If a gene is found only on the x chromosome and not the y chromosome, it is said to be what?

The X Chromosome

The X chromosome is a relatively large and gene-rich chromosome compared with the Y chromosome, and it consists of about 160 Mb of genomic deoxyribonucleic acid (DNA) (seeFig. 24.4).19,33,34 This DNA contains 5% of the haploid genome and approximately 850 protein-encoding genes. Several genes on the X chromosome play an important role in sex development in males and females, gametogenesis, and hypothalamic-pituitary (gonadotrope) function (e.g., androgen receptor[AR],ANOS1 [also calledKAL1], DAX1[NR0B1], MAMLD1,SOX3). However, most X-linked genes are unrelated to reproductive function and have a diverse range of cellular functions.

The X chromosome contains PARs at the distal end of each arm, similar to the Y chromosome (seeFig. 24.4).19 These regions and several genes in their boundaries function with their homologs on the Y-chromosome PARs in an autosomal fashion. However, as large numbers of genes on the X chromosome are located outside the PARs and do not have homologs on the Y chromosome, a process must exist to maintain the balance in copy number (i.e., gene dosage) of these genes between males with a single X chromosome and females with two X chromosomes. This process is calledX inactivation.

The first insight into X inactivation came after the identification in 1949 of the X chromatin body (i.e., Barr body) in a proportion of cells in females (seeFig. 24.3). This X chromatin is derived from one of the two X chromosomes in interphase nuclei of these somatic cells. Grumbach and colleagues showed that the X chromosome giving rise to X chromatin completes DNA synthesis later than any other chromosome.35 These findings led to the concept that only one X chromosome is genetically active during interphase, whereas the other X chromosome is heterochromatinized and relatively inactive. This change in activation state occurs in early gestation in humans (12–18 days, late blastocyte stage) and is a multistep process, regulated by the geneXIST and theTSIX antisense transcript, leading to stable and epigenetic silencing of genes on all but one X chromosome (Lyon hypothesis).36 However, female germ cells beyond the stage of oogonia are exempt from X inactivation, demonstrating a need for a second X chromosome for oocyte development.

X inactivation occurs randomly in different cells.37 After inactivation has occurred, the inactive state of that particular X chromosome is transmitted to all descendants of that cell so that XX individuals effectively function as genetic mosaics for X-linked traits. If the initial population of cells is small, skewed X inactivation can occur as a chance event despite random inactivation.In these situations, heterozygous female carriers of an X-linked disorder may manifest symptoms of the condition. A subset of genes on the X chromosome may also be imprinted and only expressed from one allele. Furthermore, recent data suggest that several other X-chromosome genes (especially on the short arm) may escape X inactivation, potentially in a tissue-specific manner, and that sex chromosome gene dosage may regulate autosomal gene networks.38,39 All these phenomena might influence phenotype variability of X-linked conditions or sex chromosome aneuploidy.

Abstract

The X chromosome is one of the two sex chromosomes in humans. It is highly conserved among other mammalian species. The X chromosome accounts for about 5% of the total human genome and contains upward of 1200 genes. Many X chromosome genes, about one-fifth, appear to play a role in human cognition and brain development. The X chromosome is also unusual in that in females, who have two of these chromosomes, one undergoes inactivation as a means of dosage compensation since males have only one X chromosome (their other sex chromosome being a Y chromosome).

The X Chromosome

Aneuploidy for the X chromosome is among the most common of cytogenetic abnormalities. The relative tolerance of human development for X chromosome abnormalities can be explained in terms ofX chromosome inactivation, the process by which most genes on one of the two X chromosomes in females are silenced epigenetically, introduced inChapter 3. X inactivation and its consequences in relation to the inheritance of X-linked disorders are discussed inChapter 7. Here we discuss the chromosomal and genomic mechanisms of X inactivation and their implications for human and medical genetics (see Box at the end of this section).

Human X-Linked Disease

The most common human syndromes associated with the X chromosome are anomalies in sex chromosome number that arise through nondisjunction at meiosis. Turner syndrome occurs in approximately 1 in 2000 female births and is caused by the loss of an entire chromosome leading to an XO karyotype. To explain why the presence of a single X chromosome is deleterious in XO females but not in XY males, it has been proposed that Turner syndrome is caused by a single, not double, dose of one or more of the few genes that normally escapes from X-inactivation. This is in tune with the observation that mice with an XO karyotype do not have an overt phenotype and that there are fewer mouse genes reported that escape X-inactivation. An additional X chromosome is present in the 1 in 600 males that are Klinefelter syndrome patients, who have an XXY karyotype. More rarely, females have also been identified with XXX and XXXX complements. Mutations, or rearrangements, in genes that are important in primary or secondary sex determination can give rise to females with an XY chromosome complement and males with an XX complement.

Mutations in single X-linked genes are fully expressed in males and give rise to ‘sex-linked’ disorders, for example, Duchenne muscular dystrophy which has an incidence of around 1 in 3000 males and the fragile X-linked mental retardation syndrome which has an incidence of around 1 in 10000 males. As a result of the random inactivation of one of their two X chromosomes in early development, all females are mosaics of two populations of cells and the relative numbers of cells in these two populations will differ between individuals. Often females heterozygous for a mutated gene are completely unaffected as the population of cells expressing the nonmutated allele either provides a sufficient quantity of normal gene product, or, during development or lineage differentiation, predominates over the population of cells carrying the mutant allele. However, some female carriers for X-linked ‘recessive’ diseases manifest some disease symptoms because of a natural skew in favor of cells with the mutated X as the active chromosome. Very occasionally, carrier females may manifest the same severity of disorder as that seen in males. Mutations in X-linked genes may also give rise to X-linked ‘dominant’ disorders found only in females and in these instances it is assumed that affected males die before birth. The most common example of an X-linked dominant is Rett syndrome, a severe progressive neurological disorder affecting approximately 1 in 20000 females, which has recently been associated with mutations in the gene encoding methyl-CpG-binding protein.

Monosomy of the X Chromosome (Turner Syndrome)

The phenotype associated with a single X chromosome (45,X) was described by Henry Turner in 1938. (An earlier description was given by Otto Ullrich in 1930.) Persons with Turner syndrome are female and usually have a characteristic phenotype, including the variable presence of proportionate short stature, sexual infantilism and ovarian dysgenesis, and a pattern of major and minor malformations. The physical features can include a triangle-shaped face; posteriorly rotated external ears; and a broad, “webbed neck” (Fig. 6.13). In addition, the chest is broad and shield-like in shape. Lymphedema of the hands and feet is observable at birth. Many infants with Turner syndrome have congenital heart defects, most commonly obstructive lesions of the left side of the heart (bicuspid aortic valve in 50% of patients and coarctation [narrowing] of the aorta in 15%–30%). Severe obstructions should be surgically repaired. About 50% of persons with Turner syndrome have structural kidney defects, but they usually do not cause medical problems. There is typically some diminution in spatial perceptual ability, but intelligence is usually normal.

Girls with Turner syndrome exhibit proportionate short stature and do not undergo an adolescent growth spurt. Mature height is reduced by approximately 20 cm, on average. Growth hormone administration produces increased height somewhat in these girls, and families now commonly choose this therapy. In most persons with Turner syndrome, streaks of connective tissue, rather than ovaries, are seen (gonadal dysgenesis). Ovarian dysgenesis occursbecause two active X chromosomes are required for normal ovarian development. Lacking normal ovaries, Turner females do not usually develop secondary sexual characteristics, and most women with this condition are infertile (about 5%–10% have sufficient ovarian development to undergo menarche, and a small number have borne children). Teenagers with Turner syndrome are typically treated with estrogen to promote the development of secondary sexual characteristics. The dose is then continued at a reduced level to maintain these characteristics and to help prevent osteoporosis.

The diagnosis of Turner syndrome is often made in the newborn infant, especially if there is a noticeable webbing of the neck coupled with a heart defect. The facial features are more subtle than in the autosomal abnormalities described previously, but the experienced clinician can often diagnose Turner syndrome on the basis of one or more of the listed clues. If Turner syndrome is not recognized in infancy or childhood, it is often diagnosed later because of short stature, pubertal failure, and/or amenorrhea.

The chromosome abnormalities in persons with Turner syndrome are quite variable. About 50% of these patients have a 45,X karyotype in their peripheral lymphocytes. At least 30% to 40% have mosaicism, mostcommonly 45,X/46,XX and less commonly 45,X/46,XY. Patients with mosaicism who have Y chromosomes in some cells are predisposed to neoplasms (gonadoblastomas) in the gonadal streak tissue. About 10% to 20% of patients with Turner syndrome have structural X chromosome abnormalities involving a deletion of some or all of Xp. This variation in chromosome abnormality helps to explain the considerable phenotypic variation seen in this syndrome.

3. Sex-linked Inheritance

The X and Y chromosomes determine sex. In addition, the human X chromosome contains hundreds of other genes. Because females have two copies of the X chromosome, whereas males have only one (they are hemizygous), diseases caused by genes on the X chromosome, most of which are X-linked recessive, predominantly affect males.

Examples of X-linked recessive diseases include adrenoleukodystrophy, Fragile X syndrome, Duchenne muscular dystrophy, and red-green color blindness.

The pedigree in these disorders is characterized by affected males related through carrier females, and absence of father-to-son transmission. If females are affected, their symptoms are usually milder, and they are termed manifesting heterozygotes. This situation typically arises from skewed X-inactivation with preferential inactivation of the normal X chromosome in their cells. In the normal situation, X chromosome inactivation is random, with inactivation of a woman's paternal X chromosome in some cells, and inactivation of her maternal X chromosome in others. In other, rare cases, women with only a single copy of the X chromosome (45, X) or with structural abnormalities of the X chromosome may manifest an X-linked recessive condition.

3.2 X-chromosome Inactivation

X-chromosome dosage is compensated between both sexes in mammals via inactivation of one of the two parental X chromosomes while maintaining active expression of a subset of genes on both chromosomes. Genes that escape X inactivation are generally those associated with Y-chromosome homologs. The process of XCI has been most thoroughly studied in mice (Disteche & Berletch, 2015; Kamikawa & Donohoe, 2014). In mice, the paternal X chromosome is imprinted to be silenced during early embryo development via a mechanism whereby imprinted expression is established by expression of the noncoding RNA, Xist, that represses transcription from the paternal X chromosome (Okamoto et al., 2011). Subsequently the paternal X chromosome reactivated in the inner cell mass of the blastocyst and random XCI selection ensues as differentiated cell lineages form. In contrast, in other species including the rabbit and human, Xist is not imprinted and XCI begins later in development than occurs in mice and Xist is expressed from either the maternal or the paternal X chromosome in some cases resulting in transient inactivation of both X chromosomes (Okamoto et al., 2011). Subsequently in the rabbit as development ensues, the choice of which X chromosome will become inactive occurs downstream of Xist expression; furthering defining species-specific differences is the skewing of X inactivation in some tissues and the identity of the individual genes on both X chromosomes that escape XCI (Deng, Berletch, Nguyen, & Disteche, 2014).

Applications of ChrX Testing

X-chromosome STR typing can be helpful in some kinship analysis situations particularly with deficient paternity cases where a DNA sample from one of the parents is not available for testing. For example, if a father/daughter parentage relationship is in question, X-STRs may be helpful due to the 100% transmission of the father’s X-chromosome to his daughter (Table 15.1). On the other hand, in a father/son parentage question, Y-chromosome results would be helpful (see Chapter 13). Table 15.2 lists several applications for X-chromosome DNA testing. ChrX testing can be especially helpful in some missing persons or disaster victim identification situations (see Chapter 9) where direct reference samples are not available and biological relatives must be sought to aid human identification.

Table 15.2. Applications of X-Chromosome Analysis.

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Complex kinship cases involving at least one female

Disputed paternity to a daughter (especially in motherless cases)

Half-sister testing where the father is the common relative

Grandparent—grandchild comparisons

Paternity testing in incest cases (see Figure 15.2)

(See Figure 15.1 for Illustration of Example Pedigrees)

X-chromosome markers can help infer parent-offspring relationships that involve at least one female, such as mother-daughter, mother-son, and father-daughter duos (illustrated in Figure 15.1). In complicated kinship scenarios, such as incest (Figure 15.2), ChrX markers may aid sorting out difficult relationship questions.

X Chromosome

The X chromosome is a fairly large chromosome (Figures 5.1 and 5.3) and contains over 1000 genes (out of the 20,000–23,000 human genes). Most of these are essential genes unrelated to sex determination. Some are metabolic enzymes essential for life (so-called “housekeeping genes”). Because females have two X chromosomes and males have only one, it might be assumed that female cells make twice the quantity of proteins encoded in the X chromosome compared with males. This is not the case; in fact, males and females have similar expression of genes on the X chromosome. This is because, early in embryonic development, a female shuts down one X chromosome in each of her cells. In 1949, Murray Barr discovered that female cells, but not male cells, contain a small dot of condensed material that represents one of the X chromosomes that has been inactivated (X-chromosome inactivation). This inclusion is called the Barr body or sex chromatin (Figure 5.2). In 1961, Mary Lyon proposed that one X chromosome is inactivated randomly in female embryonic cells so that a double gene dosage is avoided. All cells that follow a particular cell line have the same X chromosome inactivated. This means that, in some regions of a woman’s body, the X chromosome she inherited from her mother is active whereas only the one inherited from her father is active in other regions (i.e. women are mosaics with respect to X chromosome expression). If more than two X chromosomes are present, as in some conditions produced by errors of fertilization (discussed later in this chapter), all of the X chromosomes are inactivated except one (Figure 5.2).

The presence of the Barr body is used to determine the sex of fetuses during procedures such as amniocentesis and chorionic villus sampling (see Chapter 10). Also, cells from the lining of the mouth membrane can be checked for the presence of a Barr body (the buccal smear test). Fluorescent dyes can be used to identify X and Y chromosomes.

The X-Chromosome

Origin and Evolution

The X-chromosome is one of the sex chromosomes in humans. With around 155 million base pairs and 1100 genes, it represents about 5% of the total human genome that comprises 20 000–25 000 genes.

The two sex chromosomes have originated from an ancestral autosomal pair (Figure 1). Around 300 Mya, this pair of autosomes started to accumulate differences and suffered structural and functional changes throughout the evolution, originating two different chromosomes – X and Y.

Figure 1. Evolution of the sex chromosomes.

Even though they have a common origin, the X- and the Y-chromosomes followed different evolutionary paths: the Y-chromosome has lost most of its genomic material and does not suffer recombination in 95% of its extension, while the X-chromosome still retains traces of its autosomal past, suffering recombination along its entire length during female gametogenesis. Homology between the two chromosomes is still present in the telomeric pseudoautosomal regions (PAR 1 and PAR 2; Figure 1).

Characteristics

The particular characteristics of the X-chromosome make it an interesting subject for genetic studies. Many genetic conditions have already been described as being related to mutations in specific genes on the X-chromosome. Hemophilia is a classic example of an X-chromosome-associated disease, among others.

In the last decade, the interest in the study of the X-chromosome markers as tools for forensic and population genetic studies has been growing, as they can help to detect underlying patterns of genetic differentiation that are not usually captured by the traditionally analyzed autosomal markers.

Humans have one pair of the sex chromosomes, but the number of X-chromosomes present in each cell varies between males and females. Females have two copies, while males have one X-chromosome and one Y-chromosome. Therefore men inherit their X-chromosome from their mothers, whereas women inherit one X-chromosome from each parent (Figure 2). The paternal X-chromosome they receive does not suffer recombination (except in the PARs) and is transmitted directly to the daughters. The maternal X-chromosome contains combined information from the two X-chromosomes present in the mother.

Figure 2. Genetic transmission of X- and Y-chromosomes.

Given the difference in copy number in males and females, the study of the X-chromosome in men allows direct access to their haplotypes. As recombination only occurs in females, in each generation, only two-thirds of X-chromosomes recombine. The X-chromosome is thus disproportionately influenced by female demography, making the study of the X-chromosome particularly useful for detecting subtle differences between the two genders.

In a population with equal number of female and male individuals, there will only be three X-chromosomes for every four autosomes present. Furthermore, for each three X-chromosomes in a population, one will be paternally and two maternally inherited. This will lead to clear differences not only in the recombination but also in the mutation rates between the two, as in the X-chromosome the rates will be lower due to the higher mutation rate in male gametogenesis.

Owing to these characteristics, and also due to its younger age, the diversity on the X-chromosome is expected to be lower than on the autosomes. As a consequence, and looking at it from a population genetic point of view, the effects of selection, genetic drift or substructure in a given population are more pronounced. The same is observed in the linkage disequilibrium (LD) patterns. LD can be defined as the nonrandom association of alleles at two or more loci. Several factors are responsible for breaking the extent of LD in a chromosome, such as the physical distance between the markers and recombination and mutation rates. Given that recombination only occurs in females, only one half of the X-chromosomes in a population will recombine in each generation, and therefore it will necessarily take more time to break down LD by recombination. As a result, LD is greater when compared to the autosomes and the size of regions with a single genetic history is larger, making it a better and more accurate tool to detect patterns of LD in populations.

The comparative analysis between the autosomes and the X-chromosome can also be used to reveal differences in demographic histories, migration, and breeding patterns of females and males. The usual studies of gender-biased demographic events compare information obtained from the Y-chromosome and mitochondrial deoxyribonucleic acid (mtDNA) markers. Unlike mtDNA and Y-chromosome analyses that inform about the history of female or male lineages respectively, the X-chromosome allows the simultaneous study on both genders, making it an ideal system for studying population genetic differences between males and females regarding mutation rates and patterns of recombination. Owing to recombination, the X-chromosome is composed by a block-like pattern with different chromosomal regions being informative of distinct genetic histories, unlike uniparental markers that are transmitted as a single locus and where all the markers share the same genealogic history.