Y chromosome

From Academic Kids

The Y chromosome is one of the two sex chromosomes in humans and most other mammals (the other is the X chromosome). The sex chromosomes are one of the 23 pairs of human chromosomes. The Y chromosome spans about 50 million base pairs (the building blocks of DNA) and represents between 0.5 and 1 percent of the total DNA in cells. The chromosome may be used to trace sexes have unpaired X chromosomess; in the other, both females and males have XX.



Each person normally has one pair of sex chromosomes in each cell. The Y chromosome is present in males, who have one X and one Y chromosome, while females have two X chromosomes. Because only males have the Y chromosome, many of the genes on this chromosome are involved in male sexual determination and development. The most important of them is a SRY gene, which seems to determine gender for primates. (Other mammals may use different gene.)

Identifying genes on each chromosome is an active area of genetic research. Because researchers use different approaches to predict the number of genes on each chromosome, the estimated number of genes varies. The human Y chromosome likely contains between 70 and 300 genes versus more than 1000 genes for X chromosome.

Human Y chromosome is unable to recombinate with X chromosome, except for small pieces on the ends, which are about 5% of their length. About 56 of the Y chromosome genes are in this area, i. e. are common between the two sex chromosomes.


Many cold-blooded 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.

X and Y chromosome diverged about 350 million years ago, when some reptile developed a gene which makes all its owners to be males. The chromosome with this gene became Y chromosome, and similar chromosome without it became X chromosome. So initially, X and Y chromosomes were almost the same. Genes which were beneficial for males and harmful for females (male genes) either moved into Y chromosome or developed in it. This was beneficial for both sexes.

However, recombination between X and Y chromosomes was harmful because it provided males without some male genes or females with some male genes. As a result, male genes assembled around the sex determining gene in order to make this less probable. Later, Y chromosome changed in such a way that the areas around the sex determining gene completely lost their ability to recombine with X chromosome.

With time, the larger and larger areas lost ability to recombine with the X chromosome. However, without recombination it is hard to get rid of harmful mutations. Therefore, harmful mutations increasingly damaged male genes until some stopped functioning and became genetic junk. The useless genes were then removed from Y chromosome.

As a result of this process, for humans 95% of Y chromosome is unable to recombine, and Y chromosome contains only 70 to 300 working genes versus more than 1000 for X chromosome. For some other animals, the degradation of Y chromosome is even more severe. For example, the Y chromosome in kangaroos contains only the SRY gene.

For humans and some other primates, the Y chromosome is able to "recombine" with itself (see below). This process, called gene conversion, may slow down the process of degradation.

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

  1. The gene is connected to X chromosome or some autosome, making it the new Y chromosome. The whole process starts again. This happened with two species of rodents.
  2. Part of some autosome is connected to both X and Y chromosome. This happened with one specie of drosophila.

Contrary to a popular belief, SRY gene cannot be destroyed in the way to extinct all males or all species. This is because any mutation which prevents SRY from functioning would remove the specie from genetic pool of males. Indeed, kangaroos who diverged from humans 130 million years ago, still have almost the same SRY as humans, even if all other genes of kangaroo's Y-chromosome have been destroyed.

Chromosomal conditions related to chromosome Y

The following conditions are caused by changes in the structure or number of copies of chromosome Y.

Klinefelter syndrome is caused by the presence of one or more extra copies of the X chromosome in the body's cells. Most males with Klinefelter syndrome have one extra copy of the X chromosome in each cell (47,XXY). Variants of the syndrome can involve more than one extra sex chromosome. In a small percentage of cases, males with variant Klinefelter syndrome have an extra copy of both the X and Y chromosomes, for a total of two X chromosomes and two Y chromosomes (48,XXYY) in each cell. The additional chromosomes disrupt normal sexual development.

47,XYY syndrome is caused by the presence of a single extra copy of the Y chromosome in each of a male's cells. Males with 47,XYY syndrome have one X chromosome and two Y chromosomes, for a total of 47 chromosomes per cell. Researchers are not yet certain why an extra copy of the Y chromosome is associated with tall stature and learning problems in some boys and men.

Other chromosomal conditions exist as well. Such conditions often affect sex determination (whether a person has the sexual characteristics of a male or a female), sexual development, and the ability to have children (fertility). The signs and symptoms of these conditions vary widely and range from mild to severe. They can be caused by missing or extra copies of the sex chromosomes or by structural changes in the chromosomes.

Rarely, males may have more than one extra copy of the Y chromosome in every cell (polysomy Y). The extra genetic material in these cases can lead to skeletal abnormalities, decreased IQ, and delayed development, but the features of these conditions are variable.

Repair of the Y chromosome

Chromosomes have robust and accurate repair mechanisms. Over time random mistakes - mutations - occur throughout all chromosomes, and the existence of some high-accuracy repair mechanism is known to be necessary for the survival of the chromosome, and thus the species carrying the chromosome.

The primary repair mechanism is dependent upon the fact that all people receive two sets of each chromosome, one from their mother and one from their father. Over time damage occurs, yet at the same time, chromosome pairs swap damaged genes out and replace them with a copy of undamaged genes. Gene sequences on chromosomes are fixed by following the template on the homologous chromosome. This repair technique is called recombination, and repairs a great many errors. Errors not caught by this technique are weeded out over time through natural selection. Until recently such error-correcting mechanisms were known for all chromosomes in humans, with the exception of the Y chromosome.

While females have two X chromosomes, males only have one Y chromosome (and one X chromosome.) Without a homologous chromosome, the Y chromosome cannot utilize this repair mechanism. It is believed that when the sex chromosomes first evolved there was effectively only one type. Over time this diverged into the X and the Y chromosomes, each having roughly 1,000 protein-coding genes. As they diverged over time, the Y chromosome became significantly different from the X chromosome so that it could not swap genes. As such, without a then-extant repair mechanism, errors and deletions built up in the Y chromosome over time. Over time many of the Y chromosome's genes were damaged and then lost.

Since the Y chromosome did not have the same error-correcting machinery that all the other chromosomes have, this gave rise to widespread speculation that no error-correcting machinery existed within this chromosome at all. Without any such machinery, random errors in copying would logically and inevitably cause the destruction and disapperance of the Y chromosome in all animals. Indeed, over time it appears that the Y chromosome has indeed lost many of its original DNA material, and has become much smaller.

If this damage and loss were to continue unabated, this would lead to the disappearance of all males in any species, including humans. As a result, the only species that would survive in the long term would be those species that naturally evolved a female-only method of reproduction. However, this line of reasoning was based on the sole assumption that lack of knowledge about Y chromosome repair meant that no possible repair mechanism could exist. This assumption was shown to be in serious error in 2003.

All other chromosomes occur in pairs. They preserve genetic integrity by exchanging information with matching genes on the homologous chromosome, a process called "crossing over." But the Y chromosome lacks that option, being the only chromosome that is unpaired. What was discovered in 2003 was that the Y chromosome exchanges genes between the two copies of repeated sequences that lie near to each other as mirror images. This phenomenon is called gene conversion. It is the non-reciprocal transfer of genetic information from one DNA molecule to another. It has been previously observed on a small scale over long evolutionary timescales between repeated sequences on the same chromosome, but not at the dramatic frequency apparently employed by the Y chromosome.

A research team, led by David C. Page, M.D., a Howard Hughes Medical Institute investigator at the Whitehead Institute for Biomedical Research in Cambridge, Mass.; Richard K. Wilson, Ph.D., director of the Genome Sequencing Center at Washington University School of Medicine in St. Louis; and Robert H. Waterston, M.D., Ph.D., formerly of Washington University's sequencing center and now at the University of Washington, Seattle, discovered that many of the sequences of chemical units -- called bases or base pairs -- that carry genetic information on the Y chromosome are arranged as palindromes. Palindromes are phrases or sentences that read the same backward or forward, such as "Madam, I'm Adam."

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 percent identical. The extensive use of gene conversion appears to 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.

Findings were confirmed by comparing similar regions of the Y chromosome in humans to the Y chromosomes of chimpanzees, bonobos (the pygmy chimpanzee) 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.

Y chromosome in 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 sons.

see also: Y-chromosomal_Adam


  • Cordum, 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.

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