Complicated organization of a single repeated DNA sequence in the chicken genome is revealed by cloning

The structural organization of a family of repeated DNA sequences in the chicken genome has been determined by hybridization of a cloned repeated DNA sequence to Southern blots of total DNA. The length of the cloned DNA fragment is 3600 nucleotide pairs. This fragment consists principally, if not entirely, of a single repeated DNA sequence occurring only once within the cloned fragment. In the chicken genome, the family of repeated DNA sequences homologous to the cloned sequence has a limited number of alternative forms. Some of the restriction fragments of total DNA to which the cloned sequence hybridizes correspond to those expected from the location of restriction endonuclease cleavage sites within the cloned sequence. There are also a limited number of other genomic restriction fragments, each present in multiple copies, to which the cloned sequence hybridizes but which do not relate in any obvious way to the length of the cloned sequence. These various restriction fragments differ from one another in that they appear to be present in unequal amounts in total DNA, and many of them do not contain the entire cloned sequence. This study provides some new information about the structure of repeated DNA sequences in the chicken genome. The copies of a repeated DNA sequence may differ from one another both by minor variations in nucleotide sequence (divergence) and in more substantial ways as would be expected to arise from processes such as insertion, deletion, and translocation. In addition to this description of a single cloned repeated DNA sequence from the chicken genome, this paper reports the cloning of more than 100 different restriction fragments of chicken DNA, each of which contains one or more repeated DNA sequences.