Originally published as Genetics Published Articles Ahead of Print on June 18, 2008.

Genetics, Vol. 179, 1693-1704, July 2008, Copyright © 2008
doi:10.1534/genetics.108.087882

Comparative Analyses of Human Single- and Multilocus Tandem Repeats

Darren Ames1, Nick Murphy1, Tim Helentjaris, Nina Sun and Vicki Chandler2

BIO5 Institute and Department of Plant Sciences, University of Arizona, Tucson, Arizona 85719

2 Corresponding author: BIO5 Institute and Department of Plant Sciences, University of Arizona, Thomas W. Keating Bioresearch Bldg., 1657 E. Helen St., Tucson, AZ 85719.
E-mail: chandler{at}ag.arizona.edu

Using the compiled human genome sequence, we systematically cataloged all tandem repeats with periods between 20 and 2000 bp and defined two subsets whose consensus sequences were found at either single-locus tandem repeats (slTRs) or multilocus tandem repeats (mlTRs). Parameters compiled for these subsets provide insights into mechanisms underlying the creation and evolution of tandem repeats. Both subsets of tandem repeats are nonrandomly distributed in the genome, being found at higher frequency at many but not all chromosome ends and internal clusters of mlTRs were also observed. Despite the integral role of recombination in the biology of tandem repeats, recombination hotspots colocalized only with shorter microsatellites and not the longer repeats examined here. An increased frequency of slTRs was observed near imprinted genes, consistent with a functional role, while both slTRs and mlTRs were found more frequently near genes implicated in triplet expansion diseases, suggesting a general instability of these regions. Using our collated parameters, we identified 2230 slTRs as candidates for highly informative molecular markers.