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Secondary structure forming sequences drive SD-MMEJ repair of DNA double-strand breaks

Published on Dec 15, 2017in Nucleic Acids Research11.15
· DOI :10.1093/nar/gkx1056
Varandt Y. Khodaverdian2
Estimated H-index: 2
(Tufts University),
Terrence Hanscom1
Estimated H-index: 1
(Tufts University)
+ 5 AuthorsMitch McVey17
Estimated H-index: 17
(Tufts University)
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  • References (65)
  • Citations (6)
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References65
Newest
Published on Dec 1, 2017in Nature Communications11.88
Alexander Zelensky4
Estimated H-index: 4
(EUR: Erasmus University Rotterdam),
Joost Schimmel1
Estimated H-index: 1
(LEI: Leiden University)
+ 2 AuthorsMarcel Tijsterman30
Estimated H-index: 30
(LEI: Leiden University)
Off-target or random integration of exogenous DNA hampers precise genomic engineering and presents a safety risk in clinical gene therapy strategies. Genetic definition of random integration has been lacking for decades. Here, we show that the A-family DNA polymerase θ (Pol θ) promotes random integration, while canonical non-homologous DNA end joining plays a secondary role; cells double deficient for polymerase θ and canonical non-homologous DNA end joining are devoid of any integration events,...
Published on Dec 1, 2017in Nature Communications11.88
Shinta Saito4
Estimated H-index: 4
,
Ryo Maeda4
Estimated H-index: 4
,
Noritaka Adachi29
Estimated H-index: 29
Homologous recombination mediated gene targeting is highly inefficient in human cells due to random integration events, Here the authors show that dual repression of polymerase θ and DNA ligase IV eliminate random integration events.
Published on Mar 1, 2017in BioEssays4.40
Stuart L. Rulten18
Estimated H-index: 18
(University of Sussex),
Gabrielle J. Grundy6
Estimated H-index: 6
(University of Sussex)
Non-homologous end-joining (NHEJ) is the dominant means of repairing chromosomal DNA double strand breaks (DSBs), and is essential in human cells. Fifteen or more proteins can be involved in the detection, signalling, synapsis, end-processing and ligation events required to repair a DSB, and must be assembled in the confined space around the DNA ends. We review here a number of interaction points between the core NHEJ components (Ku70, Ku80, DNA-PKcs, XRCC4 and Ligase IV) and accessory factors s...
Published on Jan 1, 2017in Gene2.64
Vijai Singh15
Estimated H-index: 15
(Université Paris-Saclay),
Darren Braddick2
Estimated H-index: 2
(Université Paris-Saclay),
Pawan K. Dhar3
Estimated H-index: 3
(JNU: Jawaharlal Nehru University)
Abstract CRISPR-Cas9 is an RNA-mediated adaptive immune system that protects bacteria and archaea from viruses or plasmids. Herein we discuss the recent development of CRISPR-Cas9 into a key technology for genome editing, targeting, and regulation in a wide range of organisms and cell types. It requires a custom designed single guide-RNA (sgRNA), a Cas9 endonuclease, and PAM sequences in the target region. The sgRNA-Cas9 complex binds to its target and creates a double-strand break (DSB) that ca...
Published on Dec 1, 2016in Plant Methods3.17
Simon Schiml7
Estimated H-index: 7
(KIT: Karlsruhe Institute of Technology),
Holger Puchta48
Estimated H-index: 48
(KIT: Karlsruhe Institute of Technology)
The precise manipulation of plant genomes relies on the induction of DNA double-strand breaks by site-specific nucleases to initiate DNA repair reactions that are either based on non-homologous end joining (NHEJ) or homologous recombination (HR). Recently, the CRISPR/Cas system emerged as the most important tool for genome engineering due to its simple structure and its applicability to a wide range of organisms. Here, we review the current status of its various applications in plants, where it ...
Published on Oct 18, 2016in PLOS Genetics5.22
Robin van Schendel9
Estimated H-index: 9
(LUMC: Leiden University Medical Center),
Jane van Heteren3
Estimated H-index: 3
(LUMC: Leiden University Medical Center)
+ 1 AuthorsMarcel Tijsterman30
Estimated H-index: 30
(LUMC: Leiden University Medical Center)
For more than half a century, genotoxic agents have been used to induce mutations in the genome of model organisms to establish genotype-phenotype relationships. While inaccurate replication across damaged bases can explain the formation of single nucleotide variants, it remained unknown how DNA damage induces more severe genomic alterations. Here, we demonstrate for two of the most widely used mutagens, i.e. ethyl methanesulfonate (EMS) and photo-activated trimethylpsoralen (UV/TMP), that delet...
Published on Oct 1, 2016in Biochemistry and Cell Biology2.01
Charlene H. Emerson1
Estimated H-index: 1
,
Alison A. Bertuch22
Estimated H-index: 22
DNA double strand breaks (DSBs) are dangerous sources of genome instability and must be repaired by the cell. Nonhomologous end-joining (NHEJ) is an evolutionarily conserved pathway to repair DSBs by direct ligation of the ends, with no requirement for a homologous template. While NHEJ is the primary DSB repair pathway in mammalian cells, conservation of the core NHEJ factors throughout eukaryotes makes the pathway attractive for study in model organisms. The budding yeast, Saccharomyces cerevis...
Published on Sep 21, 2016in Genes3.33
Samuel J. Black1
Estimated H-index: 1
,
Ekaterina Kashkina7
Estimated H-index: 7
+ 1 AuthorsRichard T. Pomerantz14
Estimated H-index: 14
The gene encoding DNA polymerase θ (Polθ) was discovered over ten years ago as having a role in suppressing genome instability in mammalian cells. Studies have now clearly documented an essential function for this unique A-family polymerase in the double-strand break (DSB) repair pathway alternative end-joining (alt-EJ), also known as microhomology-mediated end-joining (MMEJ), in metazoans. Biochemical and cellular studies show that Polθ exhibits a unique ability to perform alt-EJ and during thi...
Published on Aug 1, 2016in Molecular Cell14.55
Megan Van Overbeek1
Estimated H-index: 1
(University of California, Berkeley),
Daniel Capurso2
Estimated H-index: 2
(University of California, Berkeley)
+ 11 AuthorsBastien Vidal2
Estimated H-index: 2
(University of California, Berkeley)
Summary The repair outcomes at site-specific DNA double-strand breaks (DSBs) generated by the RNA-guided DNA endonuclease Cas9 determine how gene function is altered. Despite the widespread adoption of CRISPR-Cas9 technology to induce DSBs for genome engineering, the resulting repair products have not been examined in depth. Here, the DNA repair profiles of 223 sites in the human genome demonstrate that the pattern of DNA repair following Cas9 cutting at each site is nonrandom and consistent acr...
Published on Aug 1, 2016in Molecular Cell14.55
David W. Wyatt4
Estimated H-index: 4
(UNC: University of North Carolina at Chapel Hill),
Wanjuan Feng2
Estimated H-index: 2
(UNC: University of North Carolina at Chapel Hill)
+ 6 AuthorsDale A. Ramsden34
Estimated H-index: 34
(UNC: University of North Carolina at Chapel Hill)
Summary DNA polymerase theta (Pol θ)-mediated end joining (TMEJ) has been implicated in the repair of chromosome breaks, but its cellular mechanism and role relative to canonical repair pathways are poorly understood. We show that it accounts for most repairs associated with microhomologies and is made efficient by coupling a microhomology search to removal of non-homologous tails and microhomology-primed synthesis across broken ends. In contrast to non-homologous end joining (NHEJ), TMEJ effici...
Cited By6
Newest
Published on 2019in DNA Repair3.71
Sandra Bosshard2
Estimated H-index: 2
(UNIL: University of Lausanne),
Pierre-Olivier Duroy (UNIL: University of Lausanne), Nicolas Mermod30
Estimated H-index: 30
(UNIL: University of Lausanne)
Abstract CRISPR technologies greatly foster genome editing in mammalian cells through site-directed DNA double strand breaks (DSBs). However, precise editing outcomes, as mediated by homologous recombination (HR) repair, are typically infrequent and outnumbered by undesired genome alterations. By using knockdown and overexpression studies in Chinese hamster ovary (CHO) cells as well as characterizing repaired DNA junctions, we found that efficient HR-mediated genome editing depends on alternativ...
Published on Mar 18, 2019in Nucleic Acids Research11.15
Kate Liddiard9
Estimated H-index: 9
(Cardiff University),
Brian L. Ruis11
Estimated H-index: 11
(UMN: University of Minnesota)
+ 4 AuthorsDuncan Martin Baird29
Estimated H-index: 29
(Cardiff University)
Fusion of critically short or damaged telomeres is associated with the genomic rearrangements that support malignant transformation. We have demonstrated the fundamental contribution of DNA ligase 4-dependent classical non-homologous end-joining to long-range inter-chromosomal telomere fusions. In contrast, localized genomic recombinations initiated by sister chromatid fusion are predominantly mediated by alternative non-homologous end-joining activity that may employ either DNA ligase 3 or DNA ...
Published on Nov 27, 2018in bioRxiv
Inbar Bariah (BGU: Ben-Gurion University of the Negev), Danielle Keidar-Friedman (BGU: Ben-Gurion University of the Negev), Khalil Kashkush12
Estimated H-index: 12
(BGU: Ben-Gurion University of the Negev)
Following allopolyploidization, nascent polyploid wheat species react with massive genomic rearrangements, including deletion of transposable element-containing sequences. While such massive rearrangements are considered to be a prominent process in wheat genome evolution and speciation, their structure, extent, and underlying mechanisms remain poorly understood. In this study, we retrieved ~3500 insertions of a specific variant of Fatima, one of the most dynamic long-terminal repeat retrotransp...
Published on Sep 19, 2018in Nucleic Acids Research11.15
Amir Taheri-Ghahfarokhi3
Estimated H-index: 3
(AstraZeneca),
Benjamin J. M. Taylor3
Estimated H-index: 3
(AstraZeneca)
+ 9 AuthorsLorenz M. Mayr4
Estimated H-index: 4
(AstraZeneca)
Published on 2018in G3: Genes, Genomes, Genetics2.63
Laurens Pauwels17
Estimated H-index: 17
(UGent: Ghent University),
Rebecca De Clercq12
Estimated H-index: 12
(UGent: Ghent University)
+ 5 AuthorsAstrid Goossens46
Estimated H-index: 46
(UGent: Ghent University)
Reverse genetics uses loss-of-function alleles to interrogate gene function. The advent of CRISPR/Cas9-based gene editing now allows the generation of knock-out alleles for any gene and entire gene families. Even in the model plant Arabidopsis thaliana , gene editing is welcomed as T-DNA insertion lines do not always generate null alleles. Here, we show efficient generation of heritable mutations in Arabidopsis using CRISPR/Cas9 with a workload similar to generating overexpression lines. We obta...
Published on 2018in bioRxiv
Jacob V. Layer3
Estimated H-index: 3
(Harvard University),
J. Patrick Cleary1
Estimated H-index: 1
(Harvard University)
+ 7 AuthorsRichard L. Frock13
Estimated H-index: 13
(Stanford University)
Chromosomal rearrangements, including translocations, are early and essential events in the formation of many tumors. Previous studies that defined the genetic requirements for rearrangement formation have identified differences between murine and human cells, most notably in the role of classical- and alternative-nonhomologous end joining factors (NHEJ). We reported that poly(ADP)ribose polymerase 3 (PARP3) promotes chromosomal rearrangements induced by endonucleases in multiple human cell type...
Published on Jan 1, 2018in Methods in Enzymology1.86
Alexander Brown10
Estimated H-index: 10
(WSU: Washington State University),
Aneesa T. Al-Soodani1
Estimated H-index: 1
(WSU: Washington State University)
+ 5 AuthorsSteven A. Roberts23
Estimated H-index: 23
(WSU: Washington State University)
Abstract The mechanistic understanding of how DNA double-strand breaks (DSB) are repaired is rapidly advancing in part due to the advent of inducible site-specific break model systems as well as the employment of next-generation sequencing (NGS) technologies to sequence repair junctions at high depth. Unfortunately, the sheer volume of data produced by these methods makes it difficult to analyze the structure of repair junctions manually or with other general-purpose software. Here, we describe ...
Published on Jan 1, 2018
Terrence Hanscom1
Estimated H-index: 1
(Tufts University),
Varandt Y. Khodaverdian2
Estimated H-index: 2
(Tufts University),
Mitch McVey17
Estimated H-index: 17
(Tufts University)
Abstract In this chapter, we describe a method for the recovery and analysis of alternative end-joining (alt-EJ) DNA double-strand break repair junctions following I- Sce I cutting in Drosophila melanogaster embryos. Alt-EJ can be defined as a set of Ku70/80 and DNA ligase 4-independent end-joining processes that are typically mutagenic, producing deletions, insertions, and chromosomal rearrangements more frequently than higher-fidelity repair pathways such as classical nonhomologous end joining...
View next paperP IX.26 Role of DNA repair synthesis in mammalian DNA double strand break repair