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Origin and Evolution of X Chromosome Inactivation

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Origin and Evolution of X Chromosome Inactivation Available online at www.sciencedirect.com Origin and evolution of X chromosome inactivation Joost Gribnau and J Anton Grootegoed Evolution of the mammalian sex chromosomes heavily impacts chromosome pair (Figure 1a) [3]. It is thought that the on the expression of X-encoded genes, both in marsupials and region around Sry gained male beneficial genes and other placental mammals. The loss of genes from the Y chromosome modifications such as inversions, step by step limiting the forced a two-fold upregulation of dose sensitive X-linked options for meiotic recombination between the evolving homologues. As a corollary, female cells would experience a heterologous sex chromosomes. As a result, the male lethal dose of X-linked genes, if this upregulation was not specific region of Y (MSY), clonally inherited from father counteracted by evolution of X chromosome inactivation (XCI) to son, never meets a meiotic pairing partner. The X that allows for only one active X chromosome per diploid chromosome, however, spends two-third of its time in genome. Marsupials rely on imprinted XCI, which inactivates XX females, where it pairs and recombines in meiotic always the paternally inherited X chromosome. In placental prophase of oogenesis. Further to the advantage of the mammals, random XCI (rXCI) is the predominant form, X chromosome, X-linked genes are hemizygous in males, inactivating either the maternal or paternal X. In this review, we leading to rapid fixation of mutations associated with discuss recent new insights in the regulation of XCI. Based on positive natural and sexual selection. In anthropomorphic these findings, we propose an X inactivation center (Xic), terms, an arms race is going on between X and Y, resulting composed of a cis-Xic and trans-Xic that encompass all in regression of the Y and enrichment of the gene content of elements and factors acting to control rXCI either in cis or in the X. Many of the events shaping the heterologous sex trans. We also highlight that XCI may have evolved from a very chromosomes have occurred within a relatively short time small nucleation site on the X chromosome in the vicinity of the span after formation of the proto-X and proto-Y, before Sox3 gene. Finally, we discuss the possible evolutionary road radiation of the placental mammals [4–6]. Originating from maps that resulted in imprinted XCI and rXCI as observed in the spectacular evolutionary history of these particular present day mammals. chromosomes and its consequences, the X and Y chromo- somes of present-day placental mammals undergo marked Address dynamic changes of their activities in development and Department of Reproduction and Development, Erasmus MC, University gametogenesis. These activity changes have a biological Medical Center, Rotterdam, The Netherlands function to support growth and fertility of both females and males. In the present review, we aim to outline the overall Corresponding author: Gribnau, Joost ([email protected]) scheme of events and mechanisms, although we focus on X chromosome inactivation (XCI) in female somatic cells. Current Opinion in Cell Biology 2012, 24:397–404 Sex chromosomes and the need for gene This review comes from a themed issue on Nucleus and gene expression dosage compensation Edited by Asifa Akhtar and Karla Neugebauer The human X chromosome carries more than 1000 genes [7]. By contrast, only around 100 single-copy and multi- Available online 14th March 2012 copy genes are found on the human Y chromosome, 0955-0674/$ – see front matter where the MSY carries 78 genes encoding 27 different # 2012 Elsevier Ltd. All rights reserved. proteins [8]. Hence, in diploid male somatic cells, there is an X:autosome gene dosage imbalance for most genes on DOI 10.1016/j.ceb.2012.02.004 the X. Problems resulting from this imbalance can be prevented by a two-fold transcriptional upregulation of the X chromosome. Indeed, this has been observed for Introduction mouse and human, by comparing micro-array expression Meiotic recombination keeps the autosomes organized data sets [9–11]. Another study, using an RNA-sequen- in homologous pairs, stabilizing the diploid genome of cing approach, challenged these findings [12], but the mammalian species. For one pair of autosomes, this controversy is now explained [13 ,14 ]. When genes with advantage of the diploid state was partly lost, when this low transcriptional activity are excluded from the analysis, pair of autosomes started to become the present mamma- it is observed that the moderately to highly expressed X- lian X and Y chromosomes around 160 million years ago, chromosomal genes are two-fold upregulated [13 ,14 ]. shortly before separation of the metatherians (marsupials) In addition to excluding biological noise from leaky gene and eutherians (placental mammals) [1,2]. The initial expression, genes expressed at stochastically fluctuating event probably has been a mutational change of one allele low levels may not require dosage compensation. How- of the Sox3 gene, resulting in the male sex-determining ever, genes expressed at higher levels will include dose gene Sry (sex-determining region Y) on the proto-Y of this sensitive genes. From this, we suggest that evolutionary www.sciencedirect.com Current Opinion in Cell Biology 2012, 24:397–404 398 Nucleus and gene expression Figure 1 genes in female mammals is prevented by a second compensatory mechanism, called XCI, which leads to (a) degeneration of the Y inactivation of one of the two X chromosomes, resetting the global X:autosome gene expression ratio at 1:1 in recombination female cells (Figure 1c). Looking at the end result, XCI block can be viewed as a mechanism which equalizes X-chro- Sox3 Sox3 Sox3 Sry male mosomal gene dosage between males and females. beneficial genes X chromosome inactivation: cis and trans proto mechanisms autosomes X Y X Y X Y In the female mouse embryo, an imprinted form of XCI 160 million years ago now (iXCI) is initiated very early during pre-implantation development, around the 4–8 cell stage, always targeting (b) two-fold up-regulation in male the X inherited from the father [16,17]. Following iXCI, 2x 2x this paternal X (Xp) remains inactive in the extra-embryo- 2x nic tissues, but is reactivated in the developing inner cell mass that gives rise to the embryo proper [18]. This proto reactivation asks for rapid intervention, which comes from autosomes X Y X Y X Y a strong wave of random XCI (rXCI), targeting either the maternal X (Xm) or Xp, just after implantation. The (c) X inactivation in female fascinating history of the discovery of rXCI, spearheaded by Susumu Ohno and Mary Lyon around half a century Xist Xist RNA ago, is highlighted in several recent reviews [19–21]. 2x 2x Regarding the mechanism of rXCI, genetic studies per- formed in the 1980s, involving X-to-autosomal transloca- proto tions and X truncations, indicated a region of 3 autosomes X X X X Xa Xi megabases on the X, called the X inactivation center Current Opinion in Cell Biology (Xic), instrumental in the initiation of rXCI [22]. Sub- sequent studies focusing on this region revealed a non- Evolution of mammalian sex chromosomes. (a) Degeneration of the Y coding gene, Xist in mouse and XIST in human, as the key chromosome was triggered by changes on the Y, including the origin of player in the XCI process [23–25]. Xist transcription is Sry and the inclusion of male beneficial genes in a non-recombining upregulated on the future inactive X, and the spliced and region. (b) The loss of Y-encoded genes was compensated by a two- fold upregulation of expression of dose sensitive homologous X- poly-adenylated non-coding RNA molecules spread in cis, encoded genes. (c) A two-fold upregulation of X-encoded genes would thereby recruiting chromatin remodelling complexes that be lethal to female cells, and this has driven the evolution of XCI that render the X an inactive chromatin domain (reviewed in silences one X chromosome in every female cell. [26]). From what is known for mouse, Xist activation is counteracted by the non-coding Tsix gene, which fully overlaps with Xist but is transcribed anti-sense to Xist [27]. selection has employed mechanisms to keep the X:auto- To repress Xist transcription, transcription of Tsix needs to some gene expression level at a ratio near 1:1, concomi- proceed through sequences overlapping with the Xist tant with the evolution of the X and Y chromosomes, promoter [28]. This points to a transcriptional interfer- leading to a global two-fold transcriptional upregulation ence mechanism, but the repression may also involve of the X chromosome (Figure 1b). If the mechanism RNA-mediated recruitment of de novo methyltransferase leading to this two-fold upregulation has become an DNMT3A [29,30]. With this basic machinery in place, inherent and sex independent property of the X chromo- the hunt was on to find elements, genes and factors able to some, female cells encounter a 2:1 X:autosome gene exert control over Xist and Tsix, in cis or in trans. expression ratio. In some species, this is tolerated, as for instance in the red flour beetle, Tribolium castaneum, Genuine promoter and enhancer sequences control Xist where increased expression of both X chromosomes is and Tsix transcription, but flanking non-coding genes also observed in XX female cells [15]. In mammals, the play an important role in activation of both genes. developing oocyte contains two active X chromosomes, Located upstream of Tsix, the genes Xite and Tsx posi- and a certain level of tolerance might also be found at tively regulate Tsix expression (Figure 2) [31,32]. some later steps of development and in specific tissues Chromosome conformation capture (3C) studies and cell types.
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