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Mechanism of DNA Amplification -

The origin of repeated sequences with features as different as those of tandem arrays and interspersed repeats would seem likely to involve various sorts of sequence amplification events. And, indeed, several different types have been observed experimentally. Tandem arrays, especially those composed of rather simple sequences such as the satellite DNAs, may originate through a process of unequal crossover in which DNA exchange occurs between out of register chromatids during mitosis and meiosis. Within an existing array, an unequal crossover event will cause one of the resultant sister chromatids to contain more, and the other sister chromatid to correspondingly contain fewer copies of the repeating unit.

Thus unequal crossover can lead to both increase and decrease in copy number. Both increase and decrease have been observed to occur in the evolution of several well studied tandem arrays, such as those containing the genes for ribosomal RNA, and it may be reliably inferred that unequal crossover is an important source of evolutionary variation in most, if not all, tandemly repeated sequences.

Another way tandem arrays might be generated involves a circular extra chromosomal DNA molecule (such as might be created by intrachromosomal recombination between direct repeats on the same DNA strand) replicating as a rolling circle. This would lead to the production of long linear molecules made up of head to tail repeats of the parental sequence. If integration of the newly replicated DNA into a chromosome were to occur with sufficient frequency (which need not be very high), this type of amplification could also be a major evolutionary force creating tandem arrays.

Another mechanism, termed the "onion-skin model", was recently proposed. An attractive feature of this model is that it readily explains the widespread occurrence of the compound repeats that are a prominent feature of highly repeated plant DNA. If the original amplified unit consists of single copy DNA and two copies of an interspersed repeat sequence, the product will be a mixture of more highly repeated elements (the original repeats) and repeats of the formerly unique sequence between them. With several repeats in the original sequence, the recombinations required to "resolve" the structure could give rise to a bewildering array of different combinations of more or less repeated DNA.

Operation of the mechanisms described above might give rise to an interspersion of repeat units of differing copy number, but it would not disperse an individual family of repeat sequences over long distances or from one chromosome to another. However, repeat families are frequently dis­persed throughout the entire genome in just such a pattern. Using in situ hybridization of cloned DNA containing several different highly repeated sequence families from the rye genome, scientists have shown that copies of repeated sequences are represented on all the rye chromosomes

Similar results were obtained by hybridization to Southern blots of DNA from a series of wheat lines containing individual rye chromosomes. In the latter experiments it was also possible to show that, although family members were present on all chromosomes, some chromosomes contained size classes of repeated sequences not found on other chromosomes. In these cases it is logical to suggest that a particular variant. of the repeat or a combination of a repeat and unrelated DNA, has been amplified in a relatively recent secondary event.

Both the production and dispersal of many repeated sequences may also be explained by the activities of "transposable elements". Transposable elements are DNA sequences which, either alone or in combination with other helper elements, can replicate themselves independently and insert themselves at new sites in the genome. Several interspersed repeats in plants have been cloned and analyzed, such as terminal inverted repeats which are found in transposable elements. This observation, together with the presence of a large number of inverted repeats scattered throughout a large portion of the genome, suggests that transposable elements may account for a large portion of interspersed repetitive DNA.