X Chromosome Inactivation - Essay Example

X Chromosome Inactivation In nature, equilibrium is desired in terms of gene expression in both males (XY) and females (XX). In females one of the two X chromosomes gets inactivated by silencing its genes in early stages of embryogenesis. This process of dosage compensation is evolved in nature as a means of attaining equal gene expression in males and females; thereby upregulation of gene expression on X chromosome occurs. However, X chromosome inactivation (XCI) ranges from strict paternally inherited X inactivation (PXI) to unbiased random X inactivation (RXI) in order to equalize expression of both paternally and maternally inherited X chromosome. Genetic analysis of X inactivation highlights the stipulation of linkage, dominance, sex-differential selection recombination persuading evolutionary course. Recent studies postulate cis and trans acting aspects that control commencement of XCI through X inactivation centre. In mammals, the process is triggered by non-coding XIST RNA, silencing one X chromosome in female mammals. However, 25 to 30 percent of X-linked genes and micro RNA escape the process of inactivation. Further, choice of which X to inactivate is random, which is subsequently inherited. Thus, females exhibit a mixed population of cells displaying X(Xp) or paternally derived X chromosome silent and X(Xm) the maternally derived active X chromosome or vice versa. Introduction Nature has bestowed humans with 23 pairs of chromosomes encompassing 22 autosomes and 1 pair of sex chromosome. Sex chromosome is imperative in sex determination. Females have two X chromosomes (XX) while males have one X and other Y chromosome in the pair. These chromosomes are the determiners of sex of an individual. Although females have two X chromosomes while males possess only one X chromosome, under normal conditions. In the process of X chromosome inactivation (XCI), one of the female’s X chromosomes becomes shut off in early embryonic development, resulting in random or permanent inactivation in cells other than egg cells. The process is random and all the derived daughter cells inherit the same inactive X chromosome. This is a natural process so as to maintain one working X chromosome in both male and female. The phenomenon is coined as X inactivation or Lyonization, ensuring that females also have one functional X chromosome in every cell of the body (Minks & Brown, 2009). As genes synthesise protein molecules, if both the X chromosomes express themselves, then females are going to have double the number of proteins as compared to males. However, most of the genes located on X chromosome do not play any role in determination of sex or with reproduction. Therefore, X chromosome inactivation (XCI) does not upset the metabolic equilibrium in females; moreover, the phenomenon enables males and females to have equivalence in X-linked gene expression. The phenomenon was coined as dosage compensation by Muller in 1931 (Gartler & Goldman, 2001). Dosage Compensation of X- linked genes In Animal Development Animal development is usually sensitive to an imbalance in the number of genes. Under normal conditions, each gene is present in two copies. Departures from this condition either up or down resulting in abnormal phenotypes, sometimes even death of the organism. It is therefore puzzling that so many species should have a sex determination system based on females with two X chromosomes and males with only one. In these species including mammals, the phenomenon of numerical difference of X-linked genes is related to two mechanisms to compensate for this difference. Research reveals that during the process of evolution two phenomena are utilized (Gartler & Goldman, 2001): a. Each X linked gene works hard in males as it does in females. For instance, hyperactivation of X-linked genes is observed in male Drosophila while in Caenorhabditis elegans, dosage compensation involves the partial repression of X-linked genes. Dosage compensation in C. elegans therefore seems to involve a mechanism exactly opposite to Drosophila. In C. elegans a protein molecule represses the X chromosome expression while in Drosophila transcription is enhanced (Gartler & Goldman, 2001). b. One copy of each X-linked gene is inactivated in females- In placental mammals; dosage compensation of X-linked genes is achieved by the inactivation of one of the female’s X chromosomes. The phenomenon was first proposed in 1961 by British geneticist Mary Lyon, who inferred it from the studies in mice. Research by Lyon revealed that the inactivation event occurs when the mouse embryo consists of a few thousand cells. At this time, each cell makes an independent decision to silence one of its X chromosomes (Gartler & Goldman, 2001). The chromosome to be inactivated is randomly chosen, however, it remains inactive in all the descendants of that cell. Thus, female mammals are genetic mosaics containing two types of cell clones the maternally inherited X chromosome inactivated in roughly half of the clone cells and paternally inherited X which is inactivated in other half. Female heterozygous for an X-linked gene is therefore able to show two different phenotypes. For instance, light and dark coat colour variation in mammals such as cats (Gartler & Goldman, 2001; Engelsta¨dter & Haig, 2008). X Chromosome Inactivation in Mammals Organisms with a XX/XY or XX/XO sex determination system face the problem of equalizing the activity of X-linked genes in the two sexes. In mammals, this predicament is solved by randomly inactivating one of the two X chromosomes in females; each female therefore has the same number of transcriptionally active X-linked genes as a male. Three different mechanisms of X chromosome inactivation or dosage compensation has been observed in the course of evolution namely, inactivation of X chromosome as in mammals, hyperactivation as in Drosophila and hypoactivation as observed in C. elegans. However, these diverse dosage compensation processes have an important feature in common- many different genes are co-ordinately regulated because they are on the same chromosome. This chromosome-wide regulation is superimposed on all other regulatory mechanisms involved in the spatial and temporal expression of these genes. Therefore various research studies have been carried out to understand the global regulatory system of gene expression. However, the working hypothesis elucidates some factor or factors play key role in dosage compensation process, they bind to the X chromosome and alter its transcriptional activities; the hypothesis was further demonstrated to be true as the research proceeded (Gartler & Goldman, 2001). X Chromosome Inactivation In Somatic Cells The embryonic development studies carried out in mouse revealed that the two X chromosomes in female mouse are remains active in early embryonic development of the female embryo, they are not distinguished either functionally or cytologically. However, the earlier evidence of X chromosome inactivation is reported to occur during early blastocyst stage or late morula stages. Observation discloses asynchrony of DNA (deoxyribonucleic acid) replication between the two X chromosomes, sex chromatin formation and differential gene expression. XCI is first seen in the extraembryonic lineage that is responsible for the formation of membranes surrounding the developing embryo. In these cells, nevertheless, preferentially, paternal X gets inactivated (Gartler & Goldman, 2001). As soon as the development proceeds to the gastrulation stage, random, X chromosome inactivation takes place in the epiblast, these cells are responsible for the formation of embryo. Due to random inactivation, maternal or paternal X chromosome is randomly selected for inactivation. Soon after the process of inactivation, all the descending cells will have the same X quiet which are responsible for the mosaic pattern of inactive paternal X chromosome and maternal inactive X chromosome (Gartler & Goldman, 2001). X Chromosome Inactivation in Germline Somatic cells display highly stable X chromosome inactivation; germ cells display cyclic inactivation of X chromosome. In females, one X chromosome is inactive during the mitotic phase whereas, both the X chromosomes are found to be active in oogenesis. This is essential for the process of pairing and recombination during meiosis which is not possible if one of the X chromosomes remain heterochromatic or condensed. Moreover, in males, inactivation of X chromosome does not take place in somatic cells but it does occur in spermatogenesis, where single X chromosome condenses and becomes inactive in order to prevent pairing as well as recombination between chromosomes X and Y which are nonhomologus (Gartler & Goldman, 2001). Random and Nonrandom X Chromosome Inactivation In somatic cells XCI is random process where paternal and maternal X chromosomes gets inactivated with equal probability. As a result of this random inactivation, females display heterozygous traits for haemophilia. However, conditions are reported where one of the two Xs gets inactivated with greater propensity as compared to the other, resulting in either little or no production of clotting factor in female heterozygous for haemophilia (Gartler & Goldman, 2001). Stability of X Chromosome Inactivation Research studies highlight that the X chromosome maintains its inactive condition. Numerous factors contribute to repress alleles on inactivated X chromosome, these factors are found to be functional throughout life, and if these repressing factors are active reactivation of inactivated X chromosome does not occur. In case of germline, the process of inactivation of X chromosome is cyclic and no DNA methylation (repressive factor in somatic cells) takes place. Gartler & Goldman, (2001), thought that DNA methylation maintains the inactive state, therefore, genes exhibiting age-related reactivation process do not undergo DNA methylation, on the contrary, genes undergoing the process of DNA methylation are not reactivated (Gartler & Goldman, 2001). Studies carried out with transformed cell lines revealed that reactivation may occur in cells where mechanisms required for inactive state are not functional and DNA methylation is solely responsible for repression. Studies with embryonal carcinoma (EC) cells reveal that specific factors present in EC are responsible for permitting and maintaining the active condition of both Xs (Gartler & Goldman, 2001). Xist RNA gets transcribed from both the alleles in as undistinguished female ES. Visualization by FISH reveals that in differentiated ES cells as well as in somatic cells, the transcript appears a large domain which is found to be associated with the Barr body at the periphery of the nucleus. The process of developmental upregulation of Xist expression from Xi is responsible for enhanced RNA stability instead of increase in the transcription rate. Later it was revealed that stable and unstable transcripts are actually different isoforms of Xist RNA, because of the switching between diverse promoters of Xist gene produces different transcripts involved in upregulation (Duthie, 2001; Augui et al., 2011). Some Genes Escape Inactivation Process Initially it was believed that all the genes in inactivated X chromosome are transcriptionally quiet. However, later research studies showed a group of genes present in pseudoautosomal region (PAR) of short arm (tip) homologous with the Y chromosomes escapes the process of X inactivation. Genes present in the PAR region exist in X as well as in Y chromosome therefore dosage compensation is not required. However, smaller PAR is also present on the long arm of X chromosome. This region carries several genes and only one is found to be inactivated while other genes outside PAR have Y linked alleles and therefore, no dosage compensation is required. On the other hand, there are X-linked genes that do not have any Y-linked counterparts but still they escape the process of inactivation. However, such genes are present in clusters, together they escape the process of deactivation. Research reveals that the X chromosome of mouse seems to be more completely inactivated as compared to human X chromosome, indicating the episode of a longer evolutionary time in mouse for X inactivation. Meiotic sex chromosome inactivation (MSCI) during the process of spermatogenesis is regarded as transcriptional silencing of genes in both X as well as Y chromosome in the pachytene stage as both these chromosomes remain unpaired during the prophase stage of Meiosis I (Song et al., 2009). About 15 percent of the X-linked genes escape the process of inactivation while another 10 percent gets inactivated in some females only which could have an explanation through the evolutionary trajectories of sex chromosome. During the course of evolution, all genes present in mammalian X which do not have functional homologue on Y chromosome gets inactivated (Engelsta¨dter & Haig, 2008) Evolutionary trajectories of X chromosome Inactivation X inactivation in mammals follows numerous specific forms, varying from severe paternally inherited X inactivation (PXI), to diverse forms of unbiased random X inactivation (RXI). This diverse range is outstanding, as quantitative analyses of paternally and maternally derived X inactivation ratio are obtainable for reasonably few mammalian species. With the advances in modern technologies involving genome and allele-specific gene expression technologies encompassing RNA-seq, a higher level of analysis related to XCI ratios could be investigated in other mammalian species, thereby it could serve as a boon to explore persisting diversity in X inactivation patterns (Connallon & Clark, 2013). A variety of X inactivation rules engaged by different species might be useful in theoretical scaffold of sex-differential selection. The population genetic models display wider prospects for X inactivation evolution, there must be some genetic variation for X inactivation rules. For instance, there must be some alleles in mice responsible for X chromosome inactivation, in a similar manner X inactivation observed in marsupials, humans and mice imply that some degree of inactivation persist for maternally derived X is generally hostile. The evolution of the X inactivation ratio is emerging as an imperative issue for future studies. Techniques like Multiple genes, genomic imprinting and conflicting patterns of selection as well as evolution of diploidy enable one to understand different X inactivation paradigms. However, exclusive patterns of genetic variation among X-linked loci could independently favour jarring X inactivation approach (Engelsta¨dter & Haig, 2008). Evolutionary transitions between RXI and PXI Once RXI has evolved, evolutionary reversals to strict PXI might witness severe evolutionary constraints. Population with RXI, serves as a filter of genetic variation by selection in females is directly co-related with the dominance. The withholding of recessive alleles in populations with RXI downwardly modify the mean dominance of segregating alleles thereby enhancing cost of females becoming efficiently homozygous or haploid (Connallon & Clark, 2013). Species diversity for X inactivation strategies Every organism has some specific characteristic. Species-specific features of genetic variation and mutation might unavoidably influence patterns of selection for diverse X chromosome inactivation strategies (Connallon & Clark, 2013). Mechanism of X Chromosome Inactivation As there is 50 percent probability of both X chromosomes that either one of them may become inactive, the choice is subjective to the locus known as X controlling element (Xce). In mammals, X chromosome inactivation begins at a particular site called the X inactivation centre (XIC) and then spreads in opposite directions toward the ends of the chromosome. As a result not all genes on an inactivated X chromosome are transcriptionally silent. One that remains active are called Xist (X inactive specific transcript), this gene is located within XIC. Research studies show that in human beings, the Xist gene encodes a 17-kb transcript devoid of any significant open reading frames. It therefore seems unlikely that the Xist gene codes for a protein. Instead, the RNA itself is probably the functional product of the Xist gene. This RNA is restricted to the nucleus and has been specifically localized to inactivated X chromosomes; it does not appear to be associated with active X chromosomes in either males or females. These observations suggest that X chromosome inactivation in mammals is caused by the transcription of Xist gene. Perhaps these transcripts remain associated with the inactive X chromosome, repressing the transcription of other genes. In this view, the X chromosome that is not inactivated is the one that represses the transcription of the Xist gene. Any X chromosome that does not repress Xist would make Xist RNA and inactivate itself. Experiments carried out with differentiated XX ES cells, with the chromosome bearing the mutant Xist allele, always got inactivated. The region 3’of Xist plays an important role in the process of inactivation. The knockout potentially removes the Xce locus, generating a null mutant. This mutant is capable of inactivating the X carrying the null Xce allele. In majority of the cells, the choice of X inactivation is random process which depends on the Xce allele each X possesses. In certain cases, cells undergo the process of non-random inactivation due to parental imprint. The process of imprinting utilizes the logic that chromosome memorizes its parental origin (Duthie, 2001; Connallon & Clark, 2013; Gartler & Goldman, 2001). Inactive X chromosomes are readily identified in mammalian cells. During interphase, they condense into a darkly staining mass associated with the nuclear membrane. This mass called the Barr body is, an example of facultative heterochromatin i.e. heterochromatin that appears and disappears during the cell cycle. In contrast, constitutive heterochromatin, such as that found around the centromeres of chromosomes is present throughout the cell cycle. During S-phase, the Barr body decondenses to allow the inactive X chromosome to be replicated; however, because this process takes some time, the inactive X replicates later than the rest of the chromosomes. Inactive X chromosomes must therefore have a very different chromatin structure than that of other chromosomes. Recent evidence suggests that this difference is partly determined by the kind of histones associated with the DNA (Duthie, 2001; Gartler & Goldman, 2001). One of the four chore histones, H4, can be chemically modified by the addition of acetyl groups to any of several lysines in the polypeptide chain. Acetylated H4 is associated with all the chromosomes in the human genome. However, on the inactive X it seems to be restricted to three fairly narrow bands, each corresponding to a region that contains some active genes. Acetylated H4 is also depleted in areas of constitutive heterochromatin on the other chromosomes. These findings suggested that acetylated H4 is involved in the maintenance of transcriptional activity. Repressive modifications associated with X chromosome inactivation (XCI), in human and mouse was correlated with the elephant, a far off related placental mammal. However, modifications (H4K20me1), or cell cycle (H3K27me3, H3K9me2) play key role (Chaumeil et al., 2011). According to Chaumeil et al., (2011), XCI is analogous to a arrangement that evolved in the common therian. Silent chromatin of early inactive X was exapted from adjoining constitutive heterochromatin. Later in early placental evolution, was improved by the augment of XIST and the steady enrolment of definite histone amendments now characteristically related with XCI (Chaumeil et al., 2011). Conclusion An X chromosome that has been inactivated does not look or acts like other chromosomes. Chemical analysis show that its DNA is modified by addition of methyl groups and it condenses into darkly stained structures called a Barr body. The inactivated X chromosome remains in the altered state in all the somatic tissues, while in germ tissues it is reactivated, perhaps because two copies of same X-linked genes are needed for the successful completion of oogenesis. Genetic analysis have shown that in humans the X chromosome inactivation begin at a site in the long arm of the X chromosome, and that it spreads in both directions to the chromosome’s ends. The initiating site is called the X-inactivation centre (XIC). Certainly, this site is very close to a gene called XIST (X inactive specific transcript), which is not silenced by the inactivation process. Research studies suggest that the product of the XIST locus may play a key role in the mechanism of dosage compensation. References Augui, S., Noara, E. P., Heard, E. (2011). Regulation of X-chromosome inactivation by the X-inactivation centre. Nature Reviews Genetics, 12, 429-442. Chaumeil, J., Waters, P. D., Koina, E., Gilbert, C., Robinson, T. J., Graves, J. A. M. (2011). Evolution from XIST- Independent to XIST- Controlled X Chromosome Inactivation: Epigenetic Modifications in Distantly Related Mammals. PLoS ONE, 6(4), 1-11. Connallon, T & Clark, A. G. (2013). Sex-Differential Selection and the Evolution f X Inactivation Strategies. PLOS Genetics, 9(4), 1-12. Duthie, S. M. (2001). Mechanism of X-inactivation. Encyclopedia of Life Science, 1-7. Engelsta¨dter, J., & Haig, D. (2008). Sexual Antagonism and The Evolution of X Chromosome Inactivation. Evolution, 62(8), 2097-2104. Gartler, S. M. & Goldman, M. A. (2001). X-chromosome Inactivation. Encyclopedia of Life Science, 1-6 Minks, J., Brown, C. J. (2009). Getting to the centre of X chromosome inactivation: the role of transgenes. Biochem. Cell Biol, 87, 759-766. Song, R., Ro, S., Michaels, J. D., Park, C., McCarrey, J. R., Yan, W. (2009). Many X-linked microRNAs escape meiotic sex chromosome inactivation. Nature Genetics, 41(4), 488-493. Read More