Rye heterochromatin. I. Studies on clusters of the major repeating sequence and the identification of a new dispersed repetitive sequence element

Abstract

The structure of appoximately 10 kilobases of DNA originating from the subcloned DNA segments of five lambda clones from rye heterochromatin is described. The sequence data suggested that much of the variation between the 380 base pair (bp) units of the tandem arrays in hetercohromatin must have preceded the amplification events which gave rise to the arrays. Furthermore, evidence for recombination between the tandem arrays of the units (subsequent to the presumed amplification events) was obtained. A single 14-bp region which did not show any variation in sequence was found to be part of a dyad symmetry, characteristic for DNA-binding proteins. The analysis of a molecule which contained a junction between the heterochromatic "350" DNA sequence family and apparently nonheterochromatic DNA is also presented. This nonheterochromatic DNA contains a dispersed repetitive type of sequence ("5.3") which is found adjacent to a wide range of sequences as judged from genomic analyses, in situ hybridization studies and independent isolates of the sequence. The 5.3 sequence is dispersed throughout nonheterochromatic and most heterochromatic regions. However, some heterochromatic regions and the nucleolar organizing region appear not to contain the sequence or else have only very low amounts. The "5.3" element provides a novel probe for further analysis of the rye genome.Key words: rye, heterochromatin, amplification.