Title page for ETD etd-0403103-161754


Type of Document Dissertation
Author Vincent, Bethaney June
URN etd-0403103-161754
Title Following the LINEs (Long INterspersed Elements): Human Specific L1 Elements and Their Orthologous Loci in Non-Human Primates
Degree Doctor of Philosophy (Ph.D.)
Department Biological Sciences
Advisory Committee
Advisor Name Title
Mark A. Batzer Committee Chair
David D. Pollock Committee Member
David Donze Committee Member
Jacqueline Stephens Committee Member
Mark S. Hafner Committee Member
Kathy L. O'Reilly Dean's Representative
Keywords
  • parallel insertions
  • insertion polymorphism
  • homoplasy free
  • mobile element
Date of Defense 2003-04-02
Availability unrestricted
Abstract
The L1 Ta subfamily of Long INterspersed Elements (LINEs) consists exclusively of human-specific L1 elements with a copy number of ~520 in the human genome. Four hundred sixty-eight L1 Ta elements were extracted from the draft human genomic sequence and screened by polymerase chain reaction (PCR) assays to determine their phylogenetic origin and to determine their contribution to human genomic diversity. PCR analysis indicated that 45% of the L1 Ta elements screened are polymorphic for insertion presence or absence. Sequence analysis of the L1 Ta elements produced definitive evidence of 3’transduction, gene conversion involving an older pre-existing L1 element, as well as several potential retrotransposition competent elements. The average age of the L1 Ta subfamily was estimated at 1.99 million years, indicating the subfamily’s expansion subsequent to the divergence of humans from African apes.

PCR based screening in non-human primate genomes of the orthologous sites for 249 human L1 Ta elements resulted in the recovery of various types of sequence variants for ~12% of these loci. Sequence analysis was employed to capture the nature of the observed variation. Half of the orthologous loci differed from the predicted sizes due to localized sequence variants that occurred as a result of common mutational processes in ancestral sequences, often including regions containing simple sequence repeats. Additional sequence variation included genomic deletions that occurred upon L1 insertion, as well as successive mobile element insertions that accumulated within a single locus over evolutionary time. We estimate the overall frequency of parallel independent insertion events at L1 insertion sites in seven different primate species to be very low (0.52%). In addition, no cases of insertion site homoplasy involved the integration of a second L1 element at any of the loci, but rather largely involved secondary insertions of Alu elements. No independent mobile element insertion events were found at orthologous loci in the human and chimpanzee genomes. Therefore, L1 insertion polymorphisms appear to be essentially homoplasy free characters well-suited for the study of population genetics and phylogenetic relationships within closely related species.

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