Article

Specific pathways prevent duplication-mediated genome rearrangements

Ludwig Institute for Cancer Research, Department of Medicine, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0669, USA.
Nature (Impact Factor: 41.46). 08/2009; 460(7258):984-9. DOI: 10.1038/nature08217
Source: PubMed

ABSTRACT

We have investigated the ability of different regions of the left arm of Saccharomyces cerevisiae chromosome V to participate in the formation of gross chromosomal rearrangements (GCRs). We found that the 4.2-kilobase HXT13-DSF1 region sharing divergent homology with chromosomes IV, X and XIV, similar to mammalian segmental duplications, was 'at risk' for participating in duplication-mediated GCRs generated by homologous recombination. Numerous genes and pathways, including SGS1, TOP3, RMI1, SRS2, RAD6, SLX1, SLX4, SLX5, MSH2, MSH6, RAD10 and the DNA replication stress checkpoint requiring MRC1 and TOF1, were highly specific for suppressing these GCRs compared to GCRs mediated by single-copy sequences. These results indicate that the mechanisms for formation and suppression of rearrangements occurring in regions containing at-risk sequences differ from those occurring in regions of single-copy sequence. This explains how extensive genome instability is prevented in eukaryotic cells whose genomes contain numerous divergent repeated sequences.

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    • "Three classes of topoisomerase enzymes are conserved between mammals and yeast (Wang, 2002). In S. cerevisiae, the type IA, IB, and II topoisomerases are encoded by the TOP3, TOP1, and TOP2 genes, respectively, and have multiple and overlapping roles in maintaining genome integrity during transcription , DNA replication, and DNA repair (Allen-Soltero et al., 2014;Bailis et al., 1992;Bennett et al., 2000;Brill and Sternglanz, 1988;El Hage et al., 2010;Fasching et al., 2015;Putnam et al., 2009;Yadav et al., 2014). In this study, we find that the Top2 enzyme is essential for preventing GCRs at converging promoters as the rate significantly increases in a top2-1 mutant. "
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    • "Slx8 shows an E3 ubiquitin ligase activity and interacts with an E2 ubiquitin conjugating enzyme Ubc4, while Slx5 binds to polysumoylated substrates via its multiple SIMs [11] [12]. Strains lacking SLX5/8 show many features of genomic instability, such as slow growth, increased sensitivity to genotoxins, gross chromosomal rearrangements, increased rates of chromosome loss and recombination [16] [17] [18] [19] [20] [21]. Consequently, the Slx5/8 STUbL is recruited to the sites of replication stress [18] and DNA double strand breaks (DSBs) [21], mediating relocation of irreparable DSBs to the nuclear pore [19]. "
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    • "Remarkably , deletion of SLX5 and SLX8 also cause increased rates of duplication - mediated rearrangements ( Table 1 , Putnam et al . , 2009 ) , despite the fact that deletion of SLX5 causes an increase in the sumoylation of Mms21 - targets . Moreover , the deletion of SIZ2 , which also increases the sumoylation of Mms21 - targets , causes a greater defect in suppressing duplication - mediated rearrangements alone and in combination with esc2D , slx5D , mms21 - 11 , and mms2"
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    ABSTRACT: Author Summary The human genome contains many “at-risk” sequences that are prone to mutations, including diverse repeated sequences, segmental duplications and regions of copy number variations. Such repetitive sequence elements can cause genome rearrangements through non-allelic homologous recombination (NAHR) and many human diseases are caused by chromosomal rearrangements mediated by NAHR. Here we discovered that Mms21 dependent sumoylation has a major role in suppressing duplication-mediated GCRs. In addition, we showed that mutations of additional genes in sumoylation pathway cause the highest GCR defect known to date, demonstrating a critical role of sumoylation pathway in preventing duplication-mediated GCRs. We further developed a new quantitative proteomics technology to measure sumoylation levels of individual sumoylated proteins on a proteome-wide scale and applied this approach to uncover distinct and overlapping activities of SUMO ligases for substrate sumoylation. We further established the roles of Esc2 and Slx5 in regulating the SUMO proteome. Taken together these findings suggest a model in which a fine balance of Mms21 activity towards its substrates is critical for the suppression of chromosomal rearrangements. Our findings thus have important implications for cancer genetics as well as new insights into the regulation and substrate specificity of protein sumoylation enzymes.
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