Y chromosome

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)
Human Y chromosome
Allosome
Centromere positionAcrocentric[2]
(10.4 Mbp[3])
Complete gene lists
CCDSGene list
HGNCGene list
UniProtGene list
NCBIGene list
External map viewers
EnsemblChromosome Y
EntrezChromosome Y
NCBIChromosome Y
UCSCChromosome Y
Full DNA sequences
RefSeqNC_000024 (FASTA)
GenBankCM000686 (FASTA)

The Y chromosome is one of two

male gonads
. The Y chromosome is passed only from male parents to male offspring.

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, working with Hemiptera. Stevens proposed that chromosomes always existed in pairs and that the smaller chromosome (now labelled "Y") 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. In the early 1920s Theophilus Painter determined that X and Y chromosomes determined sex in humans (and other mammals).[4]

The chromosome was given the name "Y" simply to follow on from Henking's "X" alphabetically.[5][6] 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.[5]: 65–66 

Variations

Most therian mammals have only one pair of sex chromosomes in each cell. Males have one Y chromosome and one

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.[citation needed
]

There are exceptions, however. Among humans, some males are born two Xs and a Y ("XXY", see

Origins and evolution

Before Y chromosome

Many

hermaphrodites, though hermaphroditic species are most commonly sequential, meaning the organism switches sex, producing male or female gametes at different points in its life, but never producing both at the same time. This is opposed to simultaneous hermaphroditism, where the same organism produces male and female gametes at the same time. Most simultaneous hermaphrodite species are invertebrates, and among vertebrates, simultaneous hermaphroditism has only been discovered in a few orders of fish.[11]

Origin

The X and Y chromosomes are thought to have evolved from a pair of identical chromosomes,[12][13] termed autosomes, when an ancestral animal developed an allelic variation (a so-called "sex locus") and simply possessing this allele caused the organism to be male.[14] 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 by the Y chromosome through the process of translocation.[15]

Until recently, the X and Y chromosomes were thought to have diverged around 300 million years ago.

eutherian mammals are not present on the autosomes of platypus and birds.[18] The older estimate was based on erroneous reports that the platypus X chromosomes contained these sequences.[19][20]

Recombination inhibition

Most chromosomes recombine during meiosis. However, in males, the X and Y pair in a shared region known as the pseudoautosomal region (PAR).[21] The PAR undergoes frequent recombination between the X and Y chromosomes,[21] but recombination is suppressed in other regions of the Y chromosome.[14] These regions contain sex-determining and other male-specific genes.[22] Without this suppression, these genes could be lost from the Y chromosome from recombination and cause issues such as infertility.[23]

The lack of recombination across the majority of the Y chromosome makes it a useful tool in studying human evolution, since recombination complicates the mathematical models used to trace ancestries.[24]

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

selection, and genetic drift.[14]

With a 30% difference between humans and chimpanzees, the Y chromosome is one of the fastest-evolving parts of 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.[citation needed
]

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

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.[14] The increased mutation opportunity for the Y chromosome is reported by Graves as a factor 4.8.[14] However, her original reference obtains this number for the relative mutation rates in male and female germ lines for the lineage leading to humans.[30]

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[31] 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.[32]

Inefficient selection

Without the ability to recombine during

"junk" DNA. Massive accumulations of retrotransposable elements are scattered throughout the Y.[14] 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.[citation needed
]

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.[33] This means the Y chromosome has a much lower information content relative to its overall length; it is more redundant.[citation needed]

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.[14] 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.[34]

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.[35] Such a "recombination" is called gene conversion.

In the case of the Y chromosomes, the

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.[35]

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.[35]

Gene conversion tracts formed during meiosis are long, about 2,068 base pairs, and significantly biased towards the fixation of G or C nucleotides (GC biased).[36] The recombination intermediates preceding gene conversion were found to rarely take the alternate route of crossover recombination.[36] The Y-Y gene conversion rate in humans is about 1.52 x 10-5 conversions/base/year.[37] These gene conversion events may reflect a basic function of meiosis, that of conserving the integrity of the genome.

Future evolution

According to some theories, in the terminal stages of the degeneration of the Y chromosome, other chromosomes may increasingly take over genes and functions formerly associated with it and finally, within the framework of this theory, the Y chromosome disappears entirely, and a new sex-determining system arises.[14][neutrality is disputed][improper synthesis?] Several species of rodent in the sister families Muridae and Cricetidae have reached these stages,[38][39] in the following ways:

Outside of the rodents, the black muntjac, Muntiacus crinifrons, evolved new X and Y chromosomes through fusions of the ancestral sex chromosomes and autosomes.[45]

Modern data cast doubt on this hypothesis.[16] This conclusion was reached by scientists who studied the Y chromosomes of rhesus monkeys. When genomically comparing the Y chromosome of rhesus monkeys and humans, scientists found very few differences, given that humans and rhesus monkeys diverged 30 million years ago.[46]

Some organisms have lost the Y chromosome. For example, most species of Nematodes. However, in order for the complete elimination of Y to occur, it was necessary to develop an alternative way of determining sex (for example, by determining sex by the ratio of the X chromosome to autosomes), and any genes necessary for male function had to be moved to other chromosomes.[16] In the meantime, modern data demonstrate the complex mechanisms of Y chromosome evolution and the fact that the disappearance of the Y chromosome is not guaranteed.

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",[47] 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.[citation needed]

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 with a Z chromosome and a W chromosome.

butterflies; the females have ZW sex chromosomes, and males have ZZ sex chromosomes.[48][49][50]

Non-inverted Y chromosome

There are some species, such as the Japanese rice fish, in which 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.[51]

Multiple XY pairs

Monotremes like platypuses possess four or five 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.[19] 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.[52][53]: fig. 5 

Platypus sex chromosomes have strong sequence similarity with the avian Z chromosome, (indicating close homology),[17] and the SRY gene so central to sex-determination in most other mammals is apparently not involved in platypus sex-determination.[18]

Human Y chromosome

The human Y chromosome is composed of about 62 million

hemizygous (present on only one chromosome) except in cases of aneuploidy such as XYY syndrome or XXYY syndrome. Traits that are inherited via the Y chromosome are called Y-linked traits, or holandric traits (from Ancient Greek ὅλος hólos, "whole" + ἀνδρός andrós, "male").[58]

Sequence of the human Y chromosome

At the end of the Human Genome Project (and after many updates) almost half of the Y chromosome remained un-sequenced even in 2021; a different Y chromosome from the HG002 (GM24385) genome was completely sequenced in January 2022 and is included in the new "complete genome" human reference genome sequence, CHM13.[56] The complete sequencing of a human Y chromosome was shown to contain 62,460,029 base pairs and 41 additional genes.[56] This added 30 million base pairs,[56] but it was discovered that the Y chromosome can vary a lot in size between individuals, from 45.2 million to 84.9 million base pairs.[59]

Since almost half of the human Y sequence was unknown before 2022, it could not be screened out as contamination in microbial sequencing projects. As a result, the NCBI RefSeq bacterial genome database mistakenly includes some Y chromosome data.[56]

Structure

Cytogenetic band

G-banding ideograms of human Y chromosome
G-banding patterns of human Y chromosome in three different resolutions (400,[60]
550[61] and 850[3]). Band length in this diagram is based on the ideograms from ISCN (2013).[62] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[63]
G-bands of human Y chromosome in resolution 850 bphs[3]
Chr. Arm[64] Band[65] ISCN
start[66]
ISCN
stop[66]
Basepair
start
Basepair
stop
Stain[67] Density
Y p 11.32 0 149 1 300,000 gneg
Y p 11.31 149 298 300,001 600,000 gpos 50
Y p 11.2 298 1043 600,001 10,300,000 gneg
Y p 11.1 1043 1117 10,300,001 10,400,000 acen
Y q 11.1 1117 1266 10,400,001 10,600,000 acen
Y q 11.21 1266 1397 10,600,001 12,400,000 gneg
Y q 11.221 1397 1713 12,400,001 17,100,000 gpos 50
Y q 11.222 1713 1881 17,100,001 19,600,000 gneg
Y q 11.223 1881 2160 19,600,001 23,800,000 gpos 50
Y q 11.23 2160 2346 23,800,001 26,600,000 gneg
Y q 12 2346 3650 26,600,001 57,227,415 gvar

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 (PARs) 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.[68] Single-nucleotide polymorphisms (SNPs) in this region are used to trace direct paternal ancestral lines.

More specifically, PAR1 is at 0.1–2.7 Mb. PAR2 is at 56.9–57.2 Mb. The non-recombining region (NRY) or male-specific region (MSY) sits between. Their sizes is now known perfectly from CHM13: 2.77 Mb and 329.5 kb. Until CHM13 the data in PAR1 and PAR2 was just copied over from X chromosome.[59]

Sequence classes

Genes

Number of genes

The following are some of the gene count estimates of human Y chromosome. Because researchers use different approaches to

number of genes on each chromosome varies (for technical details, see gene prediction). Among various projects, 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.[69]

Estimated by
Protein-coding genes
Non-coding RNA genes Pseudogenes Source Release date
CCDS 63 [1] 2016-09-08
HGNC 45 55 381 [70] 2017-05-12
Ensembl 63 109 392 [71] 2017-03-29
UniProt 47 [72] 2018-02-28
NCBI 73 122 400 [73][74][75] 2017-05-19

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:

Genes on the non-recombining portion of the Y chromosome[76]
Name
paralog
Note
SRY
SOX3 Sex-determining region. This is the p arm [Yp].
ZFY ZFX Zinc finger.
RPS4Y1
RPS4X
Ribosomal protein S4.
AMELY AMELX Amelogenin.
TBL1Y TBL1X
PCDH11Y PDCH11X X-transposed region (XTR) from Xq21, one of two genes. Once dubbed "PAR3"[77] but later refuted.[78]
TGIF2LY TGIF2LX The other X-transposed gene.
TSPY1, TSPY2 TSPX Testis-specific protein.
AZFa
(none) Not a gene. First part of the AZF (Azoospermia factor) region on arm q. Contains the four following genes. X counterparts escape inactivation.
USP9Y USP9X Ubiquitin protease.
DDX3Y DDX3X Helicase.
UTY UTX Histone demethylase.
TB4Y TB4X
AZFb (none) Second AZF region on arm q. Prone to NAHR [non-allelic homologous recombination] with AZFc. Overlaps with AZFc. Contains three single-copy gene regions and repeats.
CYorf15 CXorf15
RPS4Y2
RPS4X
Another copy of ribosomal protein S4.
EIF1AY EIF4AX
KDM5D KDM5C
XKRY XK (protein) Found in the "yellow" amplicon.
HSFY1, HSFY2 HSFX1, HSFX2 Found in the "blue" amplicon.
PRY, PRY2 Found in the "blue" amplicon. Identified by similarity to PTPN13 (Chr. 4).
RBMY1A1
RBMY Large number of copies. Part of an RBM gene family of RNA recognition motif (RRM) proteins.
AZFc (none) Final (distal) part of the AZF. Multiple palindromes.
DAZ1, DAZ2, DAZ3, DAZ4 RRM genes in two palindromic clusters. BOLL and DAZLA are autosomal homologs.
CDY1, CDY2 CDY1 is actually two identical copies. CDY2 is two closely related copies in palindrome P5. Probably derived from autosomal CDYL.
VCY1, VCY2
VCX1
through 3
Three copies of VCX2 (BPY2). Part of the VCX/VCY family. The two copies of BPY1 are instead in Yq11.221/AZFa.

Y-chromosome-linked diseases

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

Loss of Y chromosome

Males can lose the Y chromosome in a subset of cells, known as mosaic loss. Mosaic loss is strongly associated with age,[79] and smoking is another important risk factor for mosaic loss.[80]

Mosaic loss may be related to health outcomes, indicating that the Y chromosome plays important roles outside of sex determination.

heart risks, and mortality.[83]

Further studies are needed to understand how mosaic Y chromosome loss may contribute to other sex differences in health outcomes, such as how male smokers have between 1.5 and 2 times the risk of non-respiratory cancers as female smokers.

better source needed
]

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.[citation needed]

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.[citation needed]

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

mixed gonadal dysgenesis.[citation needed
]

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.[citation needed]

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.[88]

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.[89] 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".[90]

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,[91] and increased height was the only characteristic that could be reliably associated with XYY males.[92] The "criminal karyotype" concept is therefore inaccurate.[88]

Rare

The following Y-chromosome-linked diseases are rare, but notable because of their elucidation 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 considerably more rare. The extra genetic material in these cases can lead to skeletal abnormalities, dental abnormalities, decreased IQ, delayed development, and respiratory issues, but the severity features of these conditions are variable.[93]

XX male syndrome

SRY portion of the Y chromosome to move to the X chromosome.[8] When such an X chromosome is present in a zygote, male gonads develop because of the SRY gene.[8]

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.[citation needed]

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.[94]

Microchimerism

In 1974, male chromosomes were discovered in fetal cells in the blood circulation of women.[95]

In 1996, it was found that male fetal progenitor cells could persist postpartum in the maternal blood stream for as long as 27 years.[96]

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:[97]

  • 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:[97]

  • 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 women.[98]

See also

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External links

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