Orphons: dispersed genetic elements derived from tandem repetitive genes of eucaryotes

Abstract

We have discovered in animal cells a novel class of dispersed, solitary genetic elements derived from tandem multigene families. We refer to such displaced elements as orphons. Orphons arise from both protein-coding and non-protein-coding structural gene families, including those of histone and ribosomal genes. Southern transfer hybridization experiments, on DNA digested with enzymes that do not cut the major repeat unit of the family of genes of interest, reveal histone gene orphons in the sea urchin (Lytechinus pictus), ribosomal gene orphons in yeast (Saccharomyces cerevisiae) and ribosomal and H3 histone gene orphons in Drosophila melanogaster. There are more than 50 histone gene orphons in each sea urchin genome. Each of the five histone-coding regions has a number of orphons (5--20), in addition to the several hundred copies in the clusters that are not cut by Bam HI. Most such orphons appear to contain only one coding region. Nearly all sea urchin histone gene orphon loci are polymorphic in the population; no two individuals have the same sets of histone orphons for any coding region. An H3-coding orphon, pLpH30-1, was isolated from the genome of L. pictus. The H3 region homologous to the histone gene clusters is 1200 bases long and includes the complete early H3 gene and some surrounding histone DNA. THe orphon is flanked by at least 1.7 kb of 5' and 3 kb of 3' nonhistone DNA. These flanking sequences are each moderately repetitive in the genome and are not homologous to each other. The orphon differs less than 2% in base sequence from the analogous region of pLpC and only slightly more from pLpA (the major histone gene clones). DNA sequence analysis of the junctions between the H3 region and the immediate flanking nonhistone DNA reveals no evidence of repetitive or palindromic sequences.