Distinct faces of the Ku heterodimer mediate DNA repair and telomeric functions

Ribes-Zamora, Albert; Mihalek, Ivana; Lichtarge, Olivier; Bertuch, Alison A.

doi:10.1038/nsmb1214

Cited by 90 publications

(129 citation statements)

References 49 publications

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“…Moreover telomere termini are also enriched in yKu70-yKu80, which also recruit Sir4 (Roy et al 2004;Ribes-Zamora et al 2007). Telomeric silencing can extend .10 kb , but strong silencing is confined to the first 1-2 kb (Rusche and Lynch 2009).…”

Section: Cis-acting Silencer Sequencesmentioning

confidence: 99%

Mating-Type Genes andMATSwitching inSaccharomyces cerevisiae

2012

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Mating type in Saccharomyces cerevisiae is determined by two nonhomologous alleles, MATa and MATa. These sequences encode regulators of the two different haploid mating types and of the diploids formed by their conjugation. Analysis of the MATa1, MATa1, and MATa2 alleles provided one of the earliest models of cell-type specification by transcriptional activators and repressors. Remarkably, homothallic yeast cells can switch their mating type as often as every generation by a highly choreographed, site-specific homologous recombination event that replaces one MAT allele with different DNA sequences encoding the opposite MAT allele. This replacement process involves the participation of two intact but unexpressed copies of mating-type information at the heterochromatic loci, HMLa and HMRa, which are located at opposite ends of the same chromosome-encoding MAT. The study of MAT switching has yielded important insights into the control of cell lineage, the silencing of gene expression, the formation of heterochromatin, and the regulation of accessibility of the donor sequences. Real-time analysis of MAT switching has provided the most detailed description of the molecular events that occur during the homologous recombinational repair of a programmed double-strand chromosome break. TABLE OF CONTENTS Abstract 33Introduction 34

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Section: Cis-acting Silencer Sequencesmentioning

confidence: 99%

Mating-Type Genes andMATSwitching inSaccharomyces cerevisiae

2012

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“…Ku forms an open, ringtype structure that can be threaded onto a dsDNA end [12]. One side of the ring cradles one face of the DNA while the other side is more open, presumably to allow other NHEJ factors to access the broken DNA end [13,14]. In vertebrates, Ku recruits DNA-PK CS to the sites of DNA damage during DNA DSB repair.…”

Section: Introductionmentioning

confidence: 99%

Mutations to Ku reveal differences in human somatic cell lines

2008

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NHEJ (non-homologous end joining) is the predominant mechanism for repairing DNA doublestranded breaks in human cells. One essential NHEJ factor is the Ku heterodimer, which is composed of Ku70 and Ku86. Here we have generated heterozygous loss-of-function mutations for each of these genes in two different human somatic cell lines, HCT116 and NALM-6 using gene targeting. Previous work had suggested that phenotypic differences might exist between the genes and/or between the cell lines. By providing a side-by-each comparison of the four cell lines, we demonstrate that there are indeed subtle differences between loss-of-function mutations for Ku70 versus Ku86, which is accentuated by whether the mutations were derived in the HCT116 or NALM-6 genetic background. Overall, however, the phenotypes of the four lines are quite similar and they provide a compelling argument for the hypothesis that Ku loss-of-function mutations in human somatic cells result in demonstrable haploinsufficiencies. Collectively, these studies demonstrate the importance of proper biallelic expression of these genes for NHEJ and telomere maintenance and they provide insights into why these genes are uniquely essential for primates.

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“…Some recurrent features of top-ranked ET ranks residues 27 are that: these top-ranked residues (in the 10th, 20th, 30th top-percentile rank) cluster non-randomly in protein structures 30 ; and these clusters overlap significantly with, and therefore reveal, functional sites. 31,67 These observations are highly reliable and can efficiently guide experiments, for example, to separate functions, 8,34 rewire specificity, 29 design peptide inhibitors, 63 or reveal the conformational trigger of an allosteric pathway and recode it to respond to a different ligand. 68 Beyond these varied experimental case studies, ETA function prediction further validated the basic premise that clusters of top-ranked ET residues point to functionally essential residues, but this time on a large scale.…”

Section: Discussionmentioning

confidence: 96%

“…34 The approach relies on the Evolutionary Trace, a method that integrates sequence, structure and function analyses into a single framework to characterize structural sites and functional residues. Some recurrent features of top-ranked ET ranks residues 27 are that: these top-ranked residues (in the 10th, 20th, 30th top-percentile rank) cluster non-randomly in protein structures 30 ; and these clusters overlap significantly with, and therefore reveal, functional sites.…”

Section: Discussionmentioning

confidence: 99%

“…In large-scale analyses, ET ranked amino acids by evolutionary importance 8,29 such that the top-ranked ones formed structural clusters [30][31][32] that overlapped and predicted functional sites. 33,34 Case studies further showed that bona fide ET-guided mutants could then block, separate and even swap functions in vitro and in vivo. [35][36][37][38] ET thus predicts key functional determinants and enables their rational perturbation.…”

Section: Introductionmentioning

confidence: 99%

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Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation

et al. 2010

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Protein functional sites control most biological processes and are important targets for drug design and protein engineering. To characterize them, the evolutionary trace (ET) ranks the relative importance of residues according to their evolutionary variations. Generally, top-ranked residues cluster spatially to define evolutionary hotspots that predict functional sites in structures. Here, various functions that measure the physical continuity of ET ranks among neighboring residues in the structure, or in the sequence, are shown to inform sequence selection and to improve functional site resolution. This is shown first, in 110 proteins, for which the overlap between top-ranked residues and actual functional sites rose by 8% in significance. Then, on a structural proteomic scale, optimized ET led to better 3D structure-function motifs (3D templates) and, in turn, to enzyme function prediction by the Evolutionary Trace Annotation (ETA) method with better sensitivity of (40% to 53%) and positive predictive value (93% to 94%). This suggests that the similarity of evolutionary importance among neighboring residues in the sequence and in the structure is a universal feature of protein evolution. In practice, this yields a tool for optimizing sequence selections for comparative analysis and, via ET, for better predictions of functional site and function. This should prove useful for the efficient mutational redesign of protein function and for pharmaceutical targeting.

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Distinct faces of the Ku heterodimer mediate DNA repair and telomeric functions

Cited by 90 publications

References 49 publications

Mating-Type Genes andMATSwitching inSaccharomyces cerevisiae

Mating-Type Genes andMATSwitching inSaccharomyces cerevisiae

Mutations to Ku reveal differences in human somatic cell lines

Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation

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