two good examples of matrilineal, nonmendelian heredity. A mother's important contribution to the development and health of her progeny seems to possess many uncharted depths.
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Affiliation(s)
- Marie-Christine Maurel
- Laboratoire de Biochimie de l'Evolution et Adaptabilité Moléculaire, Institut Jacques-Monod, UMR 7592, CNRS and Universités Paris 6 and 7, 75251 Paris Cedex 05, France.
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24
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Lappalainen S, Utriainen P, Kuulasmaa T, Voutilainen R, Jääskeläinen J. Androgen receptor gene CAG repeat polymorphism and X-chromosome inactivation in children with premature adrenarche. J Clin Endocrinol Metab 2008; 93:1304-9. [PMID: 18252782 DOI: 10.1210/jc.2007-2707] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
CONTEXT There is variation in the adrenal androgen levels and clinical findings of children with premature adrenarche (PA). OBJECTIVES We hypothesized that androgen sensitivity, indicated by the length of CAG repeat in the X-chromosomal androgen receptor (AR) gene has a role in the polygenic pathogenesis of PA. DESIGN AND PATIENTS We performed a cross-sectional association study among 73 Finnish Caucasian children with PA (10 boys and 63 girls) and 97 age- and gender-matched healthy controls (18 boys and 79 girls). MAIN OUTCOME MEASURES AR gene methylation-weighted CAG(n)(mwCAG(n)) via CAG(n) length and X-chromosome inactivation analysis and clinical phenotype were determined. SETTING The study took place at a university hospital. RESULTS PA subjects had significantly shorter mwCAG(n) than controls [mean difference (95% confidence interval); 0.76 (0.14-1.38); P = 0.017]. AR gene mwCAG(n) did not correlate with androgen or SHBG levels in either group. In children with PA, mwCAG(n) correlated positively with body mass index (BMI) (tau = 0.19; P = 0.02). The mean of mwCAG(n) was significantly shorter in PA children with lower BMI compared with PA children with higher BMI [BMI sd score < 0.79, n = 35, vs. BMI sd score > 0.79, n = 36; 1.13 (0.38-1.87), P = 0.004] and in PA children with lower BMI compared with healthy children with same BMI (P = 0.004). CONCLUSIONS The AR gene CAG(n) polymorphism may have a significant role in the pathogenesis of PA, especially in lean children.
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Affiliation(s)
- Saila Lappalainen
- Department of Pediatrics, Kuopio University and University Hospital, FI-70211 Kuopio, Finland.
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25
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Abstract
The compensation of the different level of transcripts of X-linked genes in male and female mammals is achieved through X chromosome inactivation, a complex process that differentially regulates the sex chromosomes of female cells. This mechanism has been dissected at evolutionary, genetic and molecular levels: here, we discuss some of the latest examples that illustrate better these intricate connections, focusing particularly on the emerging role of spatial and three-dimensional chromatin arrangements in the building of this special chromosome, the inactive X chromosome.
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Affiliation(s)
- Jamison D Feramisco
- Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
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27
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Wutz A. Xist function: bridging chromatin and stem cells. Trends Genet 2007; 23:457-64. [PMID: 17681633 DOI: 10.1016/j.tig.2007.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 06/06/2007] [Accepted: 07/18/2007] [Indexed: 11/19/2022]
Abstract
In mammals, dosage compensation is achieved by transcriptional silencing of one of the two female X chromosomes. X inactivation is dynamically regulated in development. The non-coding Xist RNA localizes to the inactive X, initiates gene repression in the early embryo, and later stabilizes the inactive state. Different functions of Xist are observed depending on which epigenetic regulatory pathways are active in a given cell. Because Xist has evolved recently, with the origin of placental mammals, the underlying pathways are also important in regulating developmental control genes. This review emphasizes the opportunity that Xist provides to functionally define epigenetic transitions in development, to understand cell identity, pluripotency and stem cell differentiation.
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Affiliation(s)
- Anton Wutz
- Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria.
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Affiliation(s)
- Sébastien Vigneau
- Unité Génétique Moléculaire Murine, CNRS URA 2578, Institut Pasteur, 25, Rue du Docteur Roux, 75724 Paris Cedex 15, France.
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Affiliation(s)
- Sandrine Augui
- Equipe Epigenèse et Développement des Mammifères, CNRS UMR 218, Institut Curie, 26, Rue d'Ulm, 75248 Paris Cedex 06, France
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Cau M, Addis M, Congiu R, Meloni C, Cao A, Santaniello S, Loi M, Emma F, Zuffardi O, Ciccone R, Sole G, Melis MA. A locus for familial skewed X chromosome inactivation maps to chromosome Xq25 in a family with a female manifesting Lowe syndrome. J Hum Genet 2006; 51:1030-1036. [PMID: 16955230 DOI: 10.1007/s10038-006-0049-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Accepted: 08/03/2006] [Indexed: 11/29/2022]
Abstract
In mammals, X-linked gene products can be dosage compensated between males and females by inactivation of one of the two X chromosomes in the developing female embryos. X inactivation choice is usually random in embryo mammals, but several mechanisms can influence the choice determining skewed X inactivation. As a consequence, females heterozygous for X-linked recessive disease can manifest the full phenotype. Herein, we report a family with extremely skewed X inactivation that produced the full phenotype of Lowe syndrome, a recessive X-linked disease, in a female. The X chromosome inactivation studies detected an extremely skewed inactivation pattern with a ratio of 100:0 in the propositus as well as in five out of seven unaffected female relatives in four generations. The OCRL1 "de novo" mutation resides in the active paternally inherited X chromosome. X chromosome haplotype analysis suggests the presence of a locus for the familial skewed X inactivation in chromosome Xq25 most likely controlling X chromosome choice in X inactivation or cell proliferation. The description of this case adds Lowe syndrome to the list of X-linked disorders which may manifest the full phenotype in females because of the skewed X inactivation.
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Affiliation(s)
- Milena Cau
- Dipartimento di Scienze Biomediche e Biotecnologie, Università di Cagliari, via Jenner s/n, 09134, Cagliari, Italy
| | - Maria Addis
- Dipartimento di Scienze Biomediche e Biotecnologie, Università di Cagliari, via Jenner s/n, 09134, Cagliari, Italy
| | - Rita Congiu
- Dipartimento di Scienze Biomediche e Biotecnologie, Università di Cagliari, via Jenner s/n, 09134, Cagliari, Italy
| | - Cristiana Meloni
- Dipartimento di Scienze Biomediche e Biotecnologie, Università di Cagliari, via Jenner s/n, 09134, Cagliari, Italy
| | - Antonio Cao
- Istituto di Neurogenetica e Neurofarmacologia, CNR, Selargius (CA), Italy
| | - Simona Santaniello
- Dipartimento di Scienze Biomediche e Biotecnologie, Università di Cagliari, via Jenner s/n, 09134, Cagliari, Italy
| | - Mario Loi
- Servizio di Neuropsichiatria. Azienda Ospedaliera G. Brotzu, Cagliari, Italy
| | - Francesco Emma
- Department of Nephrology and dialysis, Bambino Gesù, Children's Research Hospital, Rome, Italy
| | - Orsetta Zuffardi
- Genetica Medica Università di Pavia, Pavia, Italy
- IRCSS Policlinico San Matteo, Pavia, Italy
| | | | - Gabriella Sole
- Istituto di Neurogenetica e Neurofarmacologia, CNR, Selargius (CA), Italy
| | - Maria Antonietta Melis
- Dipartimento di Scienze Biomediche e Biotecnologie, Università di Cagliari, via Jenner s/n, 09134, Cagliari, Italy.
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