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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