Y - The small chromosome

The Y Chromosome: Ancestry, Genetics, and the Making of a Man

Genes on the Y Chromosome

X chromosome and Y chromosome

Because of its distinctive role in sex determination, the Y chromosome has long attracted special attention from geneticists, evolutionary biologists and even the lay public. 

It is known to consist of regions of DNA that show quite distinctive genetic behaviour and genomic characteristics. The two human sex chromosomes, X and Y, originated a few hundred million years ago from the same ancestral autosome - a non-sex chromosome - during the evolution of sex determination They then diverged in sequence over the succeeding aeons. Nowadays, there are relatively short regions at either end of the Y chromosome that are still identical to the corresponding regions of the X chromosome, reflecting the frequent exchange of DNA between these regions ('recombination') that occurs during sperm production. But more than 95% of the modern-day.
Y chromosome is male-specific, consisting of some 23 million base pairs of euchromatin - the part of our genome containing most of the genes -  and a variable amount of heterochromatin,- consisting of highly repetitive DNA and often dismissed as non-functional. 

Autosomes are the chromosomes that are NOT a gender chromosome. (Here you can se the gender chromosome X
 far right.)
A small dictionary:
Autosomes: (see above) Chromosomes that are not a gender chromosome

Locus: In genetics a locus is the specific location of a gene , DNA sequense or position on a chromosome.
Allele: A variant of the similar DNA sequence located at a given locus is called an allele.  It is the alternative form of a gene for a character producing different effects.  

Translocation:  Translocation is a type of chromosomal abnormality in which a chromosome breaks and a portion of it reattaches to a different chromosome.
Heteromorphic: Having different forms at different periods of the life cycle, as in stages of insect metamorphosis.
Phenotype:  (from Greek phainein, 'to show' + typos, 'type') is the composite of an organism's observable characteristics or traits.
Phenotypes result from the expression of an organism's genes as well as the influence of environmental factors and the interactions between the two. Like the pigment on the skin or eye colour.

 The X and Y chromosomes are thought to have evolved 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.

Every human has 23 pairs of chromosomes - organized packets of genetic information (DNA) which code for all the necessary amino acids to create a human being. The twenty-third set of chromosomes determine the gender of a person: two X chromosomes create a female, and an X paired with a Y creates a male.
The Y chromosome is much smaller than a typical X chromosome, and contains somewhere between 70-200 genes (the entire human genome comprises approximately 20,000-25,000 genes). Some important genes on the Y chromosome include:

SRY: The SRY (Sex Determining Y Region) gene determines gender.
This gene will bind to other DNA in the cell, distorting it out of shape. This single gene creates the male phenotype. In a very rare genetic event, the gene sometimes gets translocated onto an X chromosome. When this happens, the child carries a genome that should be female (46, XX), but develops as a male. Adult men with a 46, XX karyotype and a translocated SRY gene are often identified due to infertility or hypogonadism (underdeveloped testes).

SHOX: The SHOX gene (Short Stature Homeobox) is located on the X and the Y chromosome. This gene is responsible for skeletal growth. While many genes are located only on the X chromosome, this gene is present in both the X and the Y chromosome, so that each gender receives two functional copies of the gene.

USP9Y: This gene (ubiquitin specific peptidase 9, Y-linked) is found on the Y chromosome, and is only present in males. This gene is involved in the production of healthy sperm, and infertile males sometimes have a mutation in this gene.

 The Y chromosome is the shortest chromosome in humans, and most of the Y chromosome is believed to be made of junk DNA. In the 1960s, Ohno proposed that the human Y chromosome is a profoundly degenerated X chromosome with very few genes on it encoding male-specific features and some began to speculate that the continued degradation of the Y chromosome might result in the extinction of the human male.

In order to address this question, it is helpful to know the origin of the Y chromosome. Surprisingly, the most primitive Y chromosome found so far was not found in any animal, but in the papaya.
   It is found, that male and hermaphrodite papayas contain an allele that is not found in female papayas. Severe recombination suppression and DNA sequence degeneration are observed in the regions around that allele. Although no heteromorphic chromosomes in papayas were found to be in proportion to the X and Y chromosomes in humans, the newly discovered gene shares many characteristics with male-specific region of the Y chromosome (MSY).

Is the Y Chromosome Necessary to Make a Man?

The Y chromosome is not necessary for the male phenotype. The SRY gene is required, however, and it is almost always located on the Y chromosome. In a few rare cases, the SRY gene has been translocated (moved) to the X chromosome by accident. In these cases, the genotype is 46, XX – this would normally indicate a female genotype. In the rare case of translocation of the SRY gene, however, a man can be 46, XX: these men are often fully masculinized, but are infertile.

It seems that the protein produced by the SRY gene binds to the DNA molecule in specific places, and causes it to bend sharply. It is believed that this change in the three dimensional geometric structure alters the action of a range of other genes. For instance, there are many factors affecting rate of growth, both genetic and environmental, but it is believed that it accounts for the average larger size of men compared to women.
Sometimes the SRY gene is missing from the Y chromosome, or doesn't activate. The fetus grows, is born, and lives as a little girl, and later as a woman, but her chromosomes are XY. Such people are, usually, clearly women to themselves and everyone else. The first premonition that something is wrong may be when menstruation doesn't begin. Occasionally, during meiosis a piece of a Y chromosome transfers to the X, and is carried on into the sperm. Thus the female embryo that results is XX, but develops as a male.

Until recently, the X and Y chromosomes were thought to have diverged around 300 million years ago. However, research published in 2010, and particularly research published in 2008 documenting the sequencing of the platypus genome, has suggested that the XY sex-determination system would not have been present more than 166 million years ago, at the split of the monotremes from other mammals. This reestimation 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 present on the autosomes of platypus and birds.

Y Chromosome Haplogroups

About once every 7,000 years, a mutation known as a single nucleotide polymorphism (SNP) occurs on the Y chromosome. The known rate of mutation has allowed scientists to trace migration routes of early humans out of Africa.

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. 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. Only the tips of the Y and X chromosomes recombine. The tips of the Y chromosome that could recombine with the X chromosome are referred to as the pseudoautosomal region. The rest of the Y chromosome is passed on to the next generation intact. It is because of this disregard for the rules that the Y chromosome is such a superb tool for investigating recent human evolution from a male perspective.
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. 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.
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.

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 in to 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. 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.

Disorders of the Y Chromosome

Klinefelter Syndrome: This syndrome is caused by the inheritance of more than one X chromosome alongside the Y chromosome. A man with Klinefelter Syndrome will have a genotype that is XXY, XXXY, or a mosaic of XY and XXY. This syndrome often causes sterility, have a higher than average risk of developing osteoporosis, diabetes, and autoimmune disorders. Men with Klinefelter Syndrome may have a high pitched voice and have much less body hair than a man with an XY karyotype. Some of the symptoms of Klinefelter Syndrome can be alleviated with a prescription of testosterone at puberty.
XYY Syndrome: Instead of having too many X chromosomes, men with XYY syndrome have an extra Y chromosome. Adults with this syndrome are taller than average (generally over six feet tall), but are otherwise typical in appearance. Adolescents with the syndrome are likely to be very lean, prone to severe acne, and may have difficulty with coordination. Individuals with XYY Syndrome have a higher level of testosterone than typical – the syndrome is likely under-diagnosed, as there are few symptoms to trigger testing.

Turner Syndrome: When There is No X or Y Chromosome

In some individuals, the 23rd set of chromosomes is missing one of the pair. Instead of being XY or XX, the karyotype reads as XO, because there is no second chromosome present. This is known as Turner Syndrome – people with Turner Syndrome are female, because genes located on the Y chromosome is necessary for male development. Girls with Turner Syndrome are shorter than average, and are infertile. Estrogen therapy is often given to girls with Turner Syndrome around the time of puberty.

The Disappearing Y Chromosome

All chromosomes are a matched set, save one: the Y chromosome has no identical partner. This is a negative when it comes to mutations – the other chromosomes have a back-up when an error (mutation) occurs. The identical, “back-up” chromosome gives the cell the needed information when one has an error. The Y chromosome does not have this protective mechanism, so when an error occurs, the gene essentially disappears. Over time, the errors have added up and more and more of the genes on the Y chromosome have been eliminated. Scientists theorize that the Y chromosome used to have as many genes as the X chromosome (approximately 1,000 genes), but it has dwindled down to an estimated 80 genes.
The Y chromosome is not doomed, however, as it has developed protective mechanisms to ensure its survival. This is quite good news, as the survival of the human species depends on its existence. Scientists recently discovered that the Y chromosome has been making mirror-image copies of its most important genes – a mechanism known as the Y chromosome palindrome. A palindrome is a word which is read the same forward and backward: “level” is a good example. The Y chromosome palindromes contain genetic information reading forward in the first half, and then the same information is repeated in reverse. Essentially, this means the most important genes on the Y chromosome do occur in tandem: instead of appearing on two separate chromosomes, however, the information is coded within a palindrome on the same chromosome.
Y chromosome palindromes mean that the Y chromosome is well-protected from demise, and will probably not shrink far beyond its current state.

Text taken from:
Huntington F. Willard


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