RECOMBINATION AND DNA DIVERGENCE

Environmental Health Sciences

Investigators

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Abstract

Summary of Work: Interspersed repetitive sequences are an important class of at-risk motifs (ARMs) that can lead to human genome instability. Using the yeast Saccharomyces cerevisiae, we are investigating mechanisms of genomic instability caused by human ARMS. The one million Alu elements in the human genome are a major class of repetitive DNA, where the average Alu homology is 85% and Alus frequently appear as inverted repeats (IRs). We showed in yeast and mouse cells that IRs can induce recombination, suggesting that they are sources of rearrangements. We therefore determined if inverted Alu repeats (which are ~300 bp) are contributors to genomic change in humans. We developed a yeast-based recombination system to address the role of sequence divergence, distance between repeats and genetic background on the ability of an inverted pair of Alu repeats to induce genetic instability. We found that inverted Alu repeats which are more than 85% identical and separated by < 20 bp are highly efficient at stimulating mitotic recombination. The instability of diverged inverted Alus is not enhanced in msh2, msh3, msh6, pms1 or mlh1 mutants suggesting that if mismatches arise in secondary structures (i.e., intrastrand pairing), they are not processed by mismatch repair system. In a screen for mutants that increase the recombinagenic effect of inverted repeats, we found that rad27, pol3-t and mms19 mutants could greatly increase the stimulation of diverged IRs that were distantly spaced. Initial studies suggest that the instability is due to double-strand breaks and the genetic controls are being examined. Based on the yeast results, we did a computational analysis of the human genome and developed a website (Judy Stenger) for the Alu analysis (http://dir.niehs.nih.gov /ALU). As predicted from yeast, we found that closely spaced, highly homologous inverted Alus in contrast to direct Alu repeats are rare in human genome. Based on parameters for unstable inverted Alus identified in yeast, loci were identified in the human genome that might have potential for rearrangements in normal or mutant cells.