Title page for ETD etd-11072006-091228


Type of Document Dissertation
Author Wang, Hui
URN etd-11072006-091228
Title SVA Elements: Hominid Specific Retrotransposons
Degree Doctor of Philosophy (Ph.D.)
Department Biological Sciences
Advisory Committee
Advisor Name Title
Mark A. Batzer Committee Chair
David Donze Committee Member
Joomyeong Kim Committee Member
Stephania Cormier Committee Member
Karin Peterson Dean's Representative
Keywords
  • gene duplication
  • transduction
  • genomic distribution
  • SVA
  • retrotransposon
Date of Defense 2006-11-01
Availability unrestricted
Abstract
SVA is a composite repetitive element named after its main components, SINE, VNTR and Alu. There are ~3000 SVA elements in the human genome. A genomic distribution analysis indicates that SVA elements are enriched in G+C-rich regions but have no preferences for inter- or intra-genic regions. A phylogenetic analysis of these elements resulted in the recovery of six subfamilies that were named SVA_A to SVA_F. The composition, age and genomic distribution of the different subfamilies have been examined. Subfamily age estimates indicate that the expansion of four SVA subfamilies (SVA_A, SVA_B, SVA_C and SVA_D) began before the divergence of human, chimpanzee and gorilla, while subfamilies SVA_E and SVA_F are restricted to the human lineage. Furthermore, I examined the amplification dynamics of SVA elements throughout the primate order and traced their origin back to the beginnings of hominid primate evolution, approximately 18 to 25 million years ago, which makes SVA elements the youngest family of retrotransposons in the primate order. Gene duplication is one of the most important mechanisms for creating new genes and generating genomic novelty. Retrotransposon-mediated sequence transduction (i.e. the process by which a retrotransposon carries flanking sequence during its own mobilization) has been proposed as a gene duplication mechanism. SVA elements are capable transducing 3 flanking sequence during retrotransposition. I examined all the full-length SVA elements in the human genome to assess the frequency and impact of SVA-mediated 3 sequence transduction. The results showed that ~53 kb of genomic sequence has been duplicated by 143 different SVA-mediated transduction events. In particular, I identified one group of SVA elements that has duplicated the entire AMAC gene three times in the human genome via SVA-mediated transduction events, which happened before the divergence of humans and African great apes. In addition to the original AMAC gene, the three transduced AMAC copies contain intact open reading frames (ORFs) in the human genome and at least two are actively transcribed in different human tissues. Thus, duplication of entire genes and creation of new gene families via retrotransposon-mediated sequence transduction represent an important mechanism by which mobile elements impact their host genomes.
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