Superstructure of tandemly evolving array: Distribution of polymorphic repeats in the histone locus of Drosophila melanogaster

Date of Completion

January 2000

Keywords

Biology, Molecular|Biology, Genetics|Biology, Cell

Degree

Ph.D.

Abstract

Tandemly repeated gene families; are a common feature of eukaryotlc genomes. However, tandemly repetitive sequences represent a facet of genome evolution that remains a mystery. These sequences undergo a process known as concerted evolution, which is the nonindependent evolution of repetitive DNA sequences resulting in a high sequence similarity of repeating units. Although tandem repeats are now being recognized as essential components in chromosome structure and function, it has often been considered sufficient to know the consensus sequence and copy number of such repeats. However, information on polymorphic or unusual repeat types that may seem insignificant in a functional gene analysis becomes vital to the understanding of genome organization and evolutionary processes. ^ In this work the combined approaches of genome and haplatype analyses were used to characterize the histone locus of Drosophila melanogaster . The capture of an entire array within P1 clones allowed us to generate sub-clones of linked repeats and non-repeat sequences. Three distinct regions within each histone repeat were used to generate haplotypes for hundreds of subclones. Distribution of haplotypes with respect to each other, to array superstructure, and to genomic location was determined. We found that, while there is an inverse correlation between distance and repeat similarity, there is also a cline of variability, with the most haplotypes appearing at the distal end of the locus and the fewest at the proximal end. It was also found that proximity to non-repeat sequences did not significantly increase variability. Non-histone sequences were shown to contain direct and indirect evidence of mobile elements. Finally, it was confirmed that there are distinct functional groups within this complex repetitive locus. ^

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