Some cases of incomplete penetrance appear to be due to imprinting. In this phenomenon, expression of an allele is governed by whether it is derived from the mother or the father. Imprinted alleles are located on autosomes, but are "stamped" with the sex of the parent that contributed it. The chemical basis of the imprint is the addition of methyl (-CH3) groups to the allele's nucleotides, and the effect is thought to be to silence the allele so it is not expressed. For some genes the maternal allele is silenced, while for others the paternal allele is silenced. When a child inherits the two alleles, they retain these stamps, regardless of the sex of the child. However, when the child makes its own sperm or eggs, the child's own imprinting machinery stamps the alleles so that they correspond to the child's own sex. Therefore, a particular allele can be turned on or turned off as it is passed down through successive generations, from male to female and back again.

Imagine a dominant disease allele that is active when inherited from the mother, but is silenced when inherited from the father. Both the sons and daughters of the mother will develop symptoms of the disease. The daughter's children will also develop symptoms, while the son's children will not, despite having the same genotype. This is an example of incomplete pene-trance. Prader-Willi syndrome and Angelman syndrome are examples of disorders arising from imprinted genes.

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