EVOLUTION OF MICROSATELLITES IN PRIMATE GENOMES: DEFINITION OF MICROSATELLITES, CAUSES OF VARIATION, AND THE MICROSATELLITE LIFE CYCLE
Open Access
- Author:
- Kelkar, Yogeshwar Dinkar
- Graduate Program:
- Integrative Biosciences
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- September 08, 2010
- Committee Members:
- Kateryna Dmytrivna Makova, Dissertation Advisor/Co-Advisor
Kateryna Dmytrivna Makova, Committee Chair/Co-Chair
Francesca Chiaromonte, Committee Member
Ross Cameron Hardison, Committee Member
Kristin Ann Eckert, Committee Member
Mark Shriver, Committee Member - Keywords:
- transposable elements
indel
mutability
microsatellite life cycle
microsatellites
primates
multiple regression analysis - Abstract:
- Microsatellites – simple repeats of short (1-6 bp motifs) - are ubiquitous in eukaryotic genomes, and are hotspots for insertion and deletion (indel) mutations. Due to their variable nature, microsatellites have been extensively used as genetic markers in population genetic and ecological studies. More than 40 neurological diseases in humans are caused by microsatellite instability. In spite of this, there is dearth in our understanding of their mutational mechanism and their birth/death in primate genomes. My dissertation focuses on the following key questions pertaining to the microsatellite life cycle (i.e., microsatellite birth, maturation and eventual loss from genome): 1) What qualifies a repeat to be classified as a microsatellite? 2) Which microsatellite-intrinsic and regional genomic features determine the observed genome wide variation in mutability of mature microsatellites? 3) What are the salient mutational mechanisms that cause microsatellite births and losses in primate genomes? To address these questions, the project was divided into three phases. First, we examined size polymorphism (as indicator of polymerase slippage) at repeat loci found in ten ENCODE regions that were re-sequenced in multiple individuals. In parallel, an in vitro mutagenesis system was established to determine indel frequencies and their dependence on repeat number. Using this combined approach we determined a threshold requirement of 9 repeats for [A/T]n, and of 5 repeats for [GT/AC]n to distinguish their slippage rates from background rate of slippage, thereby allowing them to be classified as micro satellites. In the second phase of the project, we used repeat number variations among human-chimpanzee microsatellite orthologs as suggestive of microsatellite mutability, and implemented a multiple regression approach to determine the predictors of regional variation of microsatellite mutability. We found that microsatellite-intrinsic features, such as repeat number, motif size and motif composition are the key determinants of this variation, and other regional genomic features contribute to this variation marginally. In the third phase of the project, we implemented a maximum parsimony approach to identify mutational steps leading to microsatellite births and deaths within a five primate phylogenetic tree. We found the overwhelming importance of substitutions in causing microsatellite births and deaths. This work also revealed how transposable elements in primate genomes act as important substrates for microsatellite birth-death activity. These results have furthered our understanding of the unique mutational processes taking place at microsatellite loci in primate genomes. They reveal a very complex life cycle of these simple repeats.