ORGANIZATIONAL AND FUNCTIONAL ANALYSIS OF THE INTERSPERSED REPETITIVE DNA SEQUENCES FROM THE NEMATODE CAENORHABDITIS ELEGANS

Abstract

The model system selected for this study is that of the free-living soil nematode Caenorhabditis elegans. The low complexity of the C. elegans genome provides the opportunity to study the organization, origins, and interrelationships of single repetitive families.;Members of three distinct, non-homologous C. elegans repeat families (CeRep) have been cloned and analyzed by DNA sequencing, electron microscopy, and cross-hybridization experiments. CeRep1, present in 8-10 copies per haploid genome, is organized with 450 bp terminal inverted repeats with variably sized separating loop regions (500 bp to 2.5 kb). Each of the loop regions contains a 500 bp conserved sequence found always adjacent to one of the terminal repeats. The repetitive units are approximately 75-80% conserved, however, the terminal inverted repeats of any particular unit show a much higher level of sequence conservation from 85-100%. Based on this finding and the fact that an alteration in sequence in one half of the inverted repeat will usually be echoed in the other half, it is proposed that a gene conversion mechanism is operating to maintain sequence homogeneity between the ends of any particular unit. No evidence has been found to indicate that members of this family are transposable. CeRep2 and CeRep3 are organized as 570 bp and 1.4 kb units present in about 15-18 and 60-100 copies per haploid genome, respectively. The elements are highly dispersed and are not well conserved at the sequence level. An approximately 25-30% sequence variation exists throughout both these families. With respect to the sequence of the CeRep3 element, it was found to possess sequences homologous to the yeast autonomously replicating sequences (ARS) and to yeast centromeric (CEN) regions. Members of this family were placed into yeast and tested for both functions. The results indicate that these sequences contribute a weak ARS function but do have the ability to stabilize normally unstable ARS plasmids both mitotically and meiotically. These results are discussed with respect to the repetitive nature of the sequences and the fact that the C. elegans genome is holocentric. The analysis of the repetitive elements of the C. elegans genome has been presented in order to supply additional data and partial answers to the questions concerning the role of interspersed repetitive DNA sequences in the eukaryotic genome. (Abstract shortened with permission of author.).