CeRep25B forms chromosome-specific minisatellite arrays in Caenorhabditis elegans

With the completion of the Genome Sequencing Project, it is now possible to rapidly and accurately determine the frequency and position of a particula r repeat sequence in the Caenorhabditis elegans genome. Several repeat sequ ences with a variety of characteristics have been examined and with few exc eptions they show a near-random distribution throughout the genome. We char acterized several genes near the left end of Chromosome III in the C. elega ns genome, and found a 24-bp minisatellite repeat sequence present in the i ntrons of two unrelated genes. This prompted a search of the databank for o ther occurrences of this sequence. Multiple copy arrays of this repeat are all located on the same autosome and fall in two clusters: one near the lef t end, and one in the central region separated by similar to 10 Mb. There a re >200 copies of this repeat on the chromosome. This euchromatic repeat se quence seems unrelated to gene expression, is absent from homologous sites in a related species, is unstable in Escherichia coli, and is polymorphic b etween different wild isolates of C. elegans. Most CeRep25B units in the ar ray match the consensus sequence very well, suggesting that either this rep eat originated quite recently or its sequence is functionally constrained. Although chromosome-specific repeat sequences have been reported previously in many organisms, such sequences are usually structural and heterochromat ic (e.g., centromeric alpha-satellite) or on the mammalian sex chromosomes. This report describes the first confirmed instance from a whole genome seq uencing project of an autosomal euchromatic chromosome-specific minisatelli te repeat.