101
|
Tuttelmann F, Gromoll J. Novel genetic aspects of Klinefelter's syndrome. Mol Hum Reprod 2010; 16:386-95. [DOI: 10.1093/molehr/gaq019] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
|
102
|
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.
Collapse
Affiliation(s)
- Kristen K K Ho
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, Australia
| | | | | | | | | |
Collapse
|
103
|
Barakat TS, Jonkers I, Monkhorst K, Gribnau J. X-changing information on X inactivation. Exp Cell Res 2010; 316:679-87. [PMID: 20083102 DOI: 10.1016/j.yexcr.2010.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 01/04/2010] [Accepted: 01/10/2010] [Indexed: 10/20/2022]
Abstract
In female somatic cells of mammalian species one X chromosome is inactivated to ensure dosage equality of X-encoded genes between females and males, during development and adulthood. X chromosome inactivation (XCI) involves various epigenetic mechanisms, including RNA mediated gene silencing in cis, DNA methylation, and changes in chromatin modifications and composition. XCI therefore provides an attractive paradigm to study epigenetic gene regulation in a more general context. The XCI process starts with counting of the number of X chromosomes present in a nucleus, and initiation of XCI follows if this number exceeds one per diploid genome. Recently, X-encoded RNF12 has been identified as a dose-dependent activator of XCI. In addition, other factors, including the pluripotency factors OCT4, SOX2 and Nanog, have been implicated to play a role in suppression of initiation of XCI. In this review, we highlight and explain these new and old findings in the context of a stochastic model for X chromosome counting and XCI initiation.
Collapse
Affiliation(s)
- Tahsin Stefan Barakat
- Department of Reproduction and Development, Room Ee 09-71, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | | | | | | |
Collapse
|
104
|
Leeb M, Wutz A. Mechanistic concepts in X inactivation underlying dosage compensation in mammals. Heredity (Edinb) 2010; 105:64-70. [DOI: 10.1038/hdy.2009.181] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
|
105
|
Barakat TS, Gribnau J. X chromosome inactivation and embryonic stem cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 695:132-54. [PMID: 21222204 DOI: 10.1007/978-1-4419-7037-4_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
X chromosome inactivation (XCI) is a process required to equalize the dosage of X-encoded genes between female and male cells. XCI is initiated very early during female embryonic development or upon differentiation of female embryonic stem (ES) cells and results in inactivation of one X chromosome in every female somatic cell. The regulation of XCI involves factors that also play a crucial role in ES cell maintenance and differentiation and the XCI process therefore provides a beautiful paradigm to study ES cell biology. In this chapter we describe the important cis and trans acting regulators of XCI and introduce the models that have been postulated to explain initiation of XCI in female cells only. We also discuss the proteins involved in the establishment of the inactive X chromosome and describe the different chromatin modifications associated with the inactivation process. Finally, we describe the potential of mouse and human ES and induced pluripotent stem (iPS) cells as model systems to study the XCI process.
Collapse
Affiliation(s)
- Tahsin Stefan Barakat
- Department of Reproduction and Development, University Medical Center, Room Ee 09-71, Erasmus MC, 3015 GE, Rotterdam, Netherlands
| | | |
Collapse
|
106
|
Abstract
How do mammals count their X chromosomes and keep only one X active per cell? In this issue, Jonkers et al. (2009) show that Rnf12/RLIM, encoded by the X-linked gene Rnf12, induces X chromosome inactivation only when present above a certain threshold, a condition fulfilled when at least two Xs are active.
Collapse
Affiliation(s)
- Elphège P Nora
- Institut Curie, CNRS UMR3215, INSERM U934, 75724 Paris Cedex 05, France
| | | |
Collapse
|
107
|
Jonkers I, Barakat TS, Achame EM, Monkhorst K, Kenter A, Rentmeester E, Grosveld F, Grootegoed JA, Gribnau J. RNF12 is an X-Encoded dose-dependent activator of X chromosome inactivation. Cell 2009; 139:999-1011. [PMID: 19945382 DOI: 10.1016/j.cell.2009.10.034] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 09/03/2009] [Accepted: 10/23/2009] [Indexed: 11/17/2022]
Abstract
In somatic cells of female placental mammals, one X chromosome is inactivated to minimize sex-related dosage differences of X-encoded genes. Random X chromosome inactivation (XCI) in the embryo is a stochastic process, in which each X has an independent probability to initiate XCI, triggered by the nuclear concentration of one or more X-encoded XCI-activators. Here, we identify the E3 ubiquitin ligase RNF12 as an important XCI-activator. Additional copies of mouse Rnf12 or human RNF12 result in initiation of XCI in male mouse ES cells and on both X chromosomes in a substantial percentage of female mouse ES cells. This activity is dependent on an intact open reading frame of Rnf12 and correlates with the transgenic expression level of RNF12. Initiation of XCI is markedly reduced in differentiating female heterozygous Rnf12(+/-) ES cells. These findings provide evidence for a dose-dependent role of RNF12 in the XCI counting and initiation process.
Collapse
Affiliation(s)
- Iris Jonkers
- Department of Reproduction and Development, Erasmus MC, University Medical Center, 3000 CA Rotterdam, The Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|
108
|
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.
Collapse
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:
| |
Collapse
|
109
|
|
110
|
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]
|
111
|
Abstract
Transcriptome studies are revealing that the eukaryotic genome actively transcribes a diverse repertoire of large noncoding RNAs (ncRNAs), many of which are unannotated and distinct from the small RNAs that have garnered much attention in recent years. Why are they so pervasive, and do they have a function? X-chromosome inactivation (XCI) is a classic epigenetic phenomenon associated with many large ncRNAs. Here, I provide a perspective on how XCI is achieved in mice and suggest how this knowledge can be applied to the rest of the genome. Emerging data indicate that long ncRNAs can function as guides and tethers, and may be the molecules of choice for epigenetic regulation: First, unlike proteins and small RNAs, large ncRNAs remain tethered to the site of transcription, and can therefore uniquely direct allelic regulation. Second, ncRNAs command a much larger sequence space than proteins, and can therefore achieve very precise spatiotemporal control of development. These properties imply that long noncoding transcripts may ultimately rival small RNAs and proteins in their versatility as epigenetic regulators, particularly for locus- and allele-specific control.
Collapse
Affiliation(s)
- Jeannie T Lee
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA.
| |
Collapse
|
112
|
Wutz A. Oct4 to count 2. Cell Res 2009; 19:917-9. [PMID: 19648946 DOI: 10.1038/cr.2009.92] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Anton Wutz
- Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria.
| |
Collapse
|
113
|
Donohoe ME, Silva SS, Pinter SF, Xu N, Lee JT. The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting. Nature 2009; 460:128-32. [PMID: 19536159 PMCID: PMC3057664 DOI: 10.1038/nature08098] [Citation(s) in RCA: 228] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 04/28/2009] [Indexed: 11/09/2022]
Abstract
Pluripotency of embryonic stem (ES) cells is controlled by defined transcription factors1,2. During differentiation, mouse ES cells undergo global epigenetic reprogramming, as exemplified by X-chromosome inactivation (XCI) whereby one female X-chromosome is silenced to achieve gene dosage parity between the sexes3-5. Somatic XCI is regulated by homologous X-chromosome pairing6,7, counting8-10, and random choice of future active X (Xa) and inactive X’s. XCI and cell differentiation are tightly coupled11, as blocking one process compromises the other8,12 and dedifferentiation of somatic cells to induced pluripotent stem (iPS) cells is accompanied by X-reactivation2. Recent evidence suggests coupling of Xist expression to pluripotency factors13, but how the two are interconnected remains unknown. Here, we show that the Oct414 lies at the top of the XCI hierarchy and regulates XCI by triggering X-chromosome pairing and counting. Oct4 directly binds Tsix and Xite, two regulatory ncRNA genes of the X-inactivation center15,16, and also complexes with XCI trans-factors, Ctcf and Yy117, through protein-protein interactions. Depletion of Oct4 blocks homologous X-chromosome pairing and results in inactivation of both Xs in female cells. Thus, we have identified the first trans-factor that regulates counting and ascribed novel functions to Oct4 during X-chromosome reprogramming.
Collapse
|
114
|
van den Berg IM, Laven JS, Stevens M, Jonkers I, Galjaard RJ, Gribnau J, Hikke van Doorninck J. X chromosome inactivation is initiated in human preimplantation embryos. Am J Hum Genet 2009; 84:771-9. [PMID: 19481196 DOI: 10.1016/j.ajhg.2009.05.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Revised: 04/27/2009] [Accepted: 05/04/2009] [Indexed: 10/20/2022] Open
Abstract
X chromosome inactivation (XCI) is the mammalian mechanism that compensates for the difference in gene dosage between XX females and XY males. Genetic and epigenetic regulatory mechanisms induce transcriptional silencing of one X chromosome in female cells. In mouse embryos, XCI is initiated at the preimplantation stage following early whole-genome activation. It is widely thought that human embryos do not employ XCI prior to implantation. Here, we show that female preimplantation embryos have a progressive accumulation of XIST RNA on one of the two X chromosomes, starting around the 8-cell stage. XIST RNA accumulates at the morula and blastocyst stages and is associated with transcriptional silencing of the XIST-coated chromosomal region. These findings indicate that XCI is initiated in female human preimplantation-stage embryos and suggest that preimplantation dosage compensation is evolutionarily conserved in placental mammals.
Collapse
|
115
|
Monkhorst K, de Hoon B, Jonkers I, Mulugeta Achame E, Monkhorst W, Hoogerbrugge J, Rentmeester E, Westerhoff HV, Grosveld F, Grootegoed JA, Gribnau J. The probability to initiate X chromosome inactivation is determined by the X to autosomal ratio and X chromosome specific allelic properties. PLoS One 2009; 4:e5616. [PMID: 19440388 PMCID: PMC2680018 DOI: 10.1371/journal.pone.0005616] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Accepted: 04/15/2009] [Indexed: 11/26/2022] Open
Abstract
Background In female mammalian cells, random X chromosome inactivation (XCI) equalizes the dosage of X-encoded gene products to that in male cells. XCI is a stochastic process, in which each X chromosome has a probability to be inactivated. To obtain more insight in the factors setting up this probability, we studied the role of the X to autosome (X∶A) ratio in initiation of XCI, and have used the experimental data in a computer simulation model to study the cellular population dynamics of XCI. Methodology/Principal Findings To obtain more insight in the role of the X∶A ratio in initiation of XCI, we generated triploid mouse ES cells by fusion of haploid round spermatids with diploid female and male ES cells. These fusion experiments resulted in only XXY triploid ES cells. XYY and XXX ES lines were absent, suggesting cell death related either to insufficient X-chromosomal gene dosage (XYY) or to inheritance of an epigenetically modified X chromosome (XXX). Analysis of active (Xa) and inactive (Xi) X chromosomes in the obtained triploid XXY lines indicated that the initiation frequency of XCI is low, resulting in a mixed population of XaXiY and XaXaY cells, in which the XaXiY cells have a small proliferative advantage. This result, and findings on XCI in diploid and tetraploid ES cell lines with different X∶A ratios, provides evidence that the X∶A ratio determines the probability for a given X chromosome to be inactivated. Furthermore, we found that the kinetics of the XCI process can be simulated using a probability for an X chromosome to be inactivated that is proportional to the X∶A ratio. These simulation studies re-emphasize our hypothesis that the probability is a function of the concentration of an X-encoded activator of XCI, and of X chromosome specific allelic properties determining the threshold for this activator. Conclusions The present findings reveal that the probability for an X chromosome to be inactivated is proportional to the X∶A ratio. This finding supports the presence of an X-encoded activator of the XCI process.
Collapse
Affiliation(s)
- Kim Monkhorst
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Bas de Hoon
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Iris Jonkers
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Eskeatnaf Mulugeta Achame
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | | | - Jos Hoogerbrugge
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Eveline Rentmeester
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Hans V. Westerhoff
- Department of Molecular Cell Physiology, Free University Amsterdam, Amsterdam, the Netherlands
- Manchester Centre for Integrative Systems Biology, Manchester, United Kingdom
| | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - J. Anton Grootegoed
- 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
- * E-mail:
| |
Collapse
|
116
|
Xist gene regulation at the onset of X inactivation. Curr Opin Genet Dev 2009; 19:122-6. [DOI: 10.1016/j.gde.2009.03.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 03/03/2009] [Accepted: 03/10/2009] [Indexed: 11/21/2022]
|
117
|
Abstract
DNA and histone methylation are linked and subjected to mitotic inheritance in mammals. Yet how methylation is propagated and maintained between successive cell divisions is not fully understood. A series of enzyme families that can add methylation marks to cytosine nucleobases, and lysine and arginine amino acid residues has been discovered. Apart from methyltransferases, there are also histone modification enzymes and accessory proteins, which can facilitate and/or target epigenetic marks. Several lysine and arginine demethylases have been discovered recently, and the presence of an active DNA demethylase is speculated in mammalian cells. A mammalian methyl DNA binding protein MBD2 and de novo DNA methyltransferase DNMT3A and DNMT3B are shown experimentally to possess DNA demethylase activity. Thus, complex mammalian epigenetic mechanisms appear to be dynamic yet reversible along with a well-choreographed set of events that take place during mammalian development.
Collapse
|
118
|
Abstract
The development of genetic sex determination and cytologically distinct sex chromosomes leads to the potential problem of gene dosage imbalances between autosomes and sex chromosomes and also between males and females. To circumvent these imbalances, mammals have developed an elaborate system of dosage compensation that includes both upregulation and repression of the X chromosome. Recent advances have provided insights into the evolutionary history of how both the imprinted and random forms of X chromosome inactivation have come about. Furthermore, our understanding of the epigenetic switch at the X-inactivation center and the molecular aspects of chromosome-wide silencing has greatly improved recently. Here, we review various facets of the ever-expanding field of mammalian dosage compensation and discuss its evolutionary, developmental, and mechanistic components.
Collapse
Affiliation(s)
- Bernhard Payer
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.
| | | |
Collapse
|
119
|
Prothero KE, Stahl JM, Carrel L. Dosage compensation and gene expression on the mammalian X chromosome: one plus one does not always equal two. Chromosome Res 2009; 17:637-48. [PMID: 19802704 PMCID: PMC4941101 DOI: 10.1007/s10577-009-9063-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Counting chromosomes is not just simple math. Although normal males and females differ in sex chromosome content (XY vs. XX), X chromosome imbalance is tolerated because dosage compensation mechanisms have evolved to ensure functional equivalence. In mammals this is accomplished by two processes--X chromosome inactivation that silences most genes on one X chromosome in females, leading to functional X monosomy for most genes in both sexes, and X chromosome upregulation that results in increased gene expression on the single active X in males and females, equalizing dosage relative to autosomes. This review focuses on genes on the X chromosome, and how gene content, organization and expression levels can be influenced by these two processes. Special attention is given to genes that are not X inactivated, and are not necessarily fully dosage compensated. These genes that "escape" X inactivation are of medical importance as they explain phenotypes in individuals with sex chromosome aneuploidies and may impact normal traits and disorders that differ between men and women. Moreover, escape genes give insight into how X chromosome inactivation is spread and maintained on the X.
Collapse
Affiliation(s)
- Katie E. Prothero
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Jill M. Stahl
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Laura Carrel
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| |
Collapse
|
120
|
Abstract
X chromosome inactivation (XCI) reduces the number of actively transcribed X chromosomes to one per diploid set of autosomes, allowing for dosage equality between the sexes. In eutherians, the inactive X chromosome in XX females is randomly selected. The mechanisms for determining both how many X chromosomes are present and which to inactivate are unknown. To understand these mechanisms, researchers have created X chromosome mutations and transgenes. Here, we introduce a new model of X chromosome inactivation that aims to account for the findings in recent studies, to promote a re-interpretation of existing data and to direct future experiments.
Collapse
Affiliation(s)
- Joshua Starmer
- Department of Genetics and the Carolina Center for the Genome Sciences, and University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | |
Collapse
|
121
|
Nesterova TB, Popova BC, Cobb BS, Norton S, Senner CE, Tang YA, Spruce T, Rodriguez TA, Sado T, Merkenschlager M, Brockdorff N. Dicer regulates Xist promoter methylation in ES cells indirectly through transcriptional control of Dnmt3a. Epigenetics Chromatin 2008; 1:2. [PMID: 19014663 PMCID: PMC2577046 DOI: 10.1186/1756-8935-1-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Accepted: 10/27/2008] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND X chromosome inactivation is the mechanism used in mammals to achieve dosage compensation of X-linked genes in XX females relative to XY males. Chromosome silencing is triggered in cis by expression of the non-coding RNA Xist. As such, correct regulation of the Xist gene promoter is required to establish appropriate X chromosome activity both in males and females. Studies to date have demonstrated co-transcription of an antisense RNA Tsix and low-level sense transcription prior to onset of X inactivation. The balance of sense and antisense RNA is important in determining the probability that a given Xist allele will be expressed, termed the X inactivation choice, when X inactivation commences. RESULTS Here we investigate further the mechanism of Xist promoter regulation. We demonstrate that both sense and antisense transcription modulate Xist promoter DNA methylation in undifferentiated embryonic stem (ES) cells, suggesting a possible mechanistic basis for influencing X chromosome choice. Given the involvement of sense and antisense RNAs in promoter methylation, we investigate a possible role for the RNA interference (RNAi) pathway. We show that the Xist promoter is hypomethylated in ES cells deficient for the essential RNAi enzyme Dicer, but that this effect is probably a secondary consequence of reduced levels of de novo DNA methyltransferases in these cells. Consistent with this we find that Dicer-deficient XY and XX embryos show appropriate Xist expression patterns, indicating that Xist gene regulation has not been perturbed. CONCLUSION We conclude that Xist promoter methylation prior to the onset of random X chromosome inactivation is influenced by relative levels of sense and antisense transcription but that this probably occurs independent of the RNAi pathway. We discuss the implications for this data in terms of understanding Xist gene regulation and X chromosome choice in random X chromosome inactivation.
Collapse
Affiliation(s)
- Tatyana B Nesterova
- Developmental Epigenetics Group, MRC Clinical Sciences Centre, Faculty of Medicine ICSTM, Hammersmith Hospital, Du Cane Road, London, UK.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
122
|
Jonkers I, Monkhorst K, Rentmeester E, Grootegoed JA, Grosveld F, Gribnau J. Xist RNA is confined to the nuclear territory of the silenced X chromosome throughout the cell cycle. Mol Cell Biol 2008; 28:5583-94. [PMID: 18625719 PMCID: PMC2546918 DOI: 10.1128/mcb.02269-07] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 02/04/2008] [Accepted: 07/04/2008] [Indexed: 11/20/2022] Open
Abstract
In mammalian female cells, one X chromosome is inactivated to prevent a dose difference in the expression of X-encoded proteins between males and females. Xist RNA, required for X chromosome inactivation, is transcribed from the future inactivated X chromosome (Xi), where it spreads in cis, to initiate silencing. We have analyzed Xist RNA transcription and localization throughout the cell cycle. It was found that Xist transcription is constant and that the mature RNA remains attached to the Xi throughout mitosis. Diploid and tetraploid cell lines with an MS2-tagged Xist gene were used to investigate spreading of Xist. Most XXXX(MS2) tetraploid mouse embryonic stem (ES) cells inactivate the X(MS2) chromosome and one other X chromosome. Analysis of cells with two Xi's indicates that Xist RNA is retained by the Xi of its origin and does not spread in trans. Also, in XX(MS2) diploid mouse ES cells with an autosomal Xist transgene, there is no trans exchange of Xist RNA from the Xi to the autosome. We propose that Xist RNA does not dissociate from the Xi of its origin, which precludes a model of diffusion-mediated trans spreading of Xist RNA.
Collapse
Affiliation(s)
- Iris Jonkers
- Department of Cell Biology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | | | | | | | | | | |
Collapse
|
123
|
Fenno LE, Ptaszek LM, Cowan CA. Human embryonic stem cells: emerging technologies and practical applications. Curr Opin Genet Dev 2008; 18:324-9. [DOI: 10.1016/j.gde.2008.06.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 06/11/2008] [Accepted: 06/14/2008] [Indexed: 10/21/2022]
|
124
|
|