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 the sex-determining chromosome in many species, since
it is the presence or absence of Y that determines the male or female
sex of offspring produced in sexual reproduction. In mammals, the Y
chromosome contains the gene SRY, which triggers testis development.
DNA in the human
Y chromosome is composed of about 59 million base
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. (See Y linkage.)
2 Origins and evolution
2.1 Before Y chromosome
2.3 Recombination inhibition
2.4.1 High mutation rate
2.4.2 Inefficient selection
2.4.3 Genetic drift
2.6 Future evolution
2.7 1:1 sex ratio
3 Non-mammal Y chromosome
3.1 ZW chromosomes
3.2 Non-inverted Y chromosome
Human Y chromosome
4.1 Non-combining region of Y (NRY)
4.2.1 Number of genes
4.3 Y-chromosome-linked diseases
4.3.1 More common
Y chromosome microdeletion
188.8.131.52 Defective Y chromosome
184.108.40.206 More than two Y chromosomes
XX male syndrome
4.4 Genetic genealogy
4.5 Brain function
4.7 Cytogenetic band
5 See also
7 External links
Y chromosome was identified as a sex-determining chromosome by
Nettie Stevens at
Bryn Mawr College
Bryn Mawr College in 1905 during a study of the
mealworm Tenebrio molitor.
Edmund Beecher Wilson
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"
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.
Most mammals have only one pair of sex chromosomes in each cell. Males
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
There are exceptions, however. For example, the platypus relies on an
XY sex-determination system
XY sex-determination system based on five pairs of chromosomes.
Platypus sex chromosomes in fact appear to bear a much stronger
homology (similarity) with the avian Z chromosome, and the SRY
gene so central to sex-determination in most other mammals is
apparently not involved in platypus sex-determination. Among
humans, some men have two Xs and a Y ("XXY", see Klinefelter
syndrome), or one X and two Ys (see XYY syndrome), and some women have
three Xs or a single X instead of a double X ("X0", see Turner
syndrome). There are other exceptions in which
SRY is damaged (leading
to an XY female), or copied to the X (leading to an XX male). For
related phenomena, see
Androgen insensitivity syndrome
Androgen insensitivity syndrome and Intersex.
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).
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
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. It is because of this disregard for the
rules that the
Y chromosome is such a superb tool for investigating
recent human evolution.
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
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
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
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
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
Y chromosome at a greater risk of mutation than the rest of the
genome. The increased mutation risk 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.
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.
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
Y chromosome free of excessive mutation, it may never make it
in to 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.
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,
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.
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.[neutrality is
disputed][improper synthesis?] Several species of rodent in the sister
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
Tokudaia tokunoshimensis, have lost the
Y chromosome and
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
The wood lemming Myopus schisticolor, the Arctic lemming, Dicrostonyx
torquatus, and multiple species in the grass mouse genus
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
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
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:
Suppose male births are less common than female.
A newborn male then has better mating prospects than a newborn female,
and therefore can expect to have more offspring.
Therefore parents genetically disposed to produce males tend to have
more than average numbers of grandchildren born to them.
Therefore the genes for male-producing tendencies spread, and male
births become more common.
As the 1:1 sex ratio is approached, the advantage associated with
producing males dies away.
The same reasoning holds if females are substituted for males
throughout. Therefore 1:1 is the equilibrium ratio.
Non-mammal Y chromosome
Many groups of organisms in addition to mammals have Y chromosomes,
but these Y chromosomes do not share common ancestry with mammalian Y
chromosomes. Such groups include 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.
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.
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 holandric traits (although
biologists will usually just say "Y-linked").
Some cells, especially in older men and smokers, lack a Y chromosome.
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 "loss of Y"
(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). And yet
women, who have no Y chromosome, have lower rates of cancer. Male
smokers have between 1.5 and 2 times the risk of non-respiratory
cancers as female smokers.
Non-combining region of Y (NRY)
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. For details,
see human Y-chromosome
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
Non-coding RNA genes
See also: Category:Genes on human chromosome Y.
In general, the human
Y chromosome is extremely gene poor—it is one
of the largest gene deserts in the human genome, however there are
several notable genes coded on the Y chromosome: not including
pseudoautosomal genes, genes encoded on the human Y chromosome
NRY, with corresponding gene on X chromosome
RPS4X (Ribosomal protein S4)
X-transposed region (XTR), once dubbed "PAR3" but later
AZF1 (azoospermia factor 1)
BPY2 (basic protein on the Y chromosome)
DAZ1 (deleted in azoospermia)
DFNY1 encoding protein Deafness, Y-linked 1
PRKY (protein kinase, Y-linked)
SRY (sex-determining region)
TSPY (testis-specific protein)
UTY (ubiquitously transcribed TPR gene on Y chromosome)
ZFY (zinc finger protein)
Diseases linked to
Y chromosome can be of more common types or very
rare ones. Yet, the rare ones still have importance in understanding
the function of the
Y chromosome in the normal case.
No vital genes reside only on the Y chromosome, since roughly half of
humans (females) do not have a Y chromosome. The only well-defined
human disease linked to a defect on the
Y chromosome is defective
testicular development (due to deletion or deleterious mutation of
SRY). However, having two X chromosomes and one
Y chromosome has
similar effects. On the other hand, having
Y chromosome polysomy has
other effects than masculinization.
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.
Main article: Klinefelter syndrome
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.
Main article: XYY syndrome
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
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.
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
DNA haplogroup and Y-chromosomal
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
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
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
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 women.
G-banding ideograms of human Y chromosome
G-banding ideogram of human
Y chromosome in resolution 850 bphs. Band
length in this diagram is proportional to base-pair length. This type
of ideogram is generally used in genome browsers (e.g. Ensembl, UCSC
G-banding patterns of human
Y chromosome in three different
resolutions (400, 550 and 850). Band length in this diagram
is based on the ideograms from ISCN (2013). This type of ideogram
represents actual relative band length observed under a microscope at
the different moments during the mitotic process.
G-bands of human
Y chromosome in resolution 850 bphs
Haplodiploid sex-determination system
Single nucleotide polymorphism
Y chromosome Short Tandem Repeat (STR)
Y-chromosome haplogroups in populations of the world
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^ "p": Short arm; "q": Long arm.
^ For cytogenetic banding nomenclature, see article locus.
^ a b These values (ISCN start/stop) are based on the length of
bands/ideograms from the ISCN book, An International System for Human
Cytogenetic Nomenclature (2013). Arbitrary unit.
^ gpos: Region which is positively stained by G banding, generally
AT-rich and gene poor; gneg: Region which is negatively stained by G
banding, generally CG-rich and gene rich; acen Centromere. var:
Variable region; stalk: Stalk.
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