The Alu Ya and Yb-lineages are distinct groups of Short INterspersed Elements (SINEs) found exclusively in primates. These lineages are comprised of several distinct subfamilies, which contain elements that are evolutionarily-related because they share common diagnostic mutations. Some of these Alu subfamilies are still actively mobilizing in the human genome. We have recovered 4333 Ya and Yb-lineage elements that reside in the human genome draft sequence and focused our analyses on the 4051 autosomal Alu elements. A total of 2672 autosomal loci were subjected to polymerase chain reaction (PCR)-based assays that allow analysis of individual elements for insertion presence and absence. The polymorphism rate for the insertion presence/absence on the human autosomes was 22% and 20% for the Ya and Yb-lineages, respectively. Less than 0.5% (12/2672) of the loci analyzed by PCR displayed positive results for insertions in the orthologous loci of various non-human primate genomes. DNA sequence analysis of these inserts showed that the non-human primate orthologous loci contained older, pre-existing Y, Sc, Sg, Sq or Sx Alu subfamily elements. These PCR results were the result of various evolutionary processes within the human lineage. This is the largest analysis of human Alu mobile element lineages to date. The size, evolutionary age and variable allele insertion frequencies of the Alu Ya and Yb-lineage subfamilies, makes these elements useful tools for human population genetics, human identification and primate comparative genomics.
| Identifer | oai:union.ndltd.org:LSU/oai:etd.lsu.edu:etd-03042005-123430 |
| Date | 08 March 2005 |
| Creators | Carter, Anthony Bronson |
| Contributors | Joseph Siebenaller, John Fleeger, Craig Hart, Arthur Penn, Mark Batzer |
| Publisher | LSU |
| Source Sets | Louisiana State University |
| Language | English |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | http://etd.lsu.edu/docs/available/etd-03042005-123430/ |
| Rights | unrestricted, I hereby certify that, if appropriate, I have obtained and attached herein a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to LSU or its agents the non-exclusive license to archive and make accessible, under the conditions specified below and in appropriate University policies, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report. |
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