Y chromosome 246891 224337275 2008-07-08T12:07:25Z Jack's Revenge 1035400 /* Genes */ linkified in accordance with [[http://en.wikipedia.org/wiki/Category:Genes_on_chromosome_Y]]; more articels to come, probably [[Image:Chromosome Y.svg|125px|right]] The '''Y chromosome''' is the [[Sex-determination system|sex-determining]] [[chromosome]] in most [[mammal]]s, including [[human]]s. In mammals, it contains the gene [[SRY]], which triggers [[testicle|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 (though for example the [[platypus]] has five pairs). Males have one Y chromosome and one X chromosome, while females have two X chromosomes. In mammals, the Y chromosome contains the gene that triggers embryonic development as a male. This gene is [[SRY]]. Other genes (in addition to [[SRY]]) on the Y chromosomes of men and other mammals are needed for normal sperm production. There are exceptions, however. 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 [[triple X syndrome|some women have three Xs]] or a single X (and no Y, "X0", see [[Turner syndrome]]). There are other exceptions in which [[SRY]] is damaged (leading to an [[Swyer syndrome|XY female]]), or copied to the X (leading to an [[XX male]]). For related phenomena see [[Androgen insensitivity syndrome]] and [[Intersex]]. Presence or absence of the Y-chromosome is a method of sexual determination. == 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 [[reptile]]s, sex depends on the incubation temperature; others are [[hermaphrodite#Simultaneous_hermaphrodites|hermaphroditic]] (meaning they contain both male and female gametes in the same individual). ===Origin=== The X and Y chromosomes diverged around 300 million years ago from a pair of identical chromosomes<ref name="lahn">{{cite journal |author=Lahn B, Page D |title=Four evolutionary strata on the human X chromosome |journal=Science |volume=286 |issue=5441 |pages=964–7 |year=1999 |pmid=10542153 |doi=10.1126/science.286.5441.964}}<!--http://www.abc.net.au/science/news/stories/s63100.htm [replaced]--></ref>, 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.<ref>{{cite journal |author=Graves J.A.M. |title=Sex chromosome specialization and degeneration in mammals |journal=Cell |volume=124 |issue=5 |pages=901–14 |year=2006 |pmid=16530039 |doi=10.1016/j.cell.2006.02.024}}</ref> 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 [[chromosomal translocation|translocation]].<ref>{{cite journal |author=Graves J.A.M., Koina E., Sankovic N. |title=How the gene content of human sex chromosomes evolved |journal=Curr Opin Genet Dev |volume=16 |issue=3 |pages=219–24 |year=2006 |pmid=16650758 |doi=10.1016/j.gde.2006.04.007}}</ref> ===Recombination inhibition=== [[genetic recombination|Recombination]] between the X and Y chromosomes proved harmful - it resulted in males without necessary genes formerly found on the X 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<ref>{{cite journal |author=Graves J.A.M. |title=Sex chromosome specialization and degeneration in mammals |journal=Cell |volume=124 |issue=5 |pages=901–14 |year=2006 |pmid=16530039 |doi=10.1016/j.cell.2006.02.024}}</ref>. 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 [[Junk DNA|genetic junk]]; this was eventually removed from the Y chromosome.{{Fact|date=June 2008}} Today, the human Y chromosome itself contains only 86 working genes,<ref name="Chromosome Y">{{cite web |url = http://www.ensembl.org/Homo_sapiens/mapview?chr=Y |title = Ensembl Human MapView release 43 |date = February 2007 |accessdate = 2007-04-14}}</ref> compared to close to 1000 working genes on the X chromosome. In some animals, Y degradation is even more severe. The [[dunnart]], a marsupial carrying a [[megabase|10-12 Mb]] Y chromosome, has only four characterised genes; among them the [[SRY]] gene, is the smallest known mammalian Y chromosome. <ref>{{cite journal |author=Toder R., Wakefield M.J., Graves J.A.M. |title=The minimal mammalian Y chromosome - the marsupial Y as a model system |journal=Cytogenet Cell Genet |volume=91 |issue=1-4 |pages=285–92 |year=2000 |pmid=11173870 |doi=10.1159/000056858}}</ref> === 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.<ref name="rozen">{{cite journal |author=Rozen S, Skaletsky H, Marszalek J, Minx P, Cordum H, Waterston R, Wilson R, Page D |title=Abundant gene conversion between arms of palindromes in human and ape Y chromosomes |journal=Nature |volume=423 |issue=6942 |pages=873–6 |year=2003 |pmid=12815433 |doi=10.1038/nature01723}}</ref> Such a "recombination" is called [[gene conversion]] or ''[[RecLOH|recombinational loss of heterozygosity]]'' (RecLOH). In the case of the Y chromosomes, the [[palindrome]]s 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 [[chimpanzee]]s, [[bonobo]]s and [[gorilla]]s. 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 === 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<!-- 10.1007/s10577-007-1171-9 -->. 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 [[rodent]]s 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 pair]]s (the building blocks of [[DNA]]) and represents approximately 0.38% of the total DNA in a human [[cell (biology)|cell]]. The human Y chromosome contains 86<ref name="Chromosome Y"/> 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 region]]s at the [[telomere]]s (which comprise about 5% of the chromosome's length). These regions are relics of ancient [[Homology (biology)|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.<ref>[http://www.sciencedaily.com/releases/2008/04/080401184955.htm ScienceDaily.com Apr. 3, 2008]</ref> It is the [[Single nucleotide polymorphism|SNP]]s in this region which are used for tracing direct paternal ancestral lines. ===Genes=== *[[AMELY]] ([[amelogenin]],Y-chromosomal) *[[ANT3Y]] ([[adenine nucleotide translocator]]-3 on the Y) *[[ASMTY]] (which stands for [[acetylserotonin methyltransferase]]) *[[AZF1]] ([[azoospermia]] factor 1) *[[AZF2]] (azoospermia factor 2) *[[BPY2]] (basic protein on the Y chromosome) *[[CSF2RY]] (granulocyte-macrophage colony-stimulating factor receptor, alpha subunit on the Y chromosome) *[[DAZ1]] (deleted in azoospermia) *[[DAZ2]] *[[IL3RAY]] ([[interleukin]]-3 receptor) *[[PRKY]] (protein kinase, Y-linked) *[[RBM1]] ([[RNA]] binding motif protein, Y chromosome, family 1, member A1) *[[RBM2]] (RNA binding motif protein 2) *[[RPS4Y1]] (Ribosomal protein S4, Y-linked copy 1) *[[RPS4Y2]] (Ribosomal protein S4, Y-linked copy 2) *[[SRY]] (sex-determining region) *[[TSPY1|TSPY]] ([[testis]]-specific protein) *[[UTY (gene)|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.{{Fact|mar 2008|date=March 2008}} ====More common==== No vital genes reside only on the Y chromosome, since 50% 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. =====Defect 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===== [[Klinefelter's syndrome]] (47, XXY) is not an aneuploidy of the Y chromosome, but a condition of having an extra X chromosome. It usually results in defective postnatal testicular function, but as the extra X does not seem to be due to direct interference with expression of Y genes. The mechanism is not fully understood. =====XYY===== {{main|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 [[Genealogy|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.<ref>See [http://www.smgf.org/page.jspx?name=together www.smgf.org] for more information.</ref> See [http://www.smgf.org/page.jspx?name=together 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. == See also == * [[Human Y-chromosome DNA haplogroups]] * [[Y-DNA haplogroups by ethnic groups]] * [[DYS (DNA)|DNA Y-chromosome Segment (DYS)]] * [[List of DYS markers]] * [[Y-chromosomal Adam]] * [[Y-chromosomal Aaron]] * [[genetic genealogy]] * [[genealogical DNA test]] * [[Y-STR|Y chromosome Short Tandem Repeat (STR)]] * [[Single nucleotide polymorphism]] * [[Y linkage]] * [[X chromosome]] ==References== {{reflist}} * 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 == * [http://www.cambridgedna.com/genealogy-dna-genetic-genealogy.php 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 * [http://www.ornl.gov/sci/techresources/Human_Genome/faq/snps.shtml Human Genome Project Information] &mdash; Human Chromosome Y Launchpad * [http://www.wi.mit.edu/news/ontopic/ychromosome.html On Topic] &mdash; The Y Chromosome - From the Whitehead Institute for Biomedical Research * [http://www.nature.com/nature/focus/ychromosome/index.html Nature] &mdash; focus on the Y chomosome * [http://www.genome.gov/11007628 National Human Genome Research Institute (NHGRI)] &mdash; Use of Novel Mechanism Preserves Y Chromosome Genes * [http://www.ysearch.org/ Ysearch.org - Public Y-DNA database] * [http://ycc.biosci.arizona.edu/ Y Chromosome Consortium (YCC)] {{Chromosomes}} [[Category:Chromosomes|Chromosome Y]] [[Category:Andrology]] [[Category:Genes on chromosome Y]] [[ca:Cromosoma Y]] [[de:Y-Chromosom]] [[es:Cromosoma Y]] [[fr:Chromosome Y]] [[id:Kromosom-Y]] [[it:Cromosoma Y (umano)]] [[he:כרומוזום Y]] [[hu:Humán Y kromoszóma]] [[nl:Y-chromosoom]] [[ja:Y染色体]] [[no:Y-kromosom]] [[pl:Chromosom Y]] [[pt:Cromossoma Y (humano)]] [[sr:Y хромозом]] [[sv:Y-kromosom]] [[tr:Y Kromozomu]] [[zh:Y染色體]]