Title page for ETD etd-03182005-105307


Type of Document Dissertation
Author Otieno, Anthony Canaan
Author's Email Address aotieno@lsu.edu
URN etd-03182005-105307
Title A Comprehensive Analysis of Human Pre-Ta LINE-1 and Ya-Lineage Alu Mobile Elements
Degree Doctor of Philosophy (Ph.D.)
Department Biological Sciences
Advisory Committee
Advisor Name Title
Mark Batzer Committee Chair
Anne Grove Committee Member
David Donze Committee Member
Patrick Dimario Committee Member
Gerald Myers Dean's Representative
Keywords
  • retrotransposon
  • LINE-1
  • alu
  • PCR
  • polymorphism
Date of Defense 2005-02-11
Availability unrestricted
Abstract
Long INterspersed Elements (LINEs or L1)and Short INterspersed Elements (SINEs) have played a critical role in shaping the human genomic landscape, making up about 33% of the human genomic mass. In this work, preTa, an L1 subfamily and the Ya-lineage of Alu SINEs were examined to determine their impact on the human genomic architecture and diversity. We analyzed 362 preTa L1 elements and 2318 Ya lineage Alu elements using computational methods and polymerase chain reaction (PCR) assays. PCR analysis on a geographically distinct panel of human populations indicated that 33 (14%) of preTa L1 elements and 313 (22%) of Ya-lineage Alu elements were polymorphic for insertion presence/absence. DNA sequence analysis of the preTa and the Ya-lineage subfamilies indicated an estimated average age of 2.34 and 2.27 million years respectively. This suggests that these elements began to amplify after the human lineage radiated from the non-human primates. None of the mobile elements analyzed were also located in orthologous non-human primate loci, supporting the fact that they are homoplasy free genetic characters. The continued amplification of mobile elements throughout evolutionary time and their variable insertion frequencies in diverse human populations make them robust tools for population genetics and comparative genomics.
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