Date of Award

Fall 1996

Project Type

Dissertation

Program or Major

Genetics

Degree Name

Doctor of Philosophy

First Advisor

John J Collins

Abstract

Eukaryotic genomes are replete with transposable elements. The nematode C. elegans will be the first multicellular organism to have its genome completely sequenced. This sequence will allow identification of all the transposon and transposon-related sequences from a single genome. In anticipation of the complete genome sequence I have initiated a series of analyses of sequences from the C. elegans genome database that share significant similarity to known families of transposons. Several members of known transposon families were observed along with a plethora of sequences related to these known transposons. Cladistic analyses were used to describe the relationships among transposons and transposon families. These analyses suggest that transposons in C. elegans may be found in both autonomous and nonautonomous forms. The differences between related element families lies mostly in the length of the inverted repeats and the presence of open reading frames. Differences between sequences within an element family suggest several mechanisms for generating length variation in inverted repeats.

Characterization of the consequences of Tc1 insertion requires a means of detecting insertions. I describe reverse genetic methodology for identifying new transposon insertions. To study the regulation of transposon activity I focused on the tissue-specific and developmental regulation of Tc1. I identified sites that are frequent targets for Tc1 insertion. In the most dramatic example, insertion of Tc1 was detected at the same site in the unc-54 gene in nearly every animal screened. This site was previously shown to be a "hotspot" for germ-line insertion, although at a frequency several orders of magnitude less than the levels now detected. I believe these insertions are somatic events because they increase in frequency during development but are not transmitted to progeny based on both genetic and molecular evidence and because I detect them in animals lacking a germline. Additional sites in unc-54 and src-1, another C. elegans gene, were identified as frequent targets for insertion of Tc1; however, none are hit as frequently as the unc-54 "hotspot". Somatic insertion of Tc1 depends on genetic background and may be suppressed early in development.

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