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Y chromosome

The Y chromosome is one of the two sex chromosomes in humans (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 material of DNA) and represents between 1.5 and 2 percent of the total DNA in cells. The chromosome may be used to trace parental lineage.

It is one of two sex chromosomes; it contains the genes that cause testis development, thus determining maleness.



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.

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 Y chromosome likely contains between 70 and 300 genes. Because only males have the Y chromosome, many of the genes on this chromosome are involved in male sexual determination and development.

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 chromosomes, 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 particularly 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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