A | B | C | D | E | F | G | H | CH | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
| Human Y chromosome | |
|---|---|
 Human Y chromosome (after G-banding) | |
 Y chromosome in human male karyogram | |
| Features | |
| Length (bp) | 62,460,029 bp (CHM13) |
| No. of genes | 63 (CCDS)[1] |
| Type | Allosome |
| Centromere position | Acrocentric[2] (10.4 Mbp[3]) |
| 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 in therian mammals and other organisms. Along with the X chromosome, it is part of the XY sex-determination system, in which the Y is the sex-determining because it is the presence or absence of Y chromosome that determines the male or female sex of offspring produced in sexual reproduction. In mammals, the Y chromosome contains the SRY gene, which triggers development of 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 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.[citation needed]
There are exceptions, however. Among humans, some males are born two Xs and a Y ("XXY", see Klinefelter syndrome), one X and two Ys (see XYY syndrome). Some females have three Xs (Trisomy X), and some have a single X instead of two Xs ("X0", see Turner syndrome). There are other variations in which, during embryonic development, the WNT4 gene[7] is activated and/or the SRY gene is damaged leading to birth of an XY female (Swyer syndrome[7]). A Y chromosome may also be present but fail to result in the development of a male phenotype in individuals with androgen insensitivity syndrome, instead resulting in a female or ambiguous phenotype. In other cases, the SRY gene is copied to the X, leading to birth of an XX male.[8]
Origins and evolution
Before Y chromosome
Many ectothermic vertebrates have no sex chromosomes.[9] If these species have different sexes, sex is determined environmentally rather than genetically. For some species, especially reptiles, sex depends on the incubation temperature.[10] Some vertebrates are 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.[16] However, research published in 2008 analyzing the platypus genome[17] suggested that the XY sex-determination system would not have been present more than 166 million years ago, when monotremes split from other mammals.[18] 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 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 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.[25] 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.[14][26] 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.[14]
With a 30% difference between humans and chimpanzees, the Y chromosome is one of the fastest-evolving parts of the human genome.[27] However, these changes have been limited to non-coding sequences and 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.[28] Additionally, a scientific report in 2012 stated that only one gene had been lost since humans diverged from the rhesus macaque 25 million years ago.[29] 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.[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 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.[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 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 into 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.[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 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.[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:
- 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.[14][40][41] Tokudaia spp. have relocated some other genes ancestrally present on the Y chromosome to the X chromosome.[41] Both sexes of Tokudaia spp. and Ellobius lutescens have an XO genotype (Turner syndrome),[41] whereas all Ellobius tancrei possess an XX genotype.[14] 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.[38][42][43]
- 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.[44]
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:
- 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-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.[48] For example, the ZW sex-determination system is found in birds, snakes, and 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
 | This section may require cleanup to meet Wikipedia's quality standards. The specific problem is: Too many subsections. Article might benefit from moving h3 subsections into h2 sections, if we can somehow reconcile the gap between all therians and humans. "Origins and evolution" section has a human focus, but the discussion does include all therians. (October 2021) |
The human Y chromosome is composed of about 62 million base pairs of DNA, making it similar in size to chromosome 19 and represents almost 2% of the total DNA in a male cell.[54][55] The human Y chromosome carries 693 genes, 107 of which are protein-coding.[56] However, some genes are repeated, making the number of exclusive protein-coding genes just 42.[56] The Consensus Coding Sequence (CCDS) Project only classifies 63 out of 107 genes, though CCDS estimates are often considered lower bounds due to their conservative classification strategy.[57] All single-copy Y-linked genes are 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
 | This article is missing information about NRY/MSY structure - How there's a huge chunk of heterochromatin in q, nomenclature of the palindromes and amplicons, TTTY transcripts, etc. Best if we add a figure that mashes together the tops of Colaco 2018 Fig 1 and PMID 12815422 fig 3.. (October 2021) |
Cytogenetic band
| 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
Genesedit
Number of genesedit
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, 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 listedit
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: