Y-chromosome: Definition from Answers.com

The diploid human genome is packaged within 46 chromosomes, as two pairs of 23 discrete elements, into all cells other than the haploid gametic egg and sperm cells. During the reproductive process, each parent's gametes contribute 22 nonsex chromosomes and either one X or one Y chromosome.

Paternal Inheritance

The X and Y chromosomes are the sex chromosomes for mammals, including humans. Not only are the X and Y sex chromosomes in mammals physically distinctive, with the Y being smaller, the Y chromosome is exceptionally peculiar. The X chromosome contains considerably more genes than the Y, which has its functionality essentially limited to traits associated with being male. It is the Y chromosome that carries the major masculinity-determining gene (SRY, for sex-determining region Y), which dictates maleness. In a mating pair, if the paternal partner contributes a normal Y chromosome, male gonadal tissues (testes) develop in the offspring. Only males have the potential to transmit a Y chromosome to the next generation, and thus the father's contribution is decisive regarding an offspring's sex.

Since normally only one Y chromosome exists per cell, no pairing between X and Y occurs at meiosis, except at small regions. Normally, no crossing over occurs. Therefore, except for rare mutations that may occur during spermatogenesis, a son will inherit an identical copy of his father's Y chromosome, and this copy is also essentially identical to the Y chromosomes carried by all his paternal forefathers, across the generations. This is in contrast to the rest of his chromosomal heritage, which will be a unique mosaic of contributions from multiple ancestors created by the reshuffling process of recombination.

Sex Determination and Y Chromosome Genes

While SRY is the most dramatic gene affiliated with the Y chromosome, about thirty other genes have been identified. Some notable representatives include AZFa, b, and c, which are associated with spermatogenesis and male infertility, SMCY, associated with the immune response function responsible for transplantation rejection when male tissue is grafted to female tissue, and TSPY, which may play a role in testicular cancer.

Sex Chromosome Evolution and Peculiarities

Discussions of sex chromosome evolution raise the question of the biological risks and benefits of sexual differentiation in organisms. Overall, sexual dimorphism enhances diversity that, in turn, improves the chances for evolutionary change and potential survival during periods of environmental change.

There are risks in the specialization of the Y chromosome, however. Besides its absence in females, lack of recombination for most of its physical territory except at its tips, and the strict pattern of paternal inheritance, the solitary cellular existence of the Y chromosome reduces the opportunity for DNA repair, which normally occurs while pairing during mitosis. This may explain the prevalence of multicopy DNA sequences on the Y, and why many of its genes have lost functionality. In fact, while genes predominately specific to male function tend to accumulate on the Y chromosome, other genes that have functional counterparts elsewhere will atrophy over evolutionary time, through the accumulation of uncorrected mutations. Thus the Y chromosome is slowing evolving toward a composition with fewer and fewer essential genes.

Molecular Anthropology Using the Y Chromosome

The field of molecular anthropology is predicated on the concept that the genes of modern populations encode aspects of human history. By studying the degree of genetic molecular variation in modern organisms, one can, in principle, understand past events. The Y chromosome is uniquely suited to such studies. Secondary applications of Y chromosome variation studies include forensics (criminological investigations, such as determining whether or not an individual has been involved in a crime) and genealogical reconstruction (verifying membership in a particular family's ancestry).

DNA polymers (such as chromosomes) are composed of a four-letter alphabet of chemicals called nucleotide bases. Random unique event mutations in DNA sequences can change the identity of a single base in the DNA molecule. These "spelling changes" are the essential currency of genetic anthropological research.

What is central is the assumption that a particular mutation arose just once in human history, and all men that display such a mutation on their Y chromosome descend from a common forefather on whom the mutation first appeared. The sequential buildup of such mutational events across the generations can be readily determined and displayed as a gene tree. Informally, the last known mutation to accumulate on a particular chromosome can be used to define a particular lineage or branch tip in the tree. As long as the mutational change does not affect the individual's ability to reproduce, it may be preserved and handed down to each succeeding generation, eventually becoming widespread in a population. Such mutations are called polymorphisms or genetic markers.

Since most of the Y chromosome has the special property of not recombining during meiosis, no shuffling of DNA from different ancestors occurs. As a consequence, any Y chromosome accumulates all the mutations that have occurred during its lineal life span and thus preserves the paternal genetic legacy that has been transmitted from father to son over the generations. The discovery of numerous Y chromosome polymorphisms has allowed us to deduce a reliable genealogy composed of numerous distinctive lineages. This concept is analogous to the genealogical relationships maintained by the traditional transmission of surnames in some cultures, although the gene tree approach provides access to a prehistorically deeper set of paternal relationships.

Molecular anthropologists have exploited this knowledge in an attempt to understand the history and evolutionary relationships of contemporary populations by performing a systematic survey of Y-chromosome DNA sequence variation. The unique nature of Y-chromosome diversification provides an elegant record of human population histories allowing researchers to reconstruct a global picture, emblematic of modern human origins, affinity, differentiation, and demographic history. The evidence shows that all modern extant human Y chromosomes trace their ancestry to Africa, and that descendants left Africa perhaps less than 100,000 years (or approximately 4,000 generations) ago.

While variation in any single DNA molecule can reflect only a small portion of human diversity, by merging other genetic information, such as data from the maternally transmitted mitochondrial DNA molecule, and nongenetic knowledge derived from archeological, linguistic, and other sources, we can improve our understanding of the affinities and histories of contemporary peoples.

Bibliography

Cavalli-Sforza, Luigi L. Genes, Peoples, and Languages, Mark Seielstad, trans. New York: North Point Press, 2000.

Jobling, Mark, and Christopher Tyler-Smith. "New Uses for New Haplotypes: The Human Y Chromosome, Disease, and Selection." Trends in Genetics 16 (2000): 356-362.

Strachan, Tom, and Andrew P. Read. Human Molecular Genetics. New York: Wiley-Liss, 1996.

—Peter A. Underhill

Human Y-chromosome

The Y chromosome is the sex-determining chromosome in most mammals, including humans. In mammals, it contains the gene SRY, which triggers testis development, thus determining sex. The human Y chromosome is composed of about 60 million base pairs.

Overview

Most mammals have 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. For example, the platypus relies on an XY sex-determination system based on five pairs of chromosomes ^[1]. Platypus sex chromosomes in fact appear to bear a much stronger homology (similarity) with the avian Z chromosome^[2], and the SRY gene so central to sex-determination in most other mammals is apparently not involved in platypus sex-determination^[3]. Among humans, some men have two Xs and a Y ("XXY", see Klinefelter's 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 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).

Origin

The X and Y chromosomes are thought to have originated from a pair of identical chromosomes^[4], termed autosomes, when an ancestral mammal developed an allelic variation, a so-called 'sex locus' - simply possessing this allele caused the organism to be male^[5]. The chromosome with this allele became the Y chromosome, while the other member of the pair became the X chromosome. Over time, genes which 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.^[6].

Until recently, the X and Y chromosomes were thought to have diverged around 300 million years ago. However recent research, particularly that stemming from the sequencing of the platypus genome^[2], has suggested that the XY sex-determination system wouldn't have been present more than 166 million years ago, at the split of the monotremes from other mammals^[3]. This reduction in the age of the XY chromosomal system by around 150 million years is based on the finding that platypus X chromosomes show much stronger homology to the avian Z sex chromosome than with other mammalian X chromosomes ^[3]. This suggests that the platypus X and avian Z chromosomes both evolved from the same chromosome of a common ancestor of the two^[7].

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^[5]. 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.

Shrinking

With time, larger and larger areas became unable to recombine with the X chromosome. This caused its own problems: without recombination, the removal of harmful mutations from chromosomes becomes increasingly difficult. With no ability to remove the harmful mutations, only fortuitous mutations that permanently turned these coding regions off would give their bearer an advantage over those with still-functioning, harmful genes. This gradually turned large swaths of the chromosome into genetic junk; this was eventually removed from the Y chromosome.^{[citation needed]}

Today, the human Y chromosome itself contains only 78 working genes,^[8] compared to close to 1500 working genes on the X chromosome. In some animals, Y degradation is even more severe. The dunnart, a marsupial carrying a 10-12 Mb Y chromosome, has only four characterised genes; among them, the SRY gene is the smallest known mammalian Y chromosome. ^[9]

Gene conversion

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.^[10] Such a "recombination" is called gene conversion or recombinational loss of heterozygosity (RecLOH).

In the case of the Y chromosomes, the palindromes are not junk 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

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After only an SRY (or other sex-determining) gene remains from the whole Y chromosome, there are the following possibilities:

The gene is connected to X chromosome or some autosome, making it the new Y chromosome. The whole process starts again. This has happened in the Transcaucasian Mole Vole (Ellobius lutescens), the Northern Mole Vole (E. talpinus) and the Zaisan Mole Vole (E. tancrei). In E. lutescens, both sexes have unpaired X chromosomes; in E. talpinus and E. tancrei, both females and males have XX. A similar situation to that of the Transcaucasian Mole Vole seems to exist in the Tokudaia osimensis species complex of spinous country-rats. Among Eumuroida, Ellobius and Tokudaia are not particularly closely related. Consequently unusual mechanisms of sex determination may well be far more common among these rodents than generally assumed.
Part of some autosome is connected to both the X and Y chromosomes. This happened with one species of Drosophila.
The Y chromosome remains, containing only the SRY gene.

Human Y chromosome

In humans, the Y chromosome spans 58 million base pairs (the building blocks of DNA) and represents approximately 0.38% of the total DNA in a human cell. The human Y chromosome contains 86^[8] genes, which code for only 23 distinct proteins. Traits that are inherited via the Y chromosome are called holandric traits.

The human Y chromosome is 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.^[11] It is the SNPs in this region which are used for tracing direct paternal ancestral lines.

Genes

Not including pseudoautosomal genes, genes include:

NRY, with corresponding gene on X chromosome
- AMELY/AMELX (amelogenin)
- RPS4Y1/RPS4Y2/RPS4X (Ribosomal protein S4)

NRY, other
- AZF1 (azoospermia factor 1)
- BPY2 (basic protein on the Y chromosome)
- DAZ1 (deleted in azoospermia)
- DAZ2
- 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

Y-Chromosome-linked diseases 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.^{[citation needed]}

More common

No vital genes reside only on the Y chromosome, since roughly half of humans (females) do not have Y chromosomes. 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.

Defective Y-chromosome

This results in the person presenting a female phenotype even though that person possesses an XY karyotype (i.e., is born with female-like genitalia). The lack of the second X results in infertility. In other words, viewed from 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 46X, 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 usually is a girl with the features of Turner syndrome or mixed gonadal dysgenesis.

XXY

Main article: Klinefelter's syndrome

Klinefelter's 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; the extra X does not seem to be due to direct interference with expression of Y genes.

XYY

Main article: XYY

It is possible for an abnormal number (aneuploidy) of Y chromosomes to result in problems.

47,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. When chromosome surveys were done in the mid-1960s in British secure hospitals for the developmentally disabled, a higher than expected number of patients were found to have an extra Y chromosome. The patients were mischaracterized as aggressive and criminal, so that for a while an extra Y chromosome was believed to predispose a boy to antisocial behavior (and was dubbed the "criminal karyotype"). Subsequently, in 1968 in Scotland the only ever comprehensive nationwide chromosome survey of prisons found no overrepresentation of 47,XYY men, and later studies found 47,XYY boys and men had the same rate of criminal convictions as 46,XY boys and men of equal intelligence. Thus, the "criminal karyotype" concept is inaccurate and obsolete.

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., XYYYY) 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 since, unlike other genes, the Y chromosome is passed exclusively from father to son.^[12] See www.smgf.org for more information. Mitochondrial DNA, maternally inherited, is used in an analogous way to trace the maternal line.

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.

ZW-chromosomes

Other organisms have mirror image sex chromosomes: the female is "XY" and the male is "XX", but by convention biologists call a "female Y" a W chromosome and the other a Z chromosome. For example, female birds, snakes, and butterflies have ZW sex chromosomes, and males have ZZ sex chromosomes.

Notes

^ Grützner F, Rens W, Tsend-Ayush E, et al. (2004). "In the platypus a meiotic chain of ten sex chromosomes shares genes with the bird Z and mammal X chromosomes". Nature 432: 913–917. doi:10.1038/nature03021.
^ ^a ^b Warren WC, Hillier LDW, Graves JAM, et al. (2008). "Genome analysis of the platypus reveals unique signatures of evolution". Nature 453: 175–183. doi:10.1038/nature06936. http://www.nature.com/nature/journal/v453/n7192/full/nature06936.html.
^ ^a ^b ^c Veyrunes F, Waters PD, Miethke P, et al. (2008). "Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes". Genome Research 18: 965–973. doi:10.1101/gr.7101908. http://genome.cshlp.org/content/18/6/965.abstract.
^ Lahn B, Page D (1999). "Four evolutionary strata on the human X chromosome". Science 286 (5441): 964–7. doi:10.1126/science.286.5441.964. PMID 10542153.
^ ^a ^b Graves J.A.M. (2006). "Sex chromosome specialization and degeneration in mammals". Cell 124 (5): 901–14. doi:10.1016/j.cell.2006.02.024. PMID 16530039.
^ Graves J.A.M., Koina E., Sankovic N. (2006). "How the gene content of human sex chromosomes evolved". Curr Opin Genet Dev 16 (3): 219–24. doi:10.1016/j.gde.2006.04.007. PMID 16650758.
^ O'Brien SJ (2008). "The platypus genome unravelled". Cell 133: 953–955. doi:10.1016/j.cell.2008.05.038. PMID 18555772.
^ ^a ^b "Ensembl Human MapView release 43". February 2007. http://www.ensembl.org/Homo_sapiens/mapview?chr=Y. Retrieved 2007-04-14.
^ Toder R., Wakefield M.J., Graves J.A.M. (2000). "The minimal mammalian Y chromosome - the marsupial Y as a model system". Cytogenet Cell Genet 91 (1-4): 285–92. doi:10.1159/000056858. PMID 11173870.
^ Rozen S, Skaletsky H, Marszalek J, Minx P, Cordum H, Waterston R, Wilson R, Page D (2003). "Abundant gene conversion between arms of palindromes in human and ape Y chromosomes". Nature 423 (6942): 873–6. doi:10.1038/nature01723. PMID 12815433.
^ ScienceDaily.com Apr. 3, 2008
^ See www.smgf.org for more information.

References

Skaletsky, H.S., et al. (2003) The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature, 423, 825-837
Rozen, S., et al. (2003) Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature, 423, 873-876.

External links

Genetic Genealogy: About the use of mtDNA and Y chromosome analysis in ancestry testing
http://www.ensembl.org/Homo_sapiens/mapview?chr=Y
http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=Y
Human Genome Project Information — Human Chromosome Y Launchpad
On Topic — The Y Chromosome - From the Whitehead Institute for Biomedical Research
Nature — focus on the Y chomosome
National Human Genome Research Institute (NHGRI) — Use of Novel Mechanism Preserves Y Chromosome Genes
Ysearch.org - Public Y-DNA database
Y Chromosome Consortium (YCC)

v • d • e Human chromosomes

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Sex chromosome	X · Y · Pseudoautosomal region

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Y-chromosome

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