Exploration of long and short repetitive sequence relationships in the sea urchin genome.

Francine C Eden,Eric H Davidson,Roy J Britten,Dale E Graham

doi:10.1093/nar/4.5.1553

Abstract

Long and short repetitive sequences of sea urchin DNA were prepared by reassociation of 2000 nucleotide long fragments to Cot 4 and digestion with the single strand specific nuclease S1. The S1 resistant duplexes were separated into long repetitive and short repetitive fractions on Agarose A50. The extent of shared sequences was studied by reassociating a labeled preparation of short repetitive DNA with an excess of unlabeled long repetitive DNA. Less than 10% of the long repetitive DNA preparation was able to reassociate with the short repetitive DNA. Thus the long and short repetitive elements appear to be principally independent sequence classes in sea urchin DNA. Precisely reassociating repetitive DNA was prepared by four successive steps of reassociation and thermal chromatography on hydroxyapatite. This fraction (3% of the genome) was reassociated by itself or with a great excess of total sea urchin DNA. The thermal stability of the products was identical in both cases (Tm=81 degrees C), indicating that precisely repeated sequences do not have many imprecise copies in sea urchin DNA.

Highlights

The DNA of the sea urchin Strongylocentrotus purpuratus exhibits short period intersersion of repetitive and nonrepetitive sequences
This paper describes new measurements of the sequence relationships between long and short repetitive sequences and between precisely and imprecisely repeated DNA sequences
Sea urchin DNA with a mode length of 2000 nucleotides was reassociated to Cot 4 and digested with the single strand specific nuclease S119, as described in Materials and Methods

Summary

Introduction

The DNA of the sea urchin Strongylocentrotus purpuratus exhibits short period intersersion of repetitive and nonrepetitive sequences. The labeled long and short repetitive DNA preparations were reassociated in the presence of a great excess of total DNA driver to display the repetition frequencies present. Each fraction was reassociated with at least a 1000-fold excess of unlabeled total DNA (450-550 ntp) in 0.12 M PB at 60°C or equivalent, and the reactions were assayed by hydroxyapatite chromatorhy at 600C in 0.12 M PB; (o) total sea urchin DNA driver; (A) long repetitive tracer; (o) short repetitive tracer.

Results

Conclusion