Correction: Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation

AbstractMaintenance of genome stability is a key issue for cell fate that could be compromised by chromosome deletions and translocations caused by DNA double-strand breaks (DSBs). Thus development of precise and sensitive tools for DSBs labeling is of great importance for understanding mechanisms of DSB formation, their sensing and repair. Until now there has been no high resolution and specific DSB detection technique that would be applicable to any cells regardless of their size. Here, we present i-BLESS, a universal method for direct genome-wide DNA double-strand break labeling in cells immobilized in agarose beads. i-BLESS has three key advantages: it is the only unbiased method applicable to yeast, achieves a sensitivity of one break at a given position in 100,000 cells, and eliminates background noise while still allowing for fixation of samples. The method allows detection of ultra-rare breaks such as those forming spontaneously at G-quadruplexes.

Download Full-text

TOPOVIBL-REC114 interaction regulates meiotic DNA double-strand breaks

10.1101/2021.11.30.470517 ◽

2021 ◽

Author(s):

Alexandre Nore ◽

Ariadna B Juarez-Martinez ◽

Julie AJ Clement ◽

Christine Brun ◽

Bouboub Diagouraga ◽

...

Keyword(s):

Dna Cleavage ◽

Point Mutations ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

Catalytic Complex ◽

Strand Breaks ◽

Genome Wide ◽

Dna Cleavage Activity ◽

Meiotic Dsbs

Meiosis requires the formation of programmed DNA double strand breaks (DSBs), essential for fertility and for generating genetic diversity. In male and female meiotic cells, DSBs are induced by the catalytic activity of the TOPOVIL complex formed by SPO11 and TOPOVIBL. To ensure genomic integrity, DNA cleavage activity is tightly regulated, and several accessory factors (REC114, MEI4, IHO1, and MEI1) are needed for DSB formation in mice. How and when these proteins act is not understood. Here, we show that REC114 is a direct partner of TOPOVIBL, and identified their conserved interacting domains by structural analysis. We then analysed the role of this interaction by monitoring meiotic DSBs in female and male mice carrying point mutations in TOPOVIBL that decrease or disrupt its binding to REC114. In these mutants, DSB activity was strongly reduced genome-wide in oocytes, but only in sub-telomeric regions in spermatocytes. In addition, in mutant spermatocytes, DSB activity was delayed in autosomes. These results provide evidence that REC114 is a key member of the TOPOVIL catalytic complex, and that the REC114/TOPOVIBL interaction ensures the efficiency and timing of DSB activity by integrating specific chromosomal features.

Download Full-text

DNA Double-Strand Breaks Trigger Genome-Wide Sister-Chromatid Cohesion Through Eco1 (Ctf7)

Science ◽

10.1126/science.1140637 ◽

2007 ◽

Vol 317 (5835) ◽

pp. 245-248 ◽

Cited By ~ 219

Author(s):

E. Unal ◽

J. M. Heidinger-Pauli ◽

D. Koshland

Keyword(s):

Sister Chromatid ◽

Sister Chromatid Cohesion ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

Strand Breaks ◽

Genome Wide ◽

Chromatid Cohesion

Download Full-text

A global view of meiotic double-strand break end resection

Science ◽

10.1126/science.aak9704 ◽

2017 ◽

Vol 355 (6320) ◽

pp. 40-45 ◽

Cited By ~ 79

Author(s):

Eleni P. Mimitou ◽

Shintaro Yamada ◽

Scott Keeney

Keyword(s):

Meiotic Recombination ◽

Strand Break ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

Strand Breaks ◽

Naked Dna ◽

Global View ◽

Genome Wide ◽

End Resection

DNA double-strand breaks that initiate meiotic recombination are exonucleolytically processed. This 5′→3′ resection is a central, conserved feature of recombination but remains poorly understood. To address this lack, we mapped resection endpoints genome-wide at high resolution inSaccharomyces cerevisiae. Full-length resection requires Exo1 exonuclease and the DSB-responsive kinase Tel1, but not Sgs1 helicase. Tel1 also promotes efficient and timely resection initiation. Resection endpoints display pronounced heterogeneity between genomic loci that reflects a tendency for nucleosomes to block Exo1, yet Exo1 also appears to digest chromatin with high processivity and at rates similar to naked DNA in vitro. This paradox points to nucleosome destabilization or eviction as a defining feature of the meiotic resection landscape.

Download Full-text

Identification of regulators of poly-ADP-ribose polymerase (PARP) inhibitor response through complementary CRISPR knockout and activation screens

10.1101/871970 ◽

2019 ◽

Cited By ~ 1

Author(s):

Kristen E. Clements ◽

Anastasia Hale ◽

Nathanial J. Tolman ◽

Claudia M. Nicolae ◽

Anchal Sharma ◽

...

Keyword(s):

Histone Acetyltransferase ◽

Positive Response ◽

Parp Inhibitor ◽

Strand Break ◽

Double Strand Breaks ◽

Repair Pathway ◽

Genetic Determinants ◽

Strand Breaks ◽

Genome Wide ◽

End Resection

AbstractInhibitors of poly-ADP-ribose polymerase 1 (PARPi) are highly effective in killing cells deficient in the homologous recombination (HR) DNA repair pathway, such as those lacking BRCA2. In light of this, PARPi have been utilized in recent years to treat BRCA2-mutant tumors, with many patients deriving impressive clinical benefit. However, positive response to PARPi is not universal, even among patients with HR-deficient tumors. Here, we present the results of three genome-wide CRISPR knockout and activation screens which provide an unbiased look at genetic determinants of PARPi response in wildtype or BRCA2-knockout cells. Strikingly, we reveal that depletion of the histone acetyltransferase TIP60, a top hit from our screens, robustly reverses the PARPi sensitivity caused by BRCA2 deficiency. Mechanistically, we show that TIP60 depletion rewires double strand break repair in BRCA2-deficient cells by promoting 53BP1 binding to double strand breaks to suppress end resection. Our work provides a comprehensive set of putative biomarkers that serve to better understand and predict PARPi response, and identifies a novel pathway of PARPi resistance in BRCA2-deficient cells.

Download Full-text

END-seq: An Unbiased, High-Resolution, and Genome-Wide Approach to Map DNA Double-Strand Breaks and Resection in Human Cells

Homologous Recombination - Methods in Molecular Biology ◽

10.1007/978-1-0716-0644-5_2 ◽

2020 ◽

pp. 9-31

Author(s):

Nancy Wong ◽

Sam John ◽

André Nussenzweig ◽

Andrés Canela

Keyword(s):

High Resolution ◽

Human Cells ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

Strand Breaks ◽

Genome Wide

Download Full-text

Genome-Wide Redistribution of Meiotic Double-Strand Breaks in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.02063-06 ◽

2006 ◽

Vol 27 (5) ◽

pp. 1868-1880 ◽

Cited By ~ 63

Author(s):

Nicolas Robine ◽

Norio Uematsu ◽

Franck Amiot ◽

Xavier Gidrol ◽

Emmanuel Barillot ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Meiotic Recombination ◽

Binding Sites ◽

Chromosomal Region ◽

Double Strand Breaks ◽

Dna Binding Domain ◽

Dna Double Strand Breaks ◽

Strand Breaks ◽

Genome Wide ◽

Local Stimulation

ABSTRACT Meiotic recombination is initiated by the formation of programmed DNA double-strand breaks (DSBs) catalyzed by the Spo11 protein. DSBs are not randomly distributed along chromosomes. To better understand factors that control the distribution of DSBs in budding yeast, we have examined the genome-wide binding and cleavage properties of the Gal4 DNA binding domain (Gal4BD)-Spo11 fusion protein. We found that Gal4BD-Spo11 cleaves only a subset of its binding sites, indicating that the association of Spo11 with chromatin is not sufficient for DSB formation. In centromere-associated regions, the centromere itself prevents DSB cleavage by tethered Gal4BD-Spo11 since its displacement restores targeted DSB formation. In addition, we observed that new DSBs introduced by Gal4BD-Spo11 inhibit surrounding DSB formation over long distances (up to 60 kb), keeping constant the number of DSBs per chromosomal region. Together, these results demonstrate that the targeting of Spo11 to new chromosomal locations leads to both local stimulation and genome-wide redistribution of recombination initiation and that some chromosomal regions are inherently cold regardless of the presence of Spo11.

Download Full-text