Y chromosome

From Wikipedia, the free encyclopedia

 

Human Y chromosome
Human Y chromosome (after G-banding)
Y chromosome in human male karyogram
Features
Length (bp)	57,227,415 bp (GRCh38)
No. of genes	63 (CCDS)
Type	Allosome
Centromere position	Acrocentric (10.4 Mbp)
Complete gene lists
CCDS	Gene list
HGNC	Gene list
UniProt	Gene list
NCBI	Gene list
External map viewers
Ensembl	Chromosome Y
Entrez	Chromosome Y
NCBI	Chromosome Y
UCSC	Chromosome Y
Full DNA sequences
RefSeq	NC_000024 (FASTA)
GenBank	CM000686 (FASTA)

The Y chromosome is one of two sex chromosomes (allosomes) in mammals, including humans, and many other animals. The other is the X chromosome. Y is normally the sex-determining chromosome in many species, since it is the presence or absence of Y that typically determines the male or female sex of offspring produced in sexual reproduction. In mammals, the Y chromosome contains the gene SRY, which by default triggers male development. The DNA in the human Y chromosome is composed of about 59 million base pairs. The Y chromosome is passed only from father to son. With a 30% difference between humans and chimpanzees, the Y chromosome is one of the fastest-evolving parts of the human genome. To date, over 200 Y-linked genes have been identified. All Y-linked genes are expressed and (apart from duplicated genes) hemizygous (present on only one chromosome) except in the cases of aneuploidy such as XYY syndrome or XXYY syndrome.

Overview

Discovery

The Y chromosome was identified as a sex-determining chromosome by Nettie Stevens at Bryn Mawr College in 1905 during a study of the mealworm Tenebrio molitor. Edmund Beecher Wilson independently discovered the same mechanisms the same year. Stevens proposed that chromosomes always existed in pairs and that the Y chromosome was the pair of the X chromosome discovered in 1890 by Hermann Henking. She realized that the previous idea of Clarence Erwin McClung, that the X chromosome determines sex, was wrong and that sex determination is, in fact, due to the presence or absence of the Y chromosome. Stevens named the chromosome "Y" simply to follow on from Henking's "X" alphabetically.

The idea that the Y chromosome was named after its similarity in appearance to the letter "Y" is mistaken. All chromosomes normally appear as an amorphous blob under the microscope and only take on a well-defined shape during mitosis. This shape is vaguely X-shaped for all chromosomes. It is entirely coincidental that the Y chromosome, during mitosis, has two very short branches which can look merged under the microscope and appear as the descender of a Y-shape.

Variations

Most therian mammals have only one pair of sex chromosomes in each cell. Males have one Y chromosome and one X chromosome, while females have two X chromosomes. In mammals, the Y chromosome contains a gene, SRY, which triggers embryonic development as a male. The Y chromosomes of humans and other mammals also contain other genes needed for normal sperm production. 

There are exceptions, however. Among humans, some men have two Xs and a Y ("XXY", see Klinefelter syndrome), or one X and two Ys, and some women have three Xs or a single X instead of a double X. There are other exceptions in which SRY is damaged (leading to an XY female), or copied to the X (leading to an XX male).

Origins and evolution

Before Y chromosome

Many ectothermic vertebrates have no sex chromosomes. If they have different sexes, sex is determined environmentally rather than genetically. For some of them, especially reptiles, sex depends on the incubation temperature; others are hermaphroditic (meaning they contain both male and female gametes in the same individual).

Origin

The X and Y chromosomes are thought to have evolved from a pair of identical chromosomes, termed autosomes, when an ancestral animal developed an allelic variation, a so-called "sex locus" – simply possessing this allele caused the organism to be male. The chromosome with this allele became the Y chromosome, while the other member of the pair became the X chromosome. Over time, genes that were beneficial for males and harmful to (or had no effect on) females either developed on the Y chromosome or were acquired through the process of translocation.

Until recently, the X and Y chromosomes were thought to have diverged around 300 million years ago. However, research published in 2010, and particularly research published in 2008 documenting the sequencing of the platypus genome, has suggested that the XY sex-determination system would not have been present more than 166 million years ago, at the split of the monotremes from other mammals. This re-estimation of the age of the therian XY system is based on the finding that sequences that are on the X chromosomes of marsupials and eutherian mammals are present on the autosomes of platypus and birds. The older estimate was based on erroneous reports that the platypus X chromosomes contained these sequences.

Recombination inhibition

Recombination between the X and Y chromosomes proved harmful—it resulted in males without necessary genes formerly found on the Y chromosome, and females with unnecessary or even harmful genes previously only found on the Y chromosome. As a result, genes beneficial to males accumulated near the sex-determining genes, and recombination in this region was suppressed in order to preserve this male specific region. Over time, the Y chromosome changed in such a way as to inhibit the areas around the sex determining genes from recombining at all with the X chromosome. As a result of this process, 95% of the human Y chromosome is unable to recombine. Only the tips of the Y and X chromosomes recombine. The tips of the Y chromosome that could recombine with the X chromosome are referred to as the pseudoautosomal region. The rest of the Y chromosome is passed on to the next generation intact, allowing for its use in tracking human evolution.

Degeneration

By one estimate, the human Y chromosome has lost 1,393 of its 1,438 original genes over the course of its existence, and linear extrapolation of this 1,393-gene loss over 300 million years gives a rate of genetic loss of 4.6 genes per million years. Continued loss of genes at the rate of 4.6 genes per million years would result in a Y chromosome with no functional genes – that is the Y chromosome would lose complete function – within the next 10 million years, or half that time with the current age estimate of 160 million years. Comparative genomic analysis reveals that many mammalian species are experiencing a similar loss of function in their heterozygous sex chromosome. Degeneration may simply be the fate of all non-recombining sex chromosomes, due to three common evolutionary forces: high mutation rate, inefficient selection, and genetic drift.

However, comparisons of the human and chimpanzee Y chromosomes (first published in 2005) show that the human Y chromosome has not lost any genes since the divergence of humans and chimpanzees between 6–7 million years ago, and a scientific report in 2012 stated that only one gene had been lost since humans diverged from the rhesus macaque 25 million years ago. These facts provide direct evidence that the linear extrapolation model is flawed and suggest that the current human Y chromosome is either no longer shrinking or is shrinking at a much slower rate than the 4.6 genes per million years estimated by the linear extrapolation model.

High mutation rate

The human Y chromosome is particularly exposed to high mutation rates due to the environment in which it is housed. The Y chromosome is passed exclusively through sperm, which undergo multiple cell divisions during gametogenesis. Each cellular division provides further opportunity to accumulate base pair mutations. Additionally, sperm are stored in the highly oxidative environment of the testis, which encourages further mutation. These two conditions combined put the Y chromosome at a greater opportunity of mutation than the rest of the genome. The increased mutation opportunity for the Y chromosome is reported by Graves as a factor 4.8. However, her original reference obtains this number for the relative mutation rates in male and female germ lines for the lineage leading to humans.

The observation that the Y chromosome experiences little meiotic recombination and has an accelerated rate of mutation and degradative change compared to the rest of the genome suggests an evolutionary explanation for the adaptive function of meiosis with respect to the main body of genetic information. Brandeis proposed that the basic function of meiosis (particularly meiotic recombination) is the conservation of the integrity of the genome, a proposal consistent with the idea that meiosis is an adaptation for repairing DNA damage.

Inefficient selection

Without the ability to recombine during meiosis, the Y chromosome is unable to expose individual alleles to natural selection. Deleterious alleles are allowed to "hitchhike" with beneficial neighbors, thus propagating maladapted alleles in to the next generation. Conversely, advantageous alleles may be selected against if they are surrounded by harmful alleles (background selection). Due to this inability to sort through its gene content, the Y chromosome is particularly prone to the accumulation of "junk" DNA. Massive accumulations of retrotransposable elements are scattered throughout the Y. The random insertion of DNA segments often disrupts encoded gene sequences and renders them nonfunctional. However, the Y chromosome has no way of weeding out these "jumping genes". Without the ability to isolate alleles, selection cannot effectively act upon them.

A clear, quantitative indication of this inefficiency is the entropy rate of the Y chromosome. Whereas all other chromosomes in the human genome have entropy rates of 1.5–1.9 bits per nucleotide (compared to the theoretical maximum of exactly 2 for no redundancy), the Y chromosome's entropy rate is only 0.84. This means the Y chromosome has a much lower information content relative to its overall length; it is more redundant.

Genetic drift

Even if a well adapted Y chromosome manages to maintain genetic activity by avoiding mutation accumulation, there is no guarantee it will be passed down to the next generation. The population size of the Y chromosome is inherently limited to 1/4 that of autosomes: diploid organisms contain two copies of autosomal chromosomes while only half the population contains 1 Y chromosome. Thus, genetic drift is an exceptionally strong force acting upon the Y chromosome. Through sheer random assortment, an adult male may never pass on his Y chromosome if he only has female offspring. Thus, although a male may have a well adapted Y chromosome free of excessive mutation, it may never make it into the next gene pool. The repeat random loss of well-adapted Y chromosomes, coupled with the tendency of the Y chromosome to evolve to have more deleterious mutations rather than less for reasons described above, contributes to the species-wide degeneration of Y chromosomes through Muller's ratchet.

Gene conversion

As it has been already mentioned, the Y chromosome is unable to recombine during meiosis like the other human chromosomes; however, in 2003, researchers from MIT discovered a process which may slow down the process of degradation. They found that human Y chromosome is able to "recombine" with itself, using palindrome base pair sequences. Such a "recombination" is called gene conversion.

In the case of the Y chromosomes, the palindromes are not noncoding DNA; these strings of bases contain functioning genes important for male fertility. Most of the sequence pairs are greater than 99.97% identical. The extensive use of gene conversion may play a role in the ability of the Y chromosome to edit out genetic mistakes and maintain the integrity of the relatively few genes it carries. In other words, since the Y chromosome is single, it has duplicates of its genes on itself instead of having a second, homologous, chromosome. When errors occur, it can use other parts of itself as a template to correct them.

Findings were confirmed by comparing similar regions of the Y chromosome in humans to the Y chromosomes of chimpanzees, bonobos and gorillas. The comparison demonstrated that the same phenomenon of gene conversion appeared to be at work more than 5 million years ago, when humans and the non-human primates diverged from each other.

Future evolution

In the terminal stages of the degeneration of the Y chromosome, other chromosomes increasingly take over genes and functions formerly associated with it. Finally, the Y chromosome disappears entirely, and a new sex-determining system arises. Several species of rodent in the sister families Muridae and Cricetidae have reached these stages, in the following ways:

• The Transcaucasian mole vole, Ellobius lutescens, the Zaisan mole vole, Ellobius tancrei, and the Japanese spinous country rats Tokudaia osimensis and Tokudaia tokunoshimensis, have lost the Y chromosome and SRY entirely. Tokudaia spp. have relocated some other genes ancestrally present on the Y chromosome to the X chromosome. Both sexes of Tokudaia spp. and Ellobius lutescens have an XO genotype (Turner syndrome), whereas all Ellobius tancrei possess an XX genotype. The new sex-determining system(s) for these rodents remains unclear.
• The wood lemming Myopus schisticolor, the Arctic lemming, Dicrostonyx torquatus, and multiple species in the grass mouse genus Akodon have evolved fertile females who possess the genotype generally coding for males, XY, in addition to the ancestral XX female, through a variety of modifications to the X and Y chromosomes.
• In the creeping vole, Microtus oregoni, the females, with just one X chromosome each, produce X gametes only, and the males, XY, produce Y gametes, or gametes devoid of any sex chromosome, through nondisjunction.

Outside of the rodents, the black muntjac, Muntiacus crinifrons, evolved new X and Y chromosomes through fusions of the ancestral sex chromosomes and autosomes.

1:1 sex ratio

Fisher's principle outlines why almost all species using sexual reproduction have a sex ratio of 1:1. W. D. Hamilton gave the following basic explanation in his 1967 paper on "Extraordinary sex ratios", given the condition that males and females cost equal amounts to produce:

1. Suppose male births are less common than female.
2. A newborn male then has better mating prospects than a newborn female, and therefore can expect to have more offspring.
3. Therefore, parents genetically disposed to produce males tend to have more than average numbers of grandchildren born to them.
4. Therefore, the genes for male-producing tendencies spread, and male births become more common.
5. As the 1:1 sex ratio is approached, the advantage associated with producing males dies away.
6. The same reasoning holds if females are substituted for males throughout. Therefore, 1:1 is the equilibrium ratio.

Non-therian Y chromosome

Many groups of organisms in addition to therian mammals have Y chromosomes, but these Y chromosomes do not share common ancestry with therian Y chromosomes. Such groups include monotremes, Drosophila, some other insects, some fish, some reptiles, and some plants. In Drosophila melanogaster, the Y chromosome does not trigger male development. Instead, sex is determined by the number of X chromosomes. The D. melanogaster Y chromosome does contain genes necessary for male fertility. So XXY D. melanogaster are female, and D. melanogaster with a single X (X0), are male but sterile. There are some species of Drosophila in which X0 males are both viable and fertile.

ZW chromosomes

Other organisms have mirror image sex chromosomes: where the homogeneous sex is the male, said to have two Z chromosomes, and the female is the heterogeneous sex, and said to have a Z chromosome and a W chromosome. For example, female birds, snakes, and butterflies have ZW sex chromosomes, and males have ZZ sex chromosomes.

Non-inverted Y chromosome

There are some species, such as the Japanese rice fish, the XY system is still developing and cross over between the X and Y is still possible. Because the male specific region is very small and contains no essential genes, it is even possible to artificially induce XX males and YY females to no ill effect.

Multiple XY pairs

Monotremes possess four or five (platypus) pairs of XY sex chromosomes, each pair consisting of sex chromosomes with homologous regions. The chromosomes of neighboring pairs are partially homologous, such that a chain is formed during mitosis. The first X chromosome in the chain is also partially homologous with the last Y chromosome, indicating that profound rearrangements, some adding new pieces from autosomes, have occurred in history.

Platypus sex chromosomes have strong sequence similarity with the avian Z chromosome, (indicating close homology), and the SRY gene so central to sex-determination in most other mammals is apparently not involved in platypus sex-determination.

Human Y chromosome

In humans, the Y chromosome spans about 58 million base pairs (the building blocks of DNA) and represents approximately 1% of the total DNA in a male cell. The human Y chromosome contains over 200 genes, at least 72 of which code for proteins. Traits that are inherited via the Y chromosome are called Y-linked, or holandric traits. 

Men can lose the Y chromosome in a subset of cells, which is called the mosaic loss of chromosome Y (LOY). This post-zygotic mutation is strongly associated with age, affecting about 15% of men 70 years of age. Smoking is another important risk factor for LOY. It has been found that men with a higher percentage of hematopoietic stem cells in blood lacking the Y chromosome (and perhaps a higher percentage of other cells lacking it) have a higher risk of certain cancers and have a shorter life expectancy. Men with LOY (which was defined as no Y in at least 18% of their hematopoietic cells) have been found to die 5.5 years earlier on average than others. This has been interpreted as a sign that the Y chromosome plays a role going beyond sex determination and reproduction (although the loss of Y may be an effect rather than a cause). Male smokers have between 1.5 and 2 times the risk of non-respiratory cancers as female smokers.

Non-combining region of Y (NRY)

The human Y chromosome is normally unable to recombine with the X chromosome, except for small pieces of pseudoautosomal regions at the telomeres (which comprise about 5% of the chromosome's length). These regions are relics of ancient homology between the X and Y chromosomes. The bulk of the Y chromosome, which does not recombine, is called the "NRY", or non-recombining region of the Y chromosome. The single-nucleotide polymorphisms (SNPs) in this region are used to trace direct paternal ancestral lines.

Genes

Number of genes

The following are some of the gene count estimates of human Y chromosome. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies (for technical details, see gene prediction). Among various projects, the collaborative consensus coding sequence project (CCDS) takes an extremely conservative strategy. So CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes.

Estimated by	Protein-coding genes	Non-coding RNA genes	Pseudogenes
CCDS	63	—	—
HGNC	45	55	381
Ensembl	63	109	392
UniProt	47	—	—
NCBI	73	122	400

Gene list

In general, the human Y chromosome is extremely gene poor—it is one of the largest gene deserts in the human genome. Disregarding pseudoautosomal genes, genes encoded on the human Y chromosome include:

• NRY, with corresponding gene on X chromosome
  • AMELY (amelogenin) similar to AMELX on X
  • RPS4Y1/RPS4Y2/RPS4X (Ribosomal protein S4)
  • DDX3Y (helicase) similar to DDX3X on X
  • X-transposed region (XTR), once dubbed "PAR3" but later refuted
    • PCDH11Y (PCDH11X)
    • TGIF2LY (TGIF2LX)
• NRY, other
  • AZF1 (azoospermia factor 1)
  • BPY2 (basic protein on the Y chromosome)
  • DAZ1 (deleted in azoospermia)
  • DAZ2
  • DFNY1 encoding protein Deafness, Y-linked 1
  • PRKY (protein kinase, Y-linked)
  • RBMY1A1
  • SRY (sex-determining region)
  • TSPY (testis-specific protein)
  • USP9Y
  • UTY (ubiquitously transcribed TPR gene on Y chromosome)
  • ZFY (zinc finger protein)

Y-chromosome-linked diseases

Diseases linked to the Y chromosome typically involve an aneuploidy, an atypical number of chromosomes.

Y chromosome microdeletion

Y chromosome microdeletion (YCM) is a family of genetic disorders caused by missing genes in the Y chromosome. Many affected men exhibit no symptoms and lead normal lives. However, YCM is also known to be present in a significant number of men with reduced fertility or reduced sperm count.

Defective Y chromosome

This results in the person presenting a female phenotype (i.e., is born with female-like genitalia) even though that person possesses an XY karyotype. The lack of the second X results in infertility. In other words, viewed from the opposite direction, the person goes through defeminization but fails to complete masculinization.

The cause can be seen as an incomplete Y chromosome: the usual karyotype in these cases is 45X, plus a fragment of Y. This usually results in defective testicular development, such that the infant may or may not have fully formed male genitalia internally or externally. The full range of ambiguity of structure may occur, especially if mosaicism is present. When the Y fragment is minimal and nonfunctional, the child is usually a girl with the features of Turner syndrome or mixed gonadal dysgenesis.

XXY

Klinefelter syndrome (47, XXY) is not an aneuploidy of the Y chromosome, but a condition of having an extra X chromosome, which usually results in defective postnatal testicular function. The mechanism is not fully understood; it does not seem to be due to direct interference by the extra X with expression of Y genes.

XYY

47, XYY syndrome (simply known as XYY syndrome) is caused by the presence of a single extra copy of the Y chromosome in each of a male's cells. 47, XYY males have one X chromosome and two Y chromosomes, for a total of 47 chromosomes per cell. Researchers have found that an extra copy of the Y chromosome is associated with increased stature and an increased incidence of learning problems in some boys and men, but the effects are variable, often minimal, and the vast majority do not know their karyotype.

In 1965 and 1966 Patricia Jacobs and colleagues published a chromosome survey of 315 male patients at Scotland's only special security hospital for the developmentally disabled, finding a higher than expected number of patients to have an extra Y chromosome. The authors of this study wondered "whether an extra Y chromosome predisposes its carriers to unusually aggressive behaviour", and this conjecture "framed the next fifteen years of research on the human Y chromosome".

Through studies over the next decade, this conjecture was shown to be incorrect: the elevated crime rate of XYY males is due to lower median intelligence and not increased aggression, and increased height was the only characteristic that could be reliably associated with XYY males. The "criminal karyotype" concept is therefore inaccurate.

Rare

The following Y-chromosome-linked diseases are rare, but notable because of their elucidating of the nature of the Y chromosome.

More than two Y chromosomes

Greater degrees of Y chromosome polysomy (having more than one extra copy of the Y chromosome in every cell, e.g., XYYY) are rare. The extra genetic material in these cases can lead to skeletal abnormalities, decreased IQ, and delayed development, but the severity features of these conditions are variable.

XX male syndrome

XX male syndrome occurs when there has been a recombination in the formation of the male gametes, causing the SRY portion of the Y chromosome to move to the X chromosome. When such an X chromosome contributes to the child, the development will lead to a male, because of the SRY gene.

Genetic genealogy

In human genetic genealogy (the application of genetics to traditional genealogy), use of the information contained in the Y chromosome is of particular interest because, unlike other chromosomes, the Y chromosome is passed exclusively from father to son, on the patrilineal line. Mitochondrial DNA, maternally inherited to both sons and daughters, is used in an analogous way to trace the matrilineal line.

Brain function

Research is currently investigating whether male-pattern neural development is a direct consequence of Y-chromosome-related gene expression or an indirect result of Y-chromosome-related androgenic hormone production.

Microchimerism

The presence of male chromosomes in fetal cells in the blood circulation of women was discovered in 1974.

In 1996, it was found that male fetal progenitor cells could persist postpartum in the maternal blood stream for as long as 27 years.

A 2004 study at the Fred Hutchinson Cancer Research Center, Seattle, investigated the origin of male chromosomes found in the peripheral blood of women who had not had male progeny. A total of 120 subjects (women who had never had sons) were investigated, and it was found that 21% of them had male DNA. The subjects were categorised into four groups based on their case histories:

• Group A (8%) had had only female progeny.
• Patients in Group B (22%) had a history of one or more miscarriages.
• Patients Group C (57%) had their pregnancies medically terminated.
• Group D (10%) had never been pregnant before.

The study noted that 10% of the women had never been pregnant before, raising the question of where the Y chromosomes in their blood could have come from. The study suggests that possible reasons for occurrence of male chromosome microchimerism could be one of the following:

• miscarriages,
• pregnancies,
• vanished male twin,
• possibly from sexual intercourse.

A 2012 study at the same institute has detected cells with the Y chromosome in multiple areas of the brains of deceased

X chromosome

From Wikipedia, the free encyclopedia

 

Human X chromosome
Human X chromosome (after G-banding)
X chromosome in human male karyogram
Features
Length (bp)	156,040,895 bp (GRCh38)
No. of genes	804 (CCDS)
Type	Allosome
Centromere position	Submetacentric (61.0 Mbp)
Complete gene lists
CCDS	Gene list
HGNC	Gene list
UniProt	Gene list
NCBI	Gene list
External map viewers
Ensembl	Chromosome X
Entrez	Chromosome X
NCBI	Chromosome X
UCSC	Chromosome X
Full DNA sequences
RefSeq	NC_000023 (FASTA)
GenBank	CM000685 (FASTA)

The X chromosome is one of the two sex-determining chromosomes (allosomes) in many organisms, including mammals (the other is the Y chromosome), and is found in both males and females. It is a part of the XY sex-determination system and X0 sex-determination system. The X chromosome was named for its unique properties by early researchers, which resulted in the naming of its counterpart Y chromosome, for the next letter in the alphabet, following its subsequent discovery.

Discovery

It was first noted that the X chromosome was special in 1890 by Hermann Henking in Leipzig. Henking was studying the testicles of Pyrrhocoris and noticed that one chromosome did not take part in meiosis. Chromosomes are so named because of their ability to take up staining (chroma in Greek means color). Although the X chromosome could be stained just as well as the others, Henking was unsure whether it was a different class of object and consequently named it X element, which later became X chromosome after it was established that it was indeed a chromosome.

The idea that the X chromosome was named after its similarity to the letter "X" is mistaken. All chromosomes normally appear as an amorphous blob under the microscope and only take on a well defined shape during mitosis. This shape is vaguely X-shaped for all chromosomes. It is entirely coincidental that the Y chromosome, during mitosis, has two very short branches which can look merged under the microscope and appear as the descender of a Y-shape.

It was first suggested that the X chromosome was involved in sex determination by Clarence Erwin McClung in 1901. After comparing his work on locusts with Henking's and others, McClung noted that only half the sperm received an X chromosome. He called this chromosome an accessory chromosome, and insisted (correctly) that it was a proper chromosome, and theorized (incorrectly) that it was the male-determining chromosome.

Inheritance pattern

The number of possible ancestors on the X chromosome inheritance line at a given ancestral generation follows the Fibonacci sequence. (After Hutchison, L. "Growing the Family Tree: The Power of DNA in Reconstructing Family Relationships".)

 

Luke Hutchison noticed that a number of possible ancestors on the X chromosome inheritance line at a given ancestral generation follows the Fibonacci sequence. A male individual has an X chromosome, which he received from his mother, and a Y chromosome, which he received from his father. The male counts as the "origin" of his own X chromosome (${\displaystyle F_{1}=1}$), and at his parents' generation, his X chromosome came from a single parent (${\displaystyle F_{2}=1}$). The male's mother received one X chromosome from her mother (the son's maternal grandmother), and one from her father (the son's maternal grandfather), so two grandparents contributed to the male descendant's X chromosome (${\displaystyle F_{3}=2}$). The maternal grandfather received his X chromosome from his mother, and the maternal grandmother received X chromosomes from both of her parents, so three great-grandparents contributed to the male descendant's X chromosome (${\displaystyle F_{4}=3}$). Five great-great-grandparents contributed to the male descendant's X chromosome (${\displaystyle F_{5}=5}$), etc. (Note that this assumes that all ancestors of a given descendant are independent, but if any genealogy is traced far enough back in time, ancestors begin to appear on multiple lines of the genealogy, until eventually, a population founder appears on all lines of the genealogy.)

Humans

Function

Nucleus of a female amniotic fluid cell. Top: Both X-chromosome territories are detected by FISH. Shown is a single optical section made with a confocal microscope. Bottom: Same nucleus stained with DAPI and recorded with a CCD camera. The Barr body is indicated by the arrow, it identifies the inactive X (Xi).

 

The X chromosome in humans spans more than 153 million base pairs (the building material of DNA). It represents about 800 protein-coding genes compared to the Y chromosome containing about 70 genes, out of 20,000–25,000 total genes in the human genome. Each person usually has one pair of sex chromosomes in each cell. Females have two X chromosomes, whereas males have one X and one Y chromosome. Both males and females retain one of their mother's X chromosomes, and females retain their second X chromosome from their father. Since the father retains his X chromosome from his mother, a human female has one X chromosome from her paternal grandmother (father's side), and one X chromosome from her mother. This inheritance pattern follows the Fibonacci numbers at a given ancestral depth. 

Genetic disorders that are due to mutations in genes on the X chromosome are described as X linked. If X chromosome has a genetic disease gene, it always causes illness in male patients, since men have only one X chromosome and therefore only one copy of each gene. Females, instead, may stay healthy and only be carrier of genetic illness, since they have another X chromosome and possibility to have healthy gene copy. For example hemophilia and red-green colorblindness run in family this way. 

The X chromosome carries hundreds of genes but few, if any, of these have anything to do directly with sex determination. Early in embryonic development in females, one of the two X chromosomes is randomly and permanently inactivated in nearly all somatic cells (cells other than egg and sperm cells). This phenomenon is called X-inactivation or Lyonization, and creates a Barr body. If X-inactivation in the somatic cell meant a complete de-functionalizing of one of the X-chromosomes, it would ensure that females, like males, had only one functional copy of the X chromosome in each somatic cell. This was previously assumed to be the case. However, recent research suggests that the Barr body may be more biologically active than was previously supposed.

The partial inactivation of the X-chromosome is due to repressive heterochromatin that compacts the DNA and prevents the expression of most genes. Heterochromatin compaction is regulated by Polycomb Repressive Complex 2 (PRC2).

Genes

Number of genes

The following are some of the gene count estimates of human X chromosome. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies (for technical details, see gene prediction). Among various projects, the collaborative consensus coding sequence project (CCDS) takes an extremely conservative strategy. So CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes.

Estimated by	Protein-coding genes	Non-coding RNA genes	Pseudogenes
CCDS	804	—	—
HGNC	825	260	606
Ensembl	841	639	871
UniProt	839	—	—
NCBI	874	494	879

Gene list

The following is a partial list of genes on human chromosome X.

• APOO: encoding protein Apolipoprotein O
• ARMCX6: encoding protein Armadillo repeat containing X-linked 6
• BEX1: encoding protein Brain-expressed X-linked protein 1
• BEX2: encoding protein Brain-expressed X-linked protein 2
• BEX4: encoding protein Brain expressed, X-linked 4
• CCDC120: encoding protein Coiled coil domain containing protein 120
• CCDC22: encoding protein Coiled-coil domain containing 22
• CD99L2: CD99 antigen-like protein 2
• CHRDL1: encoding protein Chordin-like 1
• CMTX2 encoding protein Charcot-Marie-Tooth neuropathy, X-linked 2 (recessive)
• CMTX3 encoding protein Charcot-Marie-Tooth neuropathy, X-linked 3 (dominant)
• CT45A5: encoding protein Cancer/testis antigen family 45, member A5
• CXorf36: encoding protein hypothetical protein LOC79742
• CXorf40A: Chromosome X open reading frame 40
• CXorf49: chromosome X open reading frame 49. encoding protein
• CXorf66: encoding protein Chromosome X Open Reading Frame 66
• CXorf67: encoding protein Uncharacterized protein CXorf67
• DACH2: encoding protein Dachshund homolog 2
• EFHC2: encoding protein EF-hand domain (C-terminal) containing 2
• ERCC6L encoding protein ERCC excision repair 6 like, spindle assembly checkpoint helicase
• F8A1: Factor VIII intron 22 protein
• FAM120C: encoding protein Family with sequence similarity 120C
• FAM122B: Family with sequence similarity 122 member B
• FAM122C: encoding protein Family with sequence similarity 122C
• FAM127A: CAAX box protein 1
• FAM50A: Family with sequence similarity 50 member A
• FATE1: Fetal and adult testis-expressed transcript protein
• FMR1-AS1: encoding a long non-coding RNA FMR1 antisense RNA 1
• FRMPD3: encoding protein FERM and PDZ domain containing 3
• FUNDC1: encoding protein FUN14 domain containing 1
• FUNDC2: FUN14 domain-containing protein 2
• GATA1: encoding GATA1 transcription factor
• GNL3L encoding protein G protein nucleolar 3 like
• GPRASP2: G-protein coupled receptor-associated sorting protein 2
• GRIPAP1: encoding protein GRIP1-associated protein 1
• HDHD1A: encoding enzyme Haloacid dehalogenase-like hydrolase domain-containing protein 1A
• LAS1L encoding protein LAS1-like protein
• MAGEA2: encoding protein Melanoma-associated antigen 2
• MAGEA5 encoding protein Melanoma antigen family A, 5
• MAGEA8: encoding protein Melanoma antigen family A, 8
• MAGED4B: encoding protein Melanoma-associated antigen D4
• MAGT1: encoding protein Magnesium transporter protein 1
• MBNL3: encoding protein Muscleblind-like protein 3
• MIR222: encoding microRNA MicroRNA 222
• MIR361: encoding microRNA MicroRNA 361
• MIR660: encoding protein MicroRNA 660
• MORF4L2: encoding protein Mortality factor 4-like protein 2
• MOSPD1: encoding protein Motile sperm domain containing 1
• MOSPD2: encoding protein Motile sperm domain containing 2
• NKRF: encoding protein NF-kappa-B-repressing factor
• NRK: encoding enzyme Nik-related protein kinase
• OTUD5: encoding protein OTU deubiquitinase 5
• PASD1: encoding protein PAS domain-containing protein 1
• PAGE1 :encoding a protein of unestablished function
• PBDC1: encoding a protein of unestablished function
• PCYT1B: encoding enzyme Choline-phosphate cytidylyltransferase B
• PIN4: encoding enzyme Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4
• PLAC1: encoding protein Placenta-specific protein 1
• PLP2: encoding protein Proteolipid protein 2
• RPA4: encoding protein Replication protein A 30 kDa subunit
• RPS6KA6: encoding protein Ribosomal protein S6 kinase, 90kDa, polypeptide 6
• RRAGB: encoding protein Ras-related GTP-binding protein B
• SFRS17A: encoding protein Splicing factor, arginine/serine-rich 17A
• SLITRK2: encoding protein SLIT and NTRK-like protein 2
• SMARCA1: encoding protein Probable global transcription activator SNF2L1
• SMS: encoding enzyme Spermine synthase
• SSR4: encoding protein Translocon-associated protein subunit delta
• TAF7l: encoding protein TATA-box binding protein associated factor 7-like
• TCEAL1: encoding protein Transcription elongation factor A protein-like 1
• TCEAL4: encoding protein Transcription elongation factor A protein-like 4
• THOC2: encoding protein THO complex subunit 2
• TMEM29: encoding protein Protein FAM156A
• TMEM47: encoding protein Transmembrane protein 47
• TMLHE: encoding enzyme Trimethyllysine dioxygenase, mitochondrial
• TNMD encoding protein Tenomodulin (also referred to as tendin, myodulin, Tnmd and TeM)
• TRAPPC2P1 encoding protein Trafficking protein particle complex subunit 2
• TREX2: encoding enzyme Three prime repair exonuclease 2
• TRO: encoding protein Trophinin
• TSPYL2: encoding protein Testis-specific Y-encoded-like protein 2
• USP51: encoding enzyme Ubiquitin carboxyl-terminal hydrolase 51
• YIPF6: encoding protein Protein YIPF6
• ZC3H12B: encoding protein ZC3H12B
• ZFP92: encoding protein ZFP92 zinc finger protein
• ZMYM3: encoding protein Zinc finger MYM-type protein 3
• ZNF157: encoding protein Zinc finger protein 157
• ZNF182 encoding protein Zinc finger protein 182
• ZNF275: encoding protein Zinc finger protein 275
• ZNF674: encoding protein Zinc finger protein 674

Structure

It is theorized by Ross et al. 2005 and Ohno 1967 that the X chromosome is at least partially derived from the autosomal (non-sex-related) genome of other mammals, evidenced from interspecies genomic sequence alignments. 

The X chromosome is notably larger and has a more active euchromatin region than its Y chromosome counterpart. Further comparison of the X and Y reveal regions of homology between the two. However, the corresponding region in the Y appears far shorter and lacks regions that are conserved in the X throughout primate species, implying a genetic degeneration for Y in that region. Because males have only one X chromosome, they are more likely to have an X chromosome-related disease. 

It is estimated that about 10% of the genes encoded by the X chromosome are associated with a family of "CT" genes, so named because they encode for markers found in both tumor cells (in cancer patients) as well as in the human testis (in healthy patients).

Role in diseases

Numerical abnormalities

Klinefelter syndrome:

• Klinefelter syndrome is caused by the presence of one or more extra copies of the X chromosome in a male's cells. Extra genetic material from the X chromosome interferes with male sexual development, preventing the testicles from functioning normally and reducing the levels of testosterone.
• Males with Klinefelter syndrome typically have one extra copy of the X chromosome in each cell, for a total of two X chromosomes and one Y chromosome (47,XXY). It is less common for affected males to have two or three extra X chromosomes (48,XXXY or 49,XXXXY) or extra copies of both the X and Y chromosomes (48,XXYY) in each cell. The extra genetic material may lead to tall stature, learning and reading disabilities, and other medical problems. Each extra X chromosome lowers the child's IQ by about 15 points,^[20][21] which means that the average IQ in Klinefelter syndrome is in general in the normal range, although below average. When additional X and/or Y chromosomes are present in 48,XXXY, 48,XXYY, or 49,XXXXY, developmental delays and cognitive difficulties can be more severe and mild intellectual disability may be present.
• Klinefelter syndrome can also result from an extra X chromosome in only some of the body's cells. These cases are called mosaic 46,XY/47,XXY.

Triple X syndrome (also called 47,XXX or trisomy X):

• This syndrome results from an extra copy of the X chromosome in each of a female's cells. Females with trisomy X have three X chromosomes, for a total of 47 chromosomes per cell. The average IQ of females with this syndrome is 90, while the average IQ of unaffected siblings is 100. Their stature on average is taller than normal females. They are fertile and their children do not inherit the condition.
• Females with more than one extra copy of the X chromosome (48, XXXX syndrome or 49, XXXXX syndrome) have been identified, but these conditions are rare.

Turner syndrome:

• This results when each of a female's cells has one normal X chromosome and the other sex chromosome is missing or altered. The missing genetic material affects development and causes the features of the condition, including short stature and infertility.
• About half of individuals with Turner syndrome have monosomy X (45,X), which means each cell in a woman's body has only one copy of the X chromosome instead of the usual two copies. Turner syndrome can also occur if one of the sex chromosomes is partially missing or rearranged rather than completely missing. Some women with Turner syndrome have a chromosomal change in only some of their cells. These cases are called Turner syndrome mosaics (45,X/46,XX).

X-linked recessive disorders

Sex linkage was first discovered in insects, e.g., T. H. Morgan's 1910 discovery of the pattern of inheritance of the white eyes mutation in Drosophila melanogaster. Such discoveries helped to explain x-linked disorders in humans, e.g., haemophilia A and B, adrenoleukodystrophy, and red-green color blindness.

Other disorders

XX male syndrome is a rare disorder, where the SRY region of the Y chromosome has recombined to be located on one of the X chromosomes. As a result, the XX combination after fertilization has the same effect as a XY combination, resulting in a male. However, the other genes of the X chromosome cause feminization as well.

X-linked endothelial corneal dystrophy is an extremely rare disease of cornea associated with Xq25 region. Lisch epithelial corneal dystrophy is associated with Xp22.3. 

Megalocornea 1 is associated with Xq21.3-q22

Adrenoleukodystrophy, a rare and fatal disorder that is carried by the mother on the x-cell. It affects only boys between the ages of 5 and 10 and destroys the protective cell surrounding the nerves, myelin, in the brain. The female carrier hardly shows any symptoms because females have a copy of the x-cell. This disorder causes a once healthy boy to lose all abilities to walk, talk, see, hear, and even swallow. Within 2 years after diagnosis, most boys with Adrenoleukodystrophy die.

Role in mental abilities and intelligence

The X-chromosome has played a crucial role in the development of sexually selected characteristics for over 300 million years. During that time it has accumulated a disproportionate number of genes concerned with mental functions. For reasons that are not yet understood, there is an excess proportion of genes on the X-chromosome that are associated with the development of intelligence, with no obvious links to other significant biological functions. In other words, a significant proportion of genes associated with intelligence is passed on to the male offspring from the maternal side and to the female offspring from either/both maternal and paternal side. There has also been interest in the possibility that haploinsufficiency for one or more X-linked genes has a specific impact on development of the Amygdala and its connections with cortical centres involved in social–cognition processing or the ‘social brain'.