Everything about Y-chromosome totally explained
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 (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
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
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've 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 diverged around 300 million years ago from a pair of identical chromosomes, 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. 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.
Recombination inhibition
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. 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. These harmful mutations continued to damage Y-unique genes until several finally stopped functioning and became
genetic junk; this was eventually removed from the Y chromosome.
Today, the human Y chromosome itself contains only 86 working genes, 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
10-12 Mb Y chromosome, has only four characterised genes; among them the
SRY gene, is the smallest known mammalian Y chromosome.
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. 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
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 It is the
SNPs 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)
DAZ (deleted in azoospermia)
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)
RPS4Y (Ribosomal protein S4, Y-linked copy 1)
RPS4Y2 (Ribosomal protein S4, Y-linked copy 2)
SRY (sex-determining region)
TDF (testis determining factor)
TSPY (testis-specific protein)
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.
More common
No vital genes reside only on the Y chromosome, since 50% of humans (females) don't 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 (for example, 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) isn't 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 doesn't seem to be due to direct interference with expression of Y genes. The mechanism isn't fully understood.
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 don't 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, for example, 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. 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 don't 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 doesn't 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.
Further Information
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