51
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Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science 2013; 343:80-4. [PMID: 24336569 DOI: 10.1126/science.1246981] [Citation(s) in RCA: 1983] [Impact Index Per Article: 180.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system for genome editing has greatly expanded the toolbox for mammalian genetics, enabling the rapid generation of isogenic cell lines and mice with modified alleles. Here, we describe a pooled, loss-of-function genetic screening approach suitable for both positive and negative selection that uses a genome-scale lentiviral single-guide RNA (sgRNA) library. sgRNA expression cassettes were stably integrated into the genome, which enabled a complex mutant pool to be tracked by massively parallel sequencing. We used a library containing 73,000 sgRNAs to generate knockout collections and performed screens in two human cell lines. A screen for resistance to the nucleotide analog 6-thioguanine identified all expected members of the DNA mismatch repair pathway, whereas another for the DNA topoisomerase II (TOP2A) poison etoposide identified TOP2A, as expected, and also cyclin-dependent kinase 6, CDK6. A negative selection screen for essential genes identified numerous gene sets corresponding to fundamental processes. Last, we show that sgRNA efficiency is associated with specific sequence motifs, enabling the prediction of more effective sgRNAs. Collectively, these results establish Cas9/sgRNA screens as a powerful tool for systematic genetic analysis in mammalian cells.
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Affiliation(s)
- Tim Wang
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
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Cotton AM, Ge B, Light N, Adoue V, Pastinen T, Brown CJ. Analysis of expressed SNPs identifies variable extents of expression from the human inactive X chromosome. Genome Biol 2013; 14:R122. [PMID: 24176135 PMCID: PMC4053723 DOI: 10.1186/gb-2013-14-11-r122] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 11/01/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND X-chromosome inactivation (XCI) results in the silencing of most genes on one X chromosome, yielding mono-allelic expression in individual cells. However, random XCI results in expression of both alleles in most females. Allelic imbalances have been used genome-wide to detect mono-allelically expressed genes. Analysis of X-linked allelic imbalance in females with skewed XCI offers the opportunity to identify genes that escape XCI with bi-allelic expression in contrast to those with mono-allelic expression and which are therefore subject to XCI. RESULTS We determine XCI status for 409 genes, all of which have at least five informative females in our dataset. The majority of genes are subject to XCI and genes that escape from XCI show a continuum of expression from the inactive X. Inactive X expression corresponds to differences in the level of histone modification detected by allelic imbalance after chromatin immunoprecipitation. Differences in XCI between populations and between cell lines derived from different tissues are observed. CONCLUSIONS We demonstrate that allelic imbalance can be used to determine an inactivation status for X-linked genes, even without completely non-random XCI. There is a range of expression from the inactive X. Genes escaping XCI, including those that do so in only a subset of females, cluster together, demonstrating that XCI and location on the X chromosome are related. In addition to revealing mechanisms involved in cis-gene regulation, determining which genes escape XCI can expand our understanding of the contributions of X-linked genes to sexual dimorphism.
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Lee SE, Lee SY, Lee KA. Rhox in mammalian reproduction and development. Clin Exp Reprod Med 2013; 40:107-14. [PMID: 24179867 PMCID: PMC3811726 DOI: 10.5653/cerm.2013.40.3.107] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 09/10/2013] [Accepted: 09/10/2013] [Indexed: 01/06/2023] Open
Abstract
Homeobox genes play essential roles in embryonic development and reproduction. Recently, a large cluster of homeobox genes, reproductive homeobox genes on the X chromosome (Rhox) genes, was discovered as three gene clusters, α, β, and γ in mice. It was found that Rhox genes were selectively expressed in reproduction-associated tissues, such as those of the testes, epididymis, ovaries, and placenta. Hence, it was proposed that Rhox genes are important for regulating various reproductive features, especially gametogenesis in male as well as in female mammals. It was first determined that 12 Rhox genes are clustered into α (Rhox1-4), β (Rhox5-9), and γ (Rhox10-12) subclusters, and recently Rhox13 has also been found. At present, 33 Rhox genes have been identified in the mouse genome, 11 in the rat, and three in the human. Rhox genes are also responsible for embryonic development, with considerable amounts of Rhox expression in trophoblasts, placenta tissue, embryonic stem cells, and primordial germ cells. In this article we summarized the current understanding of Rhox family genes involved in reproduction and embryonic development and elucidated a previously unreported cell-specific expression in ovarian cells.
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Affiliation(s)
- Sang-Eun Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Korea
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Hernando-Herraez I, Prado-Martinez J, Garg P, Fernandez-Callejo M, Heyn H, Hvilsom C, Navarro A, Esteller M, Sharp AJ, Marques-Bonet T. Dynamics of DNA methylation in recent human and great ape evolution. PLoS Genet 2013; 9:e1003763. [PMID: 24039605 PMCID: PMC3764194 DOI: 10.1371/journal.pgen.1003763] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 07/18/2013] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex disease. However, the dynamics of DNA methylation changes between humans and their closest relatives are still poorly understood. We performed a comparative analysis of CpG methylation patterns between 9 humans and 23 primate samples including all species of great apes (chimpanzee, bonobo, gorilla and orangutan) using Illumina Methylation450 bead arrays. Our analysis identified ∼800 genes with significantly altered methylation patterns among the great apes, including ∼170 genes with a methylation pattern unique to human. Some of these are known to be involved in developmental and neurological features, suggesting that epigenetic changes have been frequent during recent human and primate evolution. We identified a significant positive relationship between the rate of coding variation and alterations of methylation at the promoter level, indicative of co-occurrence between evolution of protein sequence and gene regulation. In contrast, and supporting the idea that many phenotypic differences between humans and great apes are not due to amino acid differences, our analysis also identified 184 genes that are perfectly conserved at protein level between human and chimpanzee, yet show significant epigenetic differences between these two species. We conclude that epigenetic alterations are an important force during primate evolution and have been under-explored in evolutionary comparative genomics. Differences in protein coding sequences between humans and their closest relatives are too small to account for their phenotypic differences. It has been hypothesized that these differences may be explained by alterations of gene regulation rather than primary genome sequence. DNA methylation is an important epigenetic modification that is involved in many biological processes, but from an evolutionary point of view this modification is still poorly understood. To this end, we performed a comparative analysis of CpG methylation patterns between humans and great apes. Using this approach, we were able to study the dynamics of DNA methylation in recent primate evolution and to identify regions showing species-specific methylation pattern among humans and great apes. We find that genes with alterations of promoter methylation tend to show increased rates of divergence in their protein sequence, and in contrast we also identify many genes with regulatory changes between human and chimpanzee that have perfectly conserved protein sequence. Our study provides the first global view of evolutionary epigenetic changes that have occurred in the genomes of all species of great apes.
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Affiliation(s)
| | | | - Paras Garg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai School, New York, New York, United States of America
| | | | - Holger Heyn
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | | | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain
| | - Andrew J. Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai School, New York, New York, United States of America
- * E-mail: (AJS); (TMB)
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- * E-mail: (AJS); (TMB)
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55
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Casimir GJ, Lefèvre N, Corazza F, Duchateau J. Sex and inflammation in respiratory diseases: a clinical viewpoint. Biol Sex Differ 2013; 4:16. [PMID: 24128344 PMCID: PMC3765878 DOI: 10.1186/2042-6410-4-16] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 08/07/2013] [Indexed: 12/15/2022] Open
Abstract
This review discusses sex differences in the prognosis of acute or chronic inflammatory diseases. The consequences of severe inflammation vary in relation to sex, depending on illness duration. In the majority of acute diseases, males present higher mortality rates, whereas continuous chronic inflammation associated with tissue damage is more deleterious in females. The recruitment of cells, along with its clinical expression, is more significant in females, as reflected by higher inflammatory markers. Given that estrogens or androgens are known to modulate inflammation, their different levels in males and females cannot account for the sexual dimorphism observed in humans and animals from birth to death with regard to inflammation. Numerous studies evaluated receptors, cytokine production, and clinical outcomes in both animals and humans, revealing that estrogens clearly modulate the immune response, but the results are contradictory and difficult to link to hormone concentrations. Even in prepubescent children, the presentation of acute pneumonia or chronic diseases mimics the adult pattern. Several genes located on the X chromosome have been shown to encode molecules involved in inflammation. Moreover, 10% to 15% of the genes from silenced X chromosome may escape inhibition. Females are also a mosaic of cells with genes from either paternal or maternal X chromosome. Therefore, polymorphism of X-linked genes would result in the presence of two cell populations with distinct regulatory arsenals, providing females with greater diversity to fight against infectious challenges, in comparison with the uniform cell populations in hemizygous males. The similarities observed between males and Turner syndrome patients using an endotoxin stimulation model support the difference in gene expression between monosomy and disomy for the X chromosome. Considering the enhanced inflammation in females, cytokine production may be assumed to be higher in females than males. Even if all results are not clear-cut, nonetheless, many studies have reported higher cytokine levels in both male humans and animals than in females. High IL-6 levels in males correlated with poorer prognosis and shorter longevity. A sound understanding of the basic regulatory mechanisms responsible for these gender differences may lead to new therapeutic targets.
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Affiliation(s)
- Georges J Casimir
- Department of Pulmonology, Allergology and Cystic Fibrosis, Hôpital Universitaire des Enfants Reine Fabiola, Avenue JJ. Crocq 15, B-1020, Brussels, Belgium ; Laboratory of Pediatrics, Université Libre de Bruxelles (ULB), Place Arthur Van Gehuchten 4, B-1020, Brussels, Belgium
| | - Nicolas Lefèvre
- Department of Pulmonology, Allergology and Cystic Fibrosis, Hôpital Universitaire des Enfants Reine Fabiola, Avenue JJ. Crocq 15, B-1020, Brussels, Belgium ; Laboratory of Immunology, Hôpital Universitaire Brugmann, Place Arthur Van Gehuchten, 4, B-1020, Brussels, Belgium
| | - Francis Corazza
- Laboratory of Immunology, Hôpital Universitaire Brugmann, Place Arthur Van Gehuchten, 4, B-1020, Brussels, Belgium
| | - Jean Duchateau
- Laboratory of Pediatrics, Université Libre de Bruxelles (ULB), Place Arthur Van Gehuchten 4, B-1020, Brussels, Belgium
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56
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Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork AJ, Schultz MD, Yu M, Tonti-Filippini J, Heyn H, Hu S, Wu JC, Rao A, Esteller M, He C, Haghighi FG, Sejnowski TJ, Behrens MM, Ecker JR. Global epigenomic reconfiguration during mammalian brain development. Science 2013; 341:1237905. [PMID: 23828890 PMCID: PMC3785061 DOI: 10.1126/science.1237905] [Citation(s) in RCA: 1310] [Impact Index Per Article: 119.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA methylation is implicated in mammalian brain development and plasticity underlying learning and memory. We report the genome-wide composition, patterning, cell specificity, and dynamics of DNA methylation at single-base resolution in human and mouse frontal cortex throughout their lifespan. Widespread methylome reconfiguration occurs during fetal to young adult development, coincident with synaptogenesis. During this period, highly conserved non-CG methylation (mCH) accumulates in neurons, but not glia, to become the dominant form of methylation in the human neuronal genome. Moreover, we found an mCH signature that identifies genes escaping X-chromosome inactivation. Last, whole-genome single-base resolution 5-hydroxymethylcytosine (hmC) maps revealed that hmC marks fetal brain cell genomes at putative regulatory regions that are CG-demethylated and activated in the adult brain and that CG demethylation at these hmC-poised loci depends on Tet2 activity.
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Affiliation(s)
- Ryan Lister
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.,Plant Energy Biology [Australian Research Council Center of Excellence (CoE)] and Computational Systems Biology (Western Australia CoE), School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
| | - Eran A Mukamel
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mark Urich
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Clare A Puddifoot
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nicholas D Johnson
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jacinta Lucero
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Yun Huang
- La Jolla Institute for Allergy and Immunology and Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University and The New York State Psychiatric Institute, New York, NY 10032, USA.,Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Matthew D Schultz
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.,Bioinformatics Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Miao Yu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Julian Tonti-Filippini
- Plant Energy Biology [Australian Research Council Center of Excellence (CoE)] and Computational Systems Biology (Western Australia CoE), School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
| | - Holger Heyn
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Shijun Hu
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anjana Rao
- La Jolla Institute for Allergy and Immunology and Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona 08907, Spain.,InstitucióCatalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Fatemeh G Haghighi
- Department of Psychiatry, Columbia University and The New York State Psychiatric Institute, New York, NY 10032, USA
| | - Terrence J Sejnowski
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.,Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92037, USA.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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57
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Berletch JB, Deng X, Nguyen DK, Disteche CM. Female bias in Rhox6 and 9 regulation by the histone demethylase KDM6A. PLoS Genet 2013; 9:e1003489. [PMID: 23658530 PMCID: PMC3642083 DOI: 10.1371/journal.pgen.1003489] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 03/18/2013] [Indexed: 12/20/2022] Open
Abstract
The Rhox cluster on the mouse X chromosome contains reproduction-related homeobox genes expressed in a sexually dimorphic manner. We report that two members of the Rhox cluster, Rhox6 and 9, are regulated by de-methylation of histone H3 at lysine 27 by KDM6A, a histone demethylase with female-biased expression. Consistent with other homeobox genes, Rhox6 and 9 are in bivalent domains prior to embryonic stem cell differentiation and thus poised for activation. In female mouse ES cells, KDM6A is specifically recruited to Rhox6 and 9 for gene activation, a process inhibited by Kdm6a knockdown in a dose-dependent manner. In contrast, KDM6A occupancy at Rhox6 and 9 is low in male ES cells and knockdown has no effect on expression. In mouse ovary where Rhox6 and 9 remain highly expressed, KDM6A occupancy strongly correlates with expression. Our study implicates Kdm6a, a gene that escapes X inactivation, in the regulation of genes important in reproduction, suggesting that KDM6A may play a role in the etiology of developmental and reproduction-related effects of X chromosome anomalies.
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Affiliation(s)
- Joel B. Berletch
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Xinxian Deng
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Di Kim Nguyen
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Christine M. Disteche
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, School of Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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58
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Abstract
Differentiated sex chromosomes evolved because of suppressed recombination once sex became genetically controlled. In XX/XY and ZZ/ZW systems, the heterogametic sex became partially aneuploid after degeneration of the Y or W. Often, aneuploidy causes abnormal levels of gene expression throughout the entire genome. Dosage compensation mechanisms evolved to restore balanced expression of the genome. These mechanisms include upregulation of the heterogametic chromosome as well as repression in the homogametic sex. Remarkably, strategies for dosage compensation differ between species. In organisms where more is known about molecular mechanisms of dosage compensation, specific protein complexes containing noncoding RNAs are targeted to the X chromosome. In addition, the dosage-regulated chromosome often occupies a specific nuclear compartment. Some genes escape dosage compensation, potentially resulting in sex-specific differences in gene expression. This review focuses on dosage compensation in mammals, with comparisons to fruit flies, nematodes, and birds.
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Affiliation(s)
- Christine M Disteche
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA.
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59
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Sex Differences in Inflammatory Cytokines and CD99 Expression Following In Vitro Lipopolysaccharide Stimulation. Shock 2012; 38:37-42. [DOI: 10.1097/shk.0b013e3182571e46] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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60
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Chen X, McClusky R, Chen J, Beaven SW, Tontonoz P, Arnold AP, Reue K. The number of x chromosomes causes sex differences in adiposity in mice. PLoS Genet 2012; 8:e1002709. [PMID: 22589744 PMCID: PMC3349739 DOI: 10.1371/journal.pgen.1002709] [Citation(s) in RCA: 227] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 03/28/2012] [Indexed: 12/12/2022] Open
Abstract
Sexual dimorphism in body weight, fat distribution, and metabolic disease has been attributed largely to differential effects of male and female gonadal hormones. Here, we report that the number of X chromosomes within cells also contributes to these sex differences. We employed a unique mouse model, known as the “four core genotypes,” to distinguish between effects of gonadal sex (testes or ovaries) and sex chromosomes (XX or XY). With this model, we produced gonadal male and female mice carrying XX or XY sex chromosome complements. Mice were gonadectomized to remove the acute effects of gonadal hormones and to uncover effects of sex chromosome complement on obesity. Mice with XX sex chromosomes (relative to XY), regardless of their type of gonad, had up to 2-fold increased adiposity and greater food intake during daylight hours, when mice are normally inactive. Mice with two X chromosomes also had accelerated weight gain on a high fat diet and developed fatty liver and elevated lipid and insulin levels. Further genetic studies with mice carrying XO and XXY chromosome complements revealed that the differences between XX and XY mice are attributable to dosage of the X chromosome, rather than effects of the Y chromosome. A subset of genes that escape X chromosome inactivation exhibited higher expression levels in adipose tissue and liver of XX compared to XY mice, and may contribute to the sex differences in obesity. Overall, our study is the first to identify sex chromosome complement, a factor distinguishing all male and female cells, as a cause of sex differences in obesity and metabolism. Differences exist between men and women in the development of obesity and related metabolic diseases such as type 2 diabetes and cardiovascular disease. Previous studies have focused on the sex-biasing role of hormones produced by male and female gonads, but these cannot account fully for the sex differences in metabolism. We discovered that removal of the gonads uncovers an important genetic determinant of sex differences in obesity—the presence of XX or XY sex chromosomes. We used a novel mouse model to tease apart the effects of male and female gonads from the effects of XX or XY chromosomes. Mice with XX sex chromosomes (relative to XY), regardless of their type of gonad, had increased body fat and ate more food during the sleep period. Mice with two X chromosomes also had accelerated weight gain, fatty liver, and hyperinsulinemia on a high fat diet. The higher expression levels of a subset of genes on the X chromosome that escape inactivation may influence adiposity and metabolic disease. The effect of X chromosome genes is present throughout life, but may become particularly significant with increases in longevity and extension of the period spent with reduced gonadal hormone levels.
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Affiliation(s)
- Xuqi Chen
- Department of Integrative Biology and Physiology and Laboratory of Neuroendocrinology or the Brain Research Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Rebecca McClusky
- Department of Integrative Biology and Physiology and Laboratory of Neuroendocrinology or the Brain Research Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jenny Chen
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Simon W. Beaven
- Department of Medicine, Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Howard Hughes Medical Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Peter Tontonoz
- Howard Hughes Medical Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Arthur P. Arnold
- Department of Integrative Biology and Physiology and Laboratory of Neuroendocrinology or the Brain Research Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Karen Reue
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Medicine, Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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61
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Gribnau J, Grootegoed JA. Origin and evolution of X chromosome inactivation. Curr Opin Cell Biol 2012; 24:397-404. [PMID: 22425180 DOI: 10.1016/j.ceb.2012.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 02/17/2012] [Accepted: 02/17/2012] [Indexed: 10/28/2022]
Abstract
Evolution of the mammalian sex chromosomes heavily impacts on the expression of X-encoded genes, both in marsupials and placental mammals. The loss of genes from the Y chromosome forced a two-fold upregulation of dose sensitive X-linked homologues. As a corollary, female cells would experience a lethal dose of X-linked genes, if this upregulation was not counteracted by evolution of X chromosome inactivation (XCI) that allows for only one active X chromosome per diploid genome. Marsupials rely on imprinted XCI, which inactivates always the paternally inherited X chromosome. In placental mammals, random XCI (rXCI) is the predominant form, inactivating either the maternal or paternal X. In this review, we discuss recent new insights in the regulation of XCI. Based on these findings, we propose an X inactivation center (Xic), composed of a cis-Xic and trans-Xic that encompass all elements and factors acting to control rXCI either in cis or in trans. We also highlight that XCI may have evolved from a very small nucleation site on the X chromosome in the vicinity of the Sox3 gene. Finally, we discuss the possible evolutionary road maps that resulted in imprinted XCI and rXCI as observed in present day mammals.
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Affiliation(s)
- Joost Gribnau
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
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62
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Bermejo-Alvarez P, Ramos-Ibeas P, Gutierrez-Adan A. Solving the "X" in embryos and stem cells. Stem Cells Dev 2012; 21:1215-24. [PMID: 22309156 DOI: 10.1089/scd.2011.0685] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
X-chromosome inactivation (XCI) is a complex epigenetic process that ensures that most X-linked genes are expressed equally for both sexes. Female eutherian mammals inactivate randomly the maternal or paternal inherited X-chromosome early in embryogenesis, whereas the extra-embryonic tissues experience an imprinting XCI that results in the inactivation of the paternal X-chromosome in mice. Although the phenomenon was initially described 40 years ago, many aspects remain obscure. In the last 2 years, some trademark publications have shed new light on the ongoing debate regarding the timing and mechanism of imprinted or random XCI. It has been observed that XCI is not accomplished at the blastocyst stage in bovines, rabbits, and humans, contrasting with the situation reported in mice, the standard model. All the species present 2 active X-chromosomes (Xa) in the early epiblast of the blastocyst, the cellular source for embryonic stem cells (ESCs). In this perspective, it would make sense to expect an absence of XCI in undifferentiated ESCs, but human ESCs are highly heterogeneous for this parameter and the presence of 2 Xa has been proposed as a true hallmark of ground-state pluripotency and a quality marker for female ESCs. Similarly, XCI reversal in female induced pluripotent stem cells is a key reprogramming event on the path to achieve the naïve pluripotency, and key pluripotency regulators can interact directly or indirectly with Xist. Finally, the presence of 2 Xa may lead to a sex-specific transcriptional regulation resulting in sexual dimorphism in reprogramming and differentiation.
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A novel c.2T > C mutation of the KDM5C/JARID1C gene in one large family with X-linked intellectual disability. Eur J Med Genet 2012; 55:178-84. [DOI: 10.1016/j.ejmg.2012.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 01/11/2012] [Indexed: 11/20/2022]
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Arnold AP. The end of gonad-centric sex determination in mammals. Trends Genet 2012; 28:55-61. [PMID: 22078126 PMCID: PMC3268825 DOI: 10.1016/j.tig.2011.10.004] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/16/2011] [Accepted: 10/17/2011] [Indexed: 01/18/2023]
Abstract
The 20th-century theory of mammalian sex determination states that the embryo is sexually indifferent until the differentiation of gonads, after which sex differences in phenotype are caused by the differential effects of gonadal hormones. However, this theory is inadequate because some sex differences precede differentiation of the gonads and/or are determined by non-gonadal effects of the sexual inequality in the number and type of sex chromosomes. In this article, I propose a general theory of sex determination, which recognizes multiple parallel primary sex-determining pathways initiated by genes or factors encoded by the sex chromosomes. The separate sex-specific pathways interact to synergize with or antagonize each other, enhancing or reducing sex differences in phenotype.
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Affiliation(s)
- Arthur P Arnold
- Department of Integrative Biology & Physiology, Laboratory of Neuroendocrinology of the Brain Research Institute, University of California, Los Angeles, CA 90095-7239, USA.
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Abstract
The immune system and its orchestrated response are affected by a multitude of endogenous and exogenous factors, modulators and challenges. One of the most frequent differences described in the immune response is its vigor and activity in females compared to males, leading to the consequent increase in autoimmune conditions seen in the female population as well as differences in the immune response to pathogens and viruses. The following review summarizes our present knowledge on sex differences in the immune response, detailing the hormonal and genetic effects that have been proposed as explanatory mechanisms. Sexual hormones, mostly estrogen but also progesterone and testosterone, affect immune cells quantitatively and qualitatively. Relevant research has focused on the impact of hormones on cytokine production by the different effector cells, as well as impact on immunoglobulin production by B lymphocytes and activity of granulocytes and NK cells. The biological aspects are complemented by research data on the possible modulatory role of the X chromosome. In addition to biological differences, the frequently neglected role of gender as an immunomodulator is introduced and explored. Gender affects all areas of human life and consequently affects the different steps of an immune response. Exposure to various types of antigens, access to health promotion programs and health care, as well as prioritization of health needs and household resource allocation all affect the different response of females and males to immunologic challenges.
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Knickmeyer RC, Davenport M. Turner syndrome and sexual differentiation of the brain: implications for understanding male-biased neurodevelopmental disorders. J Neurodev Disord 2011; 3:293-306. [PMID: 21818630 PMCID: PMC3261262 DOI: 10.1007/s11689-011-9089-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 07/13/2011] [Indexed: 01/24/2023] Open
Abstract
Turner syndrome (TS) is one of the most common sex chromosome abnormalities. Affected individuals often show a unique pattern of cognitive strengths and weaknesses and are at increased risk for a number of other neurodevelopmental conditions, many of which are more common in typical males than typical females (e.g., autism and attention-deficit hyperactivity disorder). This phenotype may reflect gonadal steroid deficiency, haploinsufficiency of X chromosome genes, failure to express parentally imprinted genes, and the uncovering of X chromosome mutations. Understanding the contribution of these different mechanisms to outcome has the potential to improve clinical care for individuals with TS and to better our understanding of the differential vulnerability to and expression of neurodevelopmental disorders in males and females. In this paper, we review what is currently known about cognition and brain development in individuals with TS, discuss underlying mechanisms and their relevance to understanding male-biased neurodevelopmental conditions, and suggest directions for future research.
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Affiliation(s)
- Rebecca Christine Knickmeyer
- Department of Psychiatry CB 7160, University of North Carolina at Chapel Hill, 343 Medical Wings C, Campus Box #7160, Chapel Hill, NC, 27599-7160, USA,
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Castagné R, Zeller T, Rotival M, Szymczak S, Truong V, Schillert A, Trégouët DA, Münzel T, Ziegler A, Cambien F, Blankenberg S, Tiret L. Influence of sex and genetic variability on expression of X-linked genes in human monocytes. Genomics 2011; 98:320-6. [DOI: 10.1016/j.ygeno.2011.06.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/27/2011] [Accepted: 06/28/2011] [Indexed: 11/28/2022]
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The choice of the filtering method in microarrays affects the inference regarding dosage compensation of the active X-chromosome. PLoS One 2011; 6:e23956. [PMID: 21912656 PMCID: PMC3164665 DOI: 10.1371/journal.pone.0023956] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 07/27/2011] [Indexed: 12/31/2022] Open
Abstract
Background The hypothesis of dosage compensation of genes of the X chromosome, supported by previous microarray studies, was recently challenged by RNA-sequencing data. It was suggested that microarray studies were biased toward an over-estimation of X-linked expression levels as a consequence of the filtering of genes below the detection threshold of microarrays. Methodology/Principal Findings To investigate this hypothesis, we used microarray expression data from circulating monocytes in 1,467 individuals. In total, 25,349 and 1,156 probes were unambiguously assigned to autosomes and the X chromosome, respectively. Globally, there was a clear shift of X-linked expressions toward lower levels than autosomes. We compared the ratio of expression levels of X-linked to autosomal transcripts (X∶AA) using two different filtering methods: 1. gene expressions were filtered out using a detection threshold irrespective of gene chromosomal location (the standard method in microarrays); 2. equal proportions of genes were filtered out separately on the X and on autosomes. For a wide range of filtering proportions, the X∶AA ratio estimated with the first method was not significantly different from 1, the value expected if dosage compensation was achieved, whereas it was significantly lower than 1 with the second method, leading to the rejection of the hypothesis of dosage compensation. We further showed in simulated data that the choice of the most appropriate method was dependent on biological assumptions regarding the proportion of actively expressed genes on the X chromosome comparative to the autosomes and the extent of dosage compensation. Conclusion/Significance This study shows that the method used for filtering out lowly expressed genes in microarrays may have a major impact according to the hypothesis investigated. The hypothesis of dosage compensation of X-linked genes cannot be firmly accepted or rejected using microarray-based data.
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69
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Sharp AJ, Stathaki E, Migliavacca E, Brahmachary M, Montgomery SB, Dupre Y, Antonarakis SE. DNA methylation profiles of human active and inactive X chromosomes. Genome Res 2011; 21:1592-600. [PMID: 21862626 DOI: 10.1101/gr.112680.110] [Citation(s) in RCA: 190] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
X-chromosome inactivation (XCI) is a dosage compensation mechanism that silences the majority of genes on one X chromosome in each female cell. To characterize epigenetic changes that accompany this process, we measured DNA methylation levels in 45,X patients carrying a single active X chromosome (X(a)), and in normal females, who carry one X(a) and one inactive X (X(i)). Methylated DNA was immunoprecipitated and hybridized to high-density oligonucleotide arrays covering the X chromosome, generating epigenetic profiles of active and inactive X chromosomes. We observed that XCI is accompanied by changes in DNA methylation specifically at CpG islands (CGIs). While the majority of CGIs show increased methylation levels on the X(i), XCI actually results in significant reductions in methylation at 7% of CGIs. Both intra- and inter-genic CGIs undergo epigenetic modification, with the biggest increase in methylation occurring at the promoters of genes silenced by XCI. In contrast, genes escaping XCI generally have low levels of promoter methylation, while genes that show inter-individual variation in silencing show intermediate increases in methylation. Thus, promoter methylation and susceptibility to XCI are correlated. We also observed a global correlation between CGI methylation and the evolutionary age of X-chromosome strata, and that genes escaping XCI show increased methylation within gene bodies. We used our epigenetic map to predict 26 novel genes escaping XCI, and searched for parent-of-origin-specific methylation differences, but found no evidence to support imprinting on the human X chromosome. Our study provides a detailed analysis of the epigenetic profile of active and inactive X chromosomes.
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Affiliation(s)
- Andrew J Sharp
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva 4, Switzerland.
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70
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Zhang Y, Klein K, Sugathan A, Nassery N, Dombkowski A, Zanger UM, Waxman DJ. Transcriptional profiling of human liver identifies sex-biased genes associated with polygenic dyslipidemia and coronary artery disease. PLoS One 2011; 6:e23506. [PMID: 21858147 PMCID: PMC3155567 DOI: 10.1371/journal.pone.0023506] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 07/19/2011] [Indexed: 01/23/2023] Open
Abstract
Sex-differences in human liver gene expression were characterized on a genome-wide scale using a large liver sample collection, allowing for detection of small expression differences with high statistical power. 1,249 sex-biased genes were identified, 70% showing higher expression in females. Chromosomal bias was apparent, with female-biased genes enriched on chrX and male-biased genes enriched on chrY and chr19, where 11 male-biased zinc-finger KRAB-repressor domain genes are distributed in six clusters. Top biological functions and diseases significantly enriched in sex-biased genes include transcription, chromatin organization and modification, sexual reproduction, lipid metabolism and cardiovascular disease. Notably, sex-biased genes are enriched at loci associated with polygenic dyslipidemia and coronary artery disease in genome-wide association studies. Moreover, of the 8 sex-biased genes at these loci, 4 have been directly linked to monogenic disorders of lipid metabolism and show an expression profile in females (elevated expression of ABCA1, APOA5 and LDLR; reduced expression of LIPC) that is consistent with the lower female risk of coronary artery disease. Female-biased expression was also observed for CYP7A1, which is activated by drugs used to treat hypercholesterolemia. Several sex-biased drug-metabolizing enzyme genes were identified, including members of the CYP, UGT, GPX and ALDH families. Half of 879 mouse orthologs, including many genes of lipid metabolism and homeostasis, show growth hormone-regulated sex-biased expression in mouse liver, suggesting growth hormone might play a similar regulatory role in human liver. Finally, the evolutionary rate of protein coding regions for human-mouse orthologs, revealed by dN/dS ratio, is significantly higher for genes showing the same sex-bias in both species than for non-sex-biased genes. These findings establish that human hepatic sex differences are widespread and affect diverse cell metabolic processes, and may help explain sex differences in lipid profiles associated with sex differential risk of coronary artery disease.
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Affiliation(s)
- Yijing Zhang
- Division of Cell and Molecular Biology, Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Kathrin Klein
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Aarathi Sugathan
- Division of Cell and Molecular Biology, Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Najlla Nassery
- Division of Cell and Molecular Biology, Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Alan Dombkowski
- Division of Clinical Pharmacology and Toxicology, Department of Pediatrics, Wayne State University, Detroit, Michigan, United States of America
| | - Ulrich M. Zanger
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - David J. Waxman
- Division of Cell and Molecular Biology, Department of Biology, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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71
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Zhou YH, Xia K, Wright FA. A powerful and flexible approach to the analysis of RNA sequence count data. ACTA ACUST UNITED AC 2011; 27:2672-8. [PMID: 21810900 DOI: 10.1093/bioinformatics/btr449] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
MOTIVATION A number of penalization and shrinkage approaches have been proposed for the analysis of microarray gene expression data. Similar techniques are now routinely applied to RNA sequence transcriptional count data, although the value of such shrinkage has not been conclusively established. If penalization is desired, the explicit modeling of mean-variance relationships provides a flexible testing regimen that 'borrows' information across genes, while easily incorporating design effects and additional covariates. RESULTS We describe BBSeq, which incorporates two approaches: (i) a simple beta-binomial generalized linear model, which has not been extensively tested for RNA-Seq data and (ii) an extension of an expression mean-variance modeling approach to RNA-Seq data, involving modeling of the overdispersion as a function of the mean. Our approaches are flexible, allowing for general handling of discrete experimental factors and continuous covariates. We report comparisons with other alternate methods to handle RNA-Seq data. Although penalized methods have advantages for very small sample sizes, the beta-binomial generalized linear model, combined with simple outlier detection and testing approaches, appears to have favorable characteristics in power and flexibility. AVAILABILITY An R package containing examples and sample datasets is available at http://www.bios.unc.edu/research/genomic_software/BBSeq CONTACT yzhou@bios.unc.edu; fwright@bios.unc.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yi-Hui Zhou
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA.
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72
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Berletch JB, Yang F, Xu J, Carrel L, Disteche CM. Genes that escape from X inactivation. Hum Genet 2011; 130:237-45. [PMID: 21614513 PMCID: PMC3136209 DOI: 10.1007/s00439-011-1011-z] [Citation(s) in RCA: 254] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Accepted: 05/17/2011] [Indexed: 12/30/2022]
Abstract
To achieve a balanced gene expression dosage between males (XY) and females (XX), mammals have evolved a compensatory mechanism to randomly inactivate one of the female X chromosomes. Despite this chromosome-wide silencing, a number of genes escape X inactivation: in women about 15% of X-linked genes are bi-allelically expressed and in mice, about 3%. Expression from the inactive X allele varies from a few percent of that from the active allele to near equal expression. While most genes have a stable inactivation pattern, a subset of genes exhibit tissue-specific differences in escape from X inactivation. Escape genes appear to be protected from the repressive chromatin modifications associated with X inactivation. Differences in the identity and distribution of escape genes between species and tissues suggest a role for these genes in the evolution of sex differences in specific phenotypes. The higher expression of escape genes in females than in males implies that they may have female-specific roles and may be responsible for some of the phenotypes observed in X aneuploidy.
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Affiliation(s)
- Joel B. Berletch
- Department of Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Fan Yang
- Department of Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jun Xu
- Department of Biomedical Sciences, Tufts University Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA
| | - Laura Carrel
- Department of Biochemistry and Molecular Biology, Pennsylvania State College of Medicine, Hershey, PA 17033, USA
| | - Christine M. Disteche
- Department of Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA. Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
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73
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X-chromosome inactivation: molecular mechanisms from the human perspective. Hum Genet 2011; 130:175-85. [PMID: 21553122 DOI: 10.1007/s00439-011-0994-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 04/15/2011] [Indexed: 10/18/2022]
Abstract
X-chromosome inactivation is an epigenetic process whereby one X chromosome is silenced in mammalian female cells. Since it was first proposed by Lyon in 1961, mouse models have been valuable tools to uncover the molecular mechanisms underlying X inactivation. However, there are also inherent differences between mouse and human X inactivation, ranging from sequence content of the X inactivation center to the phenotypic outcomes of X-chromosome abnormalities. X-linked gene dosage in males, females, and individuals with X aneuploidies and X/autosome translocations has demonstrated that many human genes escape X inactivation, implicating cis-regulatory elements in the spread of silencing. We discuss the potential nature of these elements and also review the elements in the X inactivation center involved in the early events in X-chromosome inactivation.
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74
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Walters JR, Hardcastle TJ. Getting a full dose? Reconsidering sex chromosome dosage compensation in the silkworm, Bombyx mori. Genome Biol Evol 2011; 3:491-504. [PMID: 21508430 PMCID: PMC3296447 DOI: 10.1093/gbe/evr036] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Dosage compensation—equalizing gene expression levels in response to differences in
gene dose or copy number—is classically considered to play a critical role in the
evolution of heteromorphic sex chromosomes. As the X and Y diverge through degradation and
gene loss on the Y (or the W in female-heterogametic ZW taxa), it is expected that dosage
compensation will evolve to correct for sex-specific differences in gene dose. Although
this is observed in some organisms, recent genome-wide expression studies in other taxa
have revealed striking exceptions. In particular, reports that both birds and the silkworm
moth (Bombyx mori) lack dosage compensation have spurred speculation that
this is the rule for all female-heterogametic taxa. Here, we revisit the issue of dosage
compensation in silkworm by replicating and extending the previous analysis. Contrary to
previous reports, our efforts reveal a pattern typically associated with dosage
compensated taxa: the global male:female expression ratio does not differ between the Z
and autosomes. We believe the previous report of unequal male:female ratios on the Z
reflects artifacts of microarray normalization in conjunction with not testing a major
assumption that the male:female global expression ratio was unbiased for autosomal loci.
However, we also find that the global Z chromosome expression is significantly reduced
relative to autosomes, a pattern not expected in dosage compensated taxa. This combination
of male:female parity with an overall reduction in expression for sex-linked loci is not
consistent with the prevailing evolutionary theory of sex chromosome evolution and dosage
compensation.
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Affiliation(s)
- James R Walters
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.
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75
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Wijchers PJ, Festenstein RJ. Epigenetic regulation of autosomal gene expression by sex chromosomes. Trends Genet 2011; 27:132-40. [DOI: 10.1016/j.tig.2011.01.004] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 01/10/2011] [Accepted: 01/12/2011] [Indexed: 12/11/2022]
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Bermejo-Alvarez P, Rizos D, Lonergan P, Gutierrez-Adan A. Transcriptional sexual dimorphism in elongating bovine embryos: implications for XCI and sex determination genes. Reproduction 2011; 141:801-8. [PMID: 21411694 DOI: 10.1530/rep-11-0006] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Sex chromosome transcripts can lead to a broad transcriptional sexual dimorphism in the absence of concomitant or previous exposure to sex hormones, especially when X-chromosome inactivation (XCI) is not complete. XCI timing has been suggested to differ greatly among species, and in bovine, most of the X-linked transcripts are upregulated in female blastocysts. To determine the timing of XCI, we analyzed in day 14 bovine embryos the sexual dimorphic transcription of seven X-linked genes known to be upregulated in female blastocysts (X24112, brain-expressed X-linked 2 (BEX2), ubiquitin-conjugating enzyme E2A (UBE2A), glucose-6-phosphate dehydrogenase (G6PD), brain-expressed X-linked 1 (BEX1), calpain 6 (CAPN6), and spermidine/spermine N-acetyltransferase 1 (SAT1)). The transcription of five genes whose expression differs between sexes at the blastocyst stage (DNMT3A, interferon tau (IFNT2), glutathione S-transferase mu 3 (GSTM3), progesterone receptor membrane component 1 (PGRMC1), and laminin alpha 1 (LAMA1)) and four genes related with sex determination (Wilms tumor 1 (WT1), gata binding protein 4 (GATA4), zinc finger protein multitype 2 (ZFPM2), and DMRT1) was also analyzed to determine the evolution of transcriptional sexual dimorphism. The expression level of five X-linked transcripts was effectively equalized among sexes suggesting that, in cattle, a substantial XCI occurs during the period between blastocyst hatching and initiation of elongation, although UBE2A and SAT1 displayed significant transcriptional differences. Similarly, sexual dimorphism was also reduced for autosomal genes with only DNMT3A and IFNT2 exhibiting sex-related differences. Among the genes potentially involved in sex determination, Wilms tumor 1 (WT1) was significantly upregulated in males and GATA4 in females, whereas no differences were observed for ZFPM2 and DMRT1. In conclusion, a major XCI occurred between the blastocyst and early elongation stages leading to a reduction in the transcriptional sexual dimorphism of autosomal genes, which makes the period the most susceptible to sex-specific embryo loss.
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Affiliation(s)
- P Bermejo-Alvarez
- Dpto. de Reproducción Animal y Conservación de Recursos Zoogenéticos, INIA, Ctra de la Coruña Km 5.9, Madrid 28040, Spain.
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Xu J, Andreassi M. Reversible histone methylation regulates brain gene expression and behavior. Horm Behav 2011; 59:383-92. [PMID: 20816965 PMCID: PMC3084016 DOI: 10.1016/j.yhbeh.2010.08.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 08/26/2010] [Accepted: 08/26/2010] [Indexed: 12/27/2022]
Abstract
Epigenetic chromatin remodeling, including reversible histone methylation, regulates gene transcription in brain development and synaptic plasticity. Aberrant chromatin modifications due to mutant chromatin enzymes or chemical exposures have been associated with neurological or psychiatric disorders such as mental retardation, schizophrenia, depression, and drug addiction. Some chromatin enzymes, such as histone demethylases JARID1C and UTX, are coded by X-linked genes which are not X-inactivated in females. The higher expression of JARID1C and UTX in females could contribute to sex differences in brain development and behavior.
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Affiliation(s)
- Jun Xu
- Tufts University, Department of Biomedical Sciences, North Grafton, MA 01536, USA.
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78
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Mulugeta Achame E, Baarends WM, Gribnau J, Grootegoed JA. Evaluating the relationship between spermatogenic silencing of the X chromosome and evolution of the Y chromosome in chimpanzee and human. PLoS One 2010; 5:e15598. [PMID: 21179482 PMCID: PMC3001880 DOI: 10.1371/journal.pone.0015598] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 11/12/2010] [Indexed: 02/06/2023] Open
Abstract
Chimpanzees and humans are genetically very similar, with the striking exception of their Y chromosomes, which have diverged tremendously. The male-specific region (MSY), representing the greater part of the Y chromosome, is inherited from father to son in a clonal fashion, with natural selection acting on the MSY as a unit. Positive selection might involve the performance of the MSY in spermatogenesis. Chimpanzees have a highly polygamous mating behavior, so that sperm competition is thought to provide a strong selective force acting on the Y chromosome in the chimpanzee lineage. In consequence of evolution of the heterologous sex chromosomes in mammals, meiotic sex chromosome inactivation (MSCI) results in a transcriptionally silenced XY body in male meiotic prophase, and subsequently also in postmeiotic repression of the sex chromosomes in haploid spermatids. This has evolved to a situation where MSCI has become a prerequisite for spermatogenesis. Here, by analysis of microarray testicular expression data representing a small number of male chimpanzees and men, we obtained information indicating that meiotic and postmeiotic X chromosome silencing might be more effective in chimpanzee than in human spermatogenesis. From this, we suggest that the remarkable reorganization of the chimpanzee Y chromosome, compared to the human Y chromosome, might have an impact on its meiotic interactions with the X chromosome and thereby on X chromosome silencing in spermatogenesis. Further studies will be required to address comparative functional aspects of MSCI in chimpanzee, human, and other placental mammals.
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Affiliation(s)
- Eskeatnaf Mulugeta Achame
- Department of Reproduction and Development, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Willy M. Baarends
- Department of Reproduction and Development, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Joost Gribnau
- Department of Reproduction and Development, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - J. Anton Grootegoed
- Department of Reproduction and Development, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
- * E-mail:
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Liu J, Ji H, Zheng W, Wu X, Zhu JJ, Arnold AP, Sandberg K. Sex differences in renal angiotensin converting enzyme 2 (ACE2) activity are 17β-oestradiol-dependent and sex chromosome-independent. Biol Sex Differ 2010; 1:6. [PMID: 21208466 PMCID: PMC3010099 DOI: 10.1186/2042-6410-1-6] [Citation(s) in RCA: 188] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 11/05/2010] [Indexed: 12/15/2022] Open
Abstract
Background Angotensin converting enzyme 2 (ACE2) is a newly discovered monocarboxypeptidase that counteracts the vasoconstrictor effects of angiotensin II (Ang II) by converting Ang II to Ang-(1-7) in the kidney and other tissues. Methods ACE2 activity from renal homogenates was investigated by using the fluorogenic peptide substrate Mca-YVADAPK(Dnp)-OH, where Mca is (7-methoxycoumarin-4-yl)-acetyl and Dnp is 2,4-dinitrophenyl. Results We found that ACE2 activity expressed in relative fluorescence units (RFU) in the MF1 mouse is higher in the male (M) compared to the female (F) kidney [ACE2 (RFU/min/μg protein): M 18.1 ± 1.0 versus F 11.1 ± 0.39; P < 0.0001; n = 6]. Substrate concentration curves revealed that the higher ACE2 activity in the male was due to increased ACE2 enzyme velocity (Vmax) rather than increased substrate affinity (Km). We used the four core genotypes mouse model in which gonadal sex (ovaries versus testes) is separated from the sex chromosome complement enabling comparisons among XX and XY gonadal females and XX and XY gonadal males. Renal ACE2 activity was greater in the male than the female kidney, regardless of the sex chromosome complement [ACE2 (RFU/min/μg protein): intact-XX-F, 7.59 ± 0.37; intact-XY-F, 7.43 ± 0.53; intact-XX-M, 12.1 ± 0.62; intact-XY-M, 12.7 ± 1.5; n = 4-6/group; P < 0.0001, F versus M, by two-way ANOVA]. Enzyme activity was increased in gonadectomized (GDX) female mice regardless of the sex chromosome complement whereas no effect of gonadectomy was observed in the males [ACE2 (RFU/min/μg protein): GDX-XX-F, 12.4 ± 1.2; GDX-XY-F, 11.1 ± 0.76; GDX-XX-M, 13.2 ± 0.97; GDX-XY-M, 11.6 ± 0.81; n = 6/group]. 17β-oestradiol (E2) treatment of GDX mice resulted in ACE2 activity that was only 40% of the activity found in the GDX mice, regardless of their being male or female, and was independent of the sex chromosome complement [ACE2 (RFU/min/μg protein): GDX+E2-XX-F, 5.56 ± 1.0; GDX+E2-XY-F, 4.60 ± 0.52; GDX+E2-XX-M, 5.35 ± 0.70; GDX+E2-XY-M, 5.12 ± 0.47; n = 6/group]. Conclusions Our findings suggest sex differences in renal ACE2 activity in intact mice are due, at least in part, to the presence of E2 in the ovarian hormone milieu and not to the testicular milieu or to differences in sex chromosome dosage (2X versus 1X; 0Y versus 1Y). E2 regulation of renal ACE2 has particular implications for women across their life span since this hormone changes radically during puberty, pregnancy and menopause.
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Affiliation(s)
- Jun Liu
- Center for the Study of Sex Differences in Health, Aging and Disease, Georgetown University, Washington DC 20057, USA.
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80
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HDHD1, which is often deleted in X-linked ichthyosis, encodes a pseudouridine-5'-phosphatase. Biochem J 2010; 431:237-44. [PMID: 20722631 DOI: 10.1042/bj20100174] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Pseudouridine, the fifth-most abundant nucleoside in RNA, is not metabolized in mammals, but is excreted intact in urine. The purpose of the present work was to search for an enzyme that would dephosphorylate pseudouridine 5'-phosphate, a potential intermediate in RNA degradation. We show that human erythrocytes contain a pseudouridine-5'-phosphatase displaying a Km ≤ 1 μM for its substrate. The activity of the partially purified enzyme was dependent on Mg2+, and was inhibited by Ca2+ and vanadate, suggesting that it belonged to the 'haloacid dehalogenase' family of phosphatases. Its low molecular mass (26 kDa) suggested that this phosphatase could correspond to the protein encoded by the HDHD1 (haloacid dehalogenase-like hydrolase domain-containing 1) gene, present next to the STS (steroid sulfatase) gene on human chromosome Xp22. Purified human recombinant HDHD1 dephosphorylated pseudouridine 5'-phosphate with a kcat of 1.6 s-1, a Km of 0.3 μM and a catalytic efficiency at least 1000-fold higher than that on which it acted on other phosphate esters, including 5'-UMP. The molecular identity of pseudouridine-5'-phosphatase was confirmed by the finding that its activity was negligible (<10% of controls) in extracts of B-cell lymphoblasts or erythrocytes from X-linked ichthyosis patients harbouring a combined deletion of the STS gene (the X-linked ichthyosis gene) and the HDHD1 gene. Furthermore, pseudouridine-5'-phosphatase activity was 1.5-fold higher in erythrocytes from women compared with men, in agreement with the HDHD1 gene undergoing only partial inactivation in females. In conclusion, HDHD1 is a phosphatase specifically involved in dephosphorylation of a modified nucleotide present in RNA.
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81
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Dementyeva E, Zakian S. Dosage compensation of sex chromosome genes in eukaryotes. Acta Naturae 2010; 2:36-43. [PMID: 22649662 PMCID: PMC3347590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sex chromosome evolution is accompanied by significant divergence in morphology and gene content and results in most genes of one of the sex chromosomes being present in two dosages in one sex and in one dosage in the other. To eliminate the difference in the expression levels of these genes between sexes and to restore equal expression levels of the genes between sex chromosomes and autosomes, mechanisms of dosage compensation have appeared. Studies of three classical objects,Drosophila melanogaster,Caenorhabditis elegans, and mammals, have shown that dosage compensation of X-linked genes can be achieved through completely different chromosome-wide mechanisms. New data on sex chromosome gene expression demonstrating that many sex chromosome genes can be expressed at different levels in males and females were recently obtained from birds and butterflies. In this review, dosage compensation mechanisms inD. melanogaster,C. elegans, and mammals are considered and the data on sex chromosome gene expression in birds and butterflies, and their influence on our view of dosage compensation, are discussed.
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Affiliation(s)
- E.V. Dementyeva
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences
| | - S.M. Zakian
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences
- Research Center of Clinical and Experimental Medicine, Siberian Branch, Russian Academy of Medical Sciences
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82
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Mank JE. Sex chromosomes and the evolution of sexual dimorphism: lessons from the genome. Am Nat 2010; 173:141-50. [PMID: 20374139 DOI: 10.1086/595754] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Females and males of many animals exhibit a striking array of sexual dimorphisms, ranging from the primary differences of the gametes and gonads to the somatic differences often seen in behavior, morphology, and physiology. These differences raise many questions regarding how such divergent phenotypes can arise from a genome that is largely shared between the sexes. Recent progress in genomics has revealed some of the actual genetic mechanisms that create separate sex-specific phenotypes, and the evidence indicates that thousands of genes across all portions of the genome contribute to male and female forms through sex-biased gene expression. Related work has begun to define the strength and influence of sex-specific evolutionary forces that shape these phenotypic dimorphisms and how they in turn affect the genome. Additionally, theory has long suggested that the evolution of sexual dimorphism is facilitated by sex chromosomes, as these are the only portions of the genome that differ between males and females. Genomic analysis indicates that there is indeed a relationship between sexual dimorphism and the sex chromosomes. However, the connection is far more complicated than current theory allows, and this may ultimately require a reexamination of the assumptions so that predictions match the accumulating empirical data.
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Affiliation(s)
- Judith E Mank
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
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83
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Li J, Liu Y, Kim T, Min R, Zhang Z. Gene expression variability within and between human populations and implications toward disease susceptibility. PLoS Comput Biol 2010; 6. [PMID: 20865155 PMCID: PMC2928754 DOI: 10.1371/journal.pcbi.1000910] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Accepted: 07/28/2010] [Indexed: 01/15/2023] Open
Abstract
Variations in gene expression level might lead to phenotypic diversity across individuals or populations. Although many human genes are found to have differential mRNA levels between populations, the extent of gene expression that could vary within and between populations largely remains elusive. To investigate the dynamic range of gene expression, we analyzed the expression variability of ∼18, 000 human genes across individuals within HapMap populations. Although ∼20% of human genes show differentiated mRNA levels between populations, our results show that expression variability of most human genes in one population is not significantly deviant from another population, except for a small fraction that do show substantially higher expression variability in a particular population. By associating expression variability with sequence polymorphism, intriguingly, we found SNPs in the untranslated regions (5′ and 3′UTRs) of these variable genes show consistently elevated population heterozygosity. We performed differential expression analysis on a genome-wide scale, and found substantially reduced expression variability for a large number of genes, prohibiting them from being differentially expressed between populations. Functional analysis revealed that genes with the greatest within-population expression variability are significantly enriched for chemokine signaling in HIV-1 infection, and for HIV-interacting proteins that control viral entry, replication, and propagation. This observation combined with the finding that known human HIV host factors show substantially elevated expression variability, collectively suggest that gene expression variability might explain differential HIV susceptibility across individuals. Many human genes have population-specific expression levels, which are linked to population-specific polymorphisms and copy-number variations. However, it is unclear whether human genes show similar dynamic range of expression between populations. In this work we analyzed HapMap gene expression compendium, and quantified the between-population and within-population expression variability for ∼18,000 human transcripts. We first concluded that the majority of the human genes have similar levels of within-population variability. However, a small fraction (∼4%) does show much higher expression variability in one population, and the deviation is consistently associated with increased SNP heterozygosity in their UTR regulatory regions. We further showed that genes with the greatest within-population expression variability are significantly enriched for chemokine signaling associated with HIV-1 infection. Combined with the finding that human HIV-1 host factors tend to have increased expression variability within populations, our analysis may explain, at least in part, different susceptibility to HIV infection within the human population. This work provides a fresh angle for analyzing gene expression variations in populations.
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Affiliation(s)
- Jingjing Li
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Yu Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - TaeHyung Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
| | - Renqiang Min
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
- * E-mail:
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84
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The X chromosome in immune functions: when a chromosome makes the difference. Nat Rev Immunol 2010; 10:594-604. [DOI: 10.1038/nri2815] [Citation(s) in RCA: 440] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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85
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Liu M, Shi S, Senthilnathan S, Yu J, Wu E, Bergmann C, Zerres K, Bogdanova N, Coto E, Deltas C, Pierides A, Demetriou K, Devuyst O, Gitomer B, Laakso M, Lumiaho A, Lamnissou K, Magistroni R, Parfrey P, Breuning M, Peters DJM, Torra R, Winearls CG, Torres VE, Harris PC, Paterson AD, Pei Y. Genetic variation of DKK3 may modify renal disease severity in ADPKD. J Am Soc Nephrol 2010; 21:1510-20. [PMID: 20616171 DOI: 10.1681/asn.2010030237] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Significant variation in the course of autosomal dominant polycystic kidney disease ( ADPKD) within families suggests the presence of effect modifiers. Recent studies of the variation within families harboring PKD1 mutations indicate that genetic background may account for 32 to 42% of the variance in estimated GFR (eGFR) before ESRD and 43 to 78% of the variance in age at ESRD onset, but the genetic modifiers are unknown. Here, we conducted a high-throughput single-nucleotide polymorphism (SNP) genotyping association study of 173 biological candidate genes in 794 white patients from 227 families with PKD1. We analyzed two primary outcomes: (1) eGFR and (2) time to ESRD (renal survival). For both outcomes, we used multidimensional scaling to correct for population structure and generalized estimating equations to account for the relatedness among individuals within the same family. We found suggestive associations between each of 12 SNPs and at least one of the renal outcomes. We genotyped these SNPs in a second set of 472 white patients from 229 families with PKD1 and performed a joint analysis on both cohorts. Three SNPs continued to show suggestive/significant association with eGFR at the Dickkopf 3 (DKK3) gene locus; no SNPs significantly associated with renal survival. DKK3 antagonizes Wnt/beta-catenin signaling, which may modulate renal cyst growth. Pending replication, our study suggests that genetic variation of DKK3 may modify severity of ADPKD resulting from PKD1 mutations.
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Affiliation(s)
- Michelle Liu
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
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86
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Abstract
A subset of X-linked genes escapes silencing by X inactivation and is expressed from both X chromosomes in mammalian females. Species-specific differences in the identity of these genes have recently been discovered, suggesting a role in the evolution of sex differences. Chromatin analyses have aimed to discover how genes remain expressed within a repressive environment.
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Affiliation(s)
- Joel B Berletch
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
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87
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Park C, Carrel L, Makova KD. Strong purifying selection at genes escaping X chromosome inactivation. Mol Biol Evol 2010; 27:2446-50. [PMID: 20534706 DOI: 10.1093/molbev/msq143] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
To achieve dosage balance of X-linked genes between mammalian males and females, one female X chromosome becomes inactivated. However, approximately 15% of genes on this inactivated chromosome escape X chromosome inactivation (XCI). Here, using a chromosome-wide analysis of primate X-linked orthologs, we test a hypothesis that such genes evolve under a unique selective pressure. We find that escape genes are subject to stronger purifying selection than inactivated genes and that positive selection does not significantly affect the evolution of these genes. The strength of selection does not differ between escape genes with similar versus different expression levels in males versus females. Intriguingly, escape genes possessing Y homologs evolve under the strongest purifying selection. We also found evidence of stronger conservation in gene expression levels in escape than inactivated genes. We hypothesize that divergence in function and expression between X and Y gametologs is driving such strong purifying selection for escape genes.
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Affiliation(s)
- Chungoo Park
- Center for Medical Genomics, Pennsylvania State University, University Park, USA
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88
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Dementyeva EV, Shevchenko AI, Anopriyenko OV, Mazurok NA, Elisaphenko EA, Nesterova TB, Brockdorff N, Zakian SM. Difference between random and imprinted X inactivation in common voles. Chromosoma 2010; 119:541-52. [PMID: 20473512 DOI: 10.1007/s00412-010-0277-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 04/15/2010] [Accepted: 04/26/2010] [Indexed: 11/24/2022]
Abstract
During early development in female mammals, most genes on one of the two X-chromosomes undergo transcriptional silencing. In the extraembryonic lineages of some eutherian species, imprinted X-inactivation of the paternal X-chromosome occurs. In the cells of the embryo proper, the choice of the future inactive X-chromosome is random. We mapped several genes on the X-chromosomes of five common vole species and compared their expression and methylation patterns in somatic and extraembryonic tissues, where random and imprinted X-inactivation occurs, respectively. In extraembryonic tissues, more genes were expressed on the inactive X-chromosome than in somatic tissues. We also found that the methylation status of the X-linked genes was always in accordance with their expression pattern in somatic, but not in extraembryonic tissues. The data provide new evidence that imprinted X-inactivation is less complete and/or stable than the random form and DNA methylation contributes less to its maintenance.
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Affiliation(s)
- Elena V Dementyeva
- Russian Academy of Sciences, Siberian Department, Institute of Cytology and Genetics, ac. Lavrentyev Avenue 10, Novosibirsk, Russia
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89
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Yang F, Babak T, Shendure J, Disteche CM. Global survey of escape from X inactivation by RNA-sequencing in mouse. Genome Res 2010; 20:614-22. [PMID: 20363980 DOI: 10.1101/gr.103200.109] [Citation(s) in RCA: 278] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
X inactivation equalizes the dosage of gene expression between the sexes, but some genes escape silencing and are thus expressed from both alleles in females. To survey X inactivation and escape in mouse, we performed RNA sequencing in Mus musculus x Mus spretus cells with complete skewing of X inactivation, relying on expression of single nucleotide polymorphisms to discriminate allelic origin. Thirteen of 393 (3.3%) mouse genes had significant expression from the inactive X, including eight novel escape genes. We estimate that mice have significantly fewer escape genes compared with humans. Furthermore, escape genes did not cluster in mouse, unlike the large escape domains in human, suggesting that expression is controlled at the level of individual genes. Our findings are consistent with the striking differences in phenotypes between female mice and women with a single X chromosome--a near normal phenotype in mice versus Turner syndrome and multiple abnormalities in humans. We found that escape genes are marked by the absence of trimethylation at lysine 27 of histone H3, a chromatin modification associated with genes subject to X inactivation. Furthermore, this epigenetic mark is developmentally regulated for some mouse genes.
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Affiliation(s)
- Fan Yang
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
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90
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Zaitoun I, Downs KM, Rosa GJM, Khatib H. Upregulation of imprinted genes in mice: an insight into the intensity of gene expression and the evolution of genomic imprinting. Epigenetics 2010; 5:149-58. [PMID: 20168089 DOI: 10.4161/epi.5.2.11081] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Imprinted genes are expressed monoallelically because one of the two copies is silenced epigentically in a parent-of-origin pattern. This pattern of expression is controlled by differential marking of parental alleles by DNA methylation and chromatin modifications, including both suppressive and permissive histone acetylation and methylation. Suppressive histone modifications mark silenced alleles of imprinted genes, while permissive histone modifications mark the active alleles, suggesting the possibility that imprinted genes would show upregulation in gene expression. However, it is currently unknown whether imprinted genes show such upregulation. To address this question in mice, we estimated the intensity of expression of 59 genes relative to the rest of the genome by analyzing microarray data. Expression levels of 24 genes were validated using quantitative real-time PCR (qPCR). Expression of imprinted genes was found to be upreguled in various adult and embryonic mouse tissues. Consistent with their functions in growth and development, imprinted genes were found to be highly expressed in extraembryonic tissues and progressively upregulated during early embryonic development. In conclusion, upregulation of imprinted genes found in this study is similar to the dosage compensation (twofold upregulation) recently reported for X-linked genes. It has been proposed that the twofold upregulation of X-linked genes has been coupled with low transcriptional variation (noise) which could lead to deleterious effects on the organism. Results of this study suggest a general need for imprinted genes in the mouse to be upregulated to certain levels in order to avoid deleterious effects of variation in gene expression.
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Affiliation(s)
- Ismail Zaitoun
- Department of Dairy Science, University of Wisconsin, Madison, WI, USA
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91
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Ho KKK, Deakin JE, Wright ML, Graves JAM, Grützner F. Replication asynchrony and differential condensation of X chromosomes in female platypus (Ornithorhynchus anatinus). Reprod Fertil Dev 2010; 21:952-63. [PMID: 19874719 DOI: 10.1071/rd09099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 09/15/2009] [Indexed: 11/23/2022] Open
Abstract
A common theme in the evolution of sex chromosomes is the massive loss of genes on the sex-specific chromosome (Y or W), leading to a gene imbalance between males (XY) and females (XX) in a male heterogametic species, or between ZZ and ZW in a female heterogametic species. Different mechanisms have evolved to compensate for this difference in dosage of X-borne genes between sexes. In therian mammals, one of the X chromosomes is inactivated, whereas bird dosage compensation is partial and gene-specific. In therian mammals, hallmarks of the inactive X are monoallelic gene expression, late DNA replication and chromatin condensation. Platypuses have five pairs of X chromosomes in females and five X and five Y chromosomes in males. Gene expression analysis suggests a more bird-like partial and gene-specific dosage compensation mechanism. We investigated replication timing and chromosome condensation of three of the five X chromosomes in female platypus. Our data suggest asynchronous replication of X-specific regions on X(1), X(3) and X(5) but show significantly different condensation between homologues for X(3) only, and not for X(1) or X(5). We discuss these results in relation to recent gene expression analysis of X-linked genes, which together give us insights into possible mechanisms of dosage compensation in platypus.
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Affiliation(s)
- Kristen K K Ho
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, Australia
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92
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X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils. Proc Natl Acad Sci U S A 2010; 107:3704-9. [PMID: 20133578 DOI: 10.1073/pnas.0914812107] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The DNA methylation status of human X chromosomes from male and female neutrophils was identified by high-throughput sequencing of HpaII and MspI digested fragments. In the intergenic and intragenic regions on the X chromosome, the sites outside CpG islands were heavily hypermethylated to the same degree in both genders. Nearly half of X chromosome promoters were either hypomethylated or hypermethylated in both females and males. Nearly one third of X chromosome promoters were a mixture of hypomethylated and heterogeneously methylated sites in females and were hypomethylated in males. Thus, a large fraction of genes that are silenced on the inactive X chromosome are hypomethylated in their promoter regions. These genes frequently belong to the evolutionarily younger strata of the X chromosome. The promoters that were hypomethylated at more than two sites contained most of the genes that escaped silencing on the inactive X chromosome. The overall levels of expression of X-linked genes were indistinguishable in females and males, regardless of the methylation state of the inactive X chromosome. Thus, in addition to DNA methylation, other factors are involved in the fine tuning of gene dosage compensation in neutrophils.
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93
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Lopes AM, Burgoyne PS, Ojarikre A, Bauer J, Sargent CA, Amorim A, Affara NA. Transcriptional changes in response to X chromosome dosage in the mouse: implications for X inactivation and the molecular basis of Turner Syndrome. BMC Genomics 2010; 11:82. [PMID: 20122165 PMCID: PMC2837040 DOI: 10.1186/1471-2164-11-82] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 02/01/2010] [Indexed: 11/12/2022] Open
Abstract
Background X monosomic mice (39,XO) have a remarkably mild phenotype when compared to women with Turner syndrome (45,XO). The generally accepted hypothesis to explain this discrepancy is that the number of genes on the mouse X chromosome which escape X inactivation, and thus are expressed at higher levels in females, is very small. However this hypothesis has never been tested and only a small number of genes have been assayed for their X-inactivation status in the mouse. We performed a global expression analysis in four somatic tissues (brain, liver, kidney and muscle) of adult 40,XX and 39,XO mice using the Illumina Mouse WG-6 v1_1 Expression BeadChip and an extensive validation by quantitative real time PCR, in order to identify which genes are expressed from both X chromosomes. Results We identified several genes on the X chromosome which are overexpressed in XX females, including those previously reported as escaping X inactivation, as well as new candidates. However, the results obtained by microarray and qPCR were not fully concordant, illustrating the difficulty in ascertaining modest fold changes, such as those expected for genes escaping X inactivation. Remarkably, considerable variation was observed between tissues, suggesting that inactivation patterns may be tissue-dependent. Our analysis also exposed several autosomal genes involved in mitochondrial metabolism and in protein translation which are differentially expressed between XX and XO mice, revealing secondary transcriptional changes to the alteration in X chromosome dosage. Conclusions Our results support the prediction that the mouse inactive X chromosome is largely silent, while providing a list of the genes potentially escaping X inactivation in rodents. Although the lower expression of X-linked genes in XO mice may not be relevant in the particular tissues/systems which are affected in human X chromosome monosomy, genes deregulated in XO mice are good candidates for further study in an involvement in Turner Syndrome phenotype.
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Affiliation(s)
- Alexandra M Lopes
- IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-465 Porto, Portugal.
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94
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Lelièvre JM, Le Bourhis D, Breton A, Hayes H, Servely JL, Vignon X. Heat-induced and spontaneous expression of Hsp70.1Luciferase transgene copies localized on Xp22 in female bovine cells. BMC Res Notes 2010; 3:17. [PMID: 20180997 PMCID: PMC2832894 DOI: 10.1186/1756-0500-3-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 01/22/2010] [Indexed: 12/03/2022] Open
Abstract
Background Expression of several copies of the heat-inducible Hsp70.1Luciferase (LUC) transgene inserted at a single X chromosome locus of a bull (Bos taurus) was assessed in females after X-chromosome inactivation (XCI). Furthermore, impact of the chromosomal environment on the spontaneous expression of these transgene copies before XCI was studied during early development in embryos obtained after in vitro fertilization (IVF), when the locus was carried by the X chromosome inherited from the bull, and after somatic cell nuclear transfer (SCNT) cloning, when the locus could be carried by the inactive Xi or the active Xa chromosome in a female donor cell, or by the (active) X in a male donor cell. Findings Transgene copies were mapped to bovine Xp22. In XXLUC female fibroblasts, i.e. after random XCI, the proportions of late-replicating inactive and early-replicating active XLUC chromosomes were not biased and the proportion of cells displaying an increase in the level of immunostained luciferase protein after heat-shock induction was similar to that in male fibroblasts. Spontaneous transgene expression occurred at the 8-16-cell stage both in transgenic (female) embryos obtained after IVF and in male and female embryos obtained after SCNT. Conclusions The XLUC chromosome is normally inactivated but at least part of the inactivated X-linked Hsp70.1Luciferase transgene copies remains heat-inducible after random XCI in somatic cells. Before XCI, the profile of the transgenes' spontaneous expression is independent of the epigenetic origin of the XLUC chromosome since it is similar in IVF female, SCNT male and SCNT female embryos.
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Affiliation(s)
- Jean-Marc Lelièvre
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy en Josas, France.
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95
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Jazin E, Cahill L. Sex differences in molecular neuroscience: from fruit flies to humans. Nat Rev Neurosci 2010; 11:9-17. [DOI: 10.1038/nrn2754] [Citation(s) in RCA: 182] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Deng X, Nguyen DK, Hansen RS, Van Dyke DL, Gartler SM, Disteche CM. Dosage regulation of the active X chromosome in human triploid cells. PLoS Genet 2009; 5:e1000751. [PMID: 19997486 PMCID: PMC2777382 DOI: 10.1371/journal.pgen.1000751] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 11/04/2009] [Indexed: 11/22/2022] Open
Abstract
In mammals, dosage compensation is achieved by doubling expression of X-linked genes in both sexes, together with X inactivation in females. Up-regulation of the active X chromosome may be controlled by DNA sequence–based and/or epigenetic mechanisms that double the X output potentially in response to autosomal factor(s). To determine whether X expression is adjusted depending on ploidy, we used expression arrays to compare X-linked and autosomal gene expression in human triploid cells. While the average X:autosome expression ratio was about 1 in normal diploid cells, this ratio was lower (0.81–0.84) in triploid cells with one active X and higher (1.32–1.4) in triploid cells with two active X's. Thus, overall X-linked gene expression in triploid cells does not strictly respond to an autosomal factor, nor is it adjusted to achieve a perfect balance. The unbalanced X:autosome expression ratios that we observed could contribute to the abnormal phenotypes associated with triploidy. Absolute autosomal expression levels per gene copy were similar in triploid versus diploid cells, indicating no apparent global effect on autosomal expression. In triploid cells with two active X's our data support a basic doubling of X-linked gene expression. However, in triploid cells with a single active X, X-linked gene expression is adjusted upward presumably by an epigenetic mechanism that senses the ratio between the number of active X chromosomes and autosomal sets. Such a mechanism may act on a subset of genes whose expression dosage in relation to autosomal expression may be critical. Indeed, we found that there was a range of individual X-linked gene expression in relation to ploidy and that a small subset (∼7%) of genes had expression levels apparently proportional to the number of autosomal sets. Many organisms have a single X chromosome in males and two in females, leading to a chromosome imbalance between autosomes and sex chromosomes and between the sexes. In mammals, this dosage imbalance is adjusted by doubling expression of X-linked genes in both sexes and by silencing one X chromosome in females. We used expression array analyses of human triploid cultures to test X chromosome expression in the presence of three sets of autosomes and address the question of an autosomal counting factor. We found that overall X-linked gene expression is not tripled in the presence of three sets of autosomes. However, in triploid cells with a single active X chromosome, its expression is adjusted upward presumably by an epigenetic mechanism that senses the active X/autosome ratio. Based on the range of individual gene expression we identified a subset of dosage-sensitive genes whose expression is apparently proportional to the ploidy. Our findings are important for understanding the regulation of the X chromosome and the role of ploidy in the balance of gene expression and associated phenotypes.
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Affiliation(s)
- Xinxian Deng
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Di Kim Nguyen
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - R. Scott Hansen
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Daniel L. Van Dyke
- Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Stanley M. Gartler
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Christine M. Disteche
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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97
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Abstract
Dosage compensation serves to equalize X chromosome gene expression in mammalian males and females and involves extensive silencing of the 2nd X chromosome in females. If dosage compensation mechanisms completely suppressed the 2nd X chromosome, then actual physical loss of this "eXtra" chromosome should have few consequences. However, X monosomy has major effects upon normal development, fertility and longevity in humans and some other species. This article reviews observations and arguments attempting to explain the phenotypic effects of X monosomy in humans and other mammals in terms of X chromosome gene dosage.
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Affiliation(s)
- Carolyn A Bondy
- Developmental Endocrinology Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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98
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Deakin JE, Chaumeil J, Hore TA, Marshall Graves JA. Unravelling the evolutionary origins of X chromosome inactivation in mammals: insights from marsupials and monotremes. Chromosome Res 2009; 17:671-85. [DOI: 10.1007/s10577-009-9058-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Entezam A, Usdin K. ATM and ATR protect the genome against two different types of tandem repeat instability in Fragile X premutation mice. Nucleic Acids Res 2009; 37:6371-7. [PMID: 19710035 PMCID: PMC2770655 DOI: 10.1093/nar/gkp666] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Expansion of a tandem repeat tract is responsible for the Repeat Expansion diseases, a group of more than 20 human genetic disorders that includes those like Fragile X (FX) syndrome that result from repeat expansion in the FMR1 gene. We have previously shown that the ATM and Rad3-related (ATR) checkpoint kinase protects the genome against one type of repeat expansion in a FX premutation mouse model. By crossing the FX premutation mice to Ataxia Telangiectasia-Mutated (Atm) mutant mice, we show here that ATM also prevents repeat expansion. However, our data suggest that the ATM-sensitive mechanism is different from the ATR-sensitive one. Specifically, the effect of the ATM deficiency is more marked when the premutation allele is paternally transmitted and expansions occur more frequently in male offspring regardless of the Atm genotype of the offspring. The gender effect is most consistent with a repair event occurring in the early embryo that is more efficient in females, perhaps as a result of the action of an X-linked DNA repair gene. Our data thus support the hypothesis that two different mechanisms of FX repeat expansion exist, an ATR-sensitive mechanism seen on maternal transmission and an ATM-sensitive mechanism that shows a male expansion bias.
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Affiliation(s)
- Ali Entezam
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
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100
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Chow J, Heard E. X inactivation and the complexities of silencing a sex chromosome. Curr Opin Cell Biol 2009; 21:359-66. [PMID: 19477626 DOI: 10.1016/j.ceb.2009.04.012] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 04/17/2009] [Accepted: 04/17/2009] [Indexed: 10/20/2022]
Abstract
X chromosome inactivation represents a paradigm for monoallelic gene expression and epigenetic regulation in mammals. Since its discovery over half a century ago, the pathways involved in the establishment of X-chromosomal silencing, assembly, and maintenance of the heterochromatic state have been the subjects of intensive research. In placental mammals, it is becoming clear that X inactivation involves an interplay between noncoding transcripts such as Xist, chromatin modifiers, and factors involved in nuclear organization. Together these result in a changed chromatin structure and in the spatial reorganization of the X chromosome. Exciting new work is starting to uncover the factors involved in some of these changes. Recent studies have also revealed surprising diversity in the kinetics and extent of gene silencing across the X chromosome, as well as in the mechanisms of XCI between mammals.
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Affiliation(s)
- Jennifer Chow
- Mammalian Developmental Epigenetics Group, Institut Curie, CNRS UMR3215, INSERM 934, 26 rue d'Ulm, Paris 75005, France.
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