scholarly journals Tissue Specific DNA Repair Outcomes Shape the Landscape of Genome Editing

2021 ◽  
Vol 12 ◽  
Author(s):  
Mathilde Meyenberg ◽  
Joana Ferreira da Silva ◽  
Joanna I. Loizou
Keyword(s):  
Dna Repair ◽  
Genome Editing ◽  
Genetic Diseases ◽  
Dna Double Strand Breaks ◽  
Dna Breaks ◽  
Dna Damage And Repair ◽  
Tissue Specific ◽  
Precise Control ◽  
Repair Processes ◽  
Recent Developments

The use of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 has moved from bench to bedside in less than 10years, realising the vision of correcting disease through genome editing. The accuracy and safety of this approach relies on the precise control of DNA damage and repair processes to achieve the desired editing outcomes. Strategies for modulating pathway choice for repairing CRISPR-mediated DNA double-strand breaks (DSBs) have advanced the genome editing field. However, the promise of correcting genetic diseases with CRISPR-Cas9 based therapies is restrained by a lack of insight into controlling desired editing outcomes in cells of different tissue origin. Here, we review recent developments and urge for a greater understanding of tissue specific DNA repair processes of CRISPR-induced DNA breaks. We propose that integrated mapping of tissue specific DNA repair processes will fundamentally empower the implementation of precise and safe genome editing therapies for a larger variety of diseases.

scholarly journals Chromothripsis as an on-target consequence of CRISPR-Cas9 genome editing

2020 ◽  
Author(s):  
Mitchell L. Leibowitz ◽  
Stamatis Papathanasiou ◽  
Phillip A. Doerfler ◽  
Logan J. Blaine ◽  
Yu Yao ◽  
...  
Keyword(s):  
Genome Editing ◽  
Chromosomal Abnormalities ◽  
Therapeutic Potential ◽  
Chromosome Rearrangement ◽  
Genetic Diseases ◽  
Cell Manipulation ◽  
Dna Double Strand Breaks ◽  
Dna Breaks ◽  
Link Type ◽  
A Genome

Genome editing has promising therapeutic potential for genetic diseases and cancer (1, 2). However, the most practicable current approaches rely on the generation of DNA double-strand breaks (DSBs), which can give rise to a poorly characterized spectrum of structural chromosomal abnormalities. Here, we show that a catastrophic mutational process called chromothripsis is a previously unappreciated consequence of CRISPR-Cas9-mediated DSBs. Chromothripsis is extensive chromosome rearrangement restricted to one or a few chromosomes that can cause human congenital disease and cancer (3–6). Using model cell systems and a genome editing protocol similar to ones in clinical trials (7) (NCT03655678, NCT03745287) we show that CRISPR-Cas9-mediated DNA breaks generate abnormal nuclear structures—micronuclei and chromosome bridges—that trigger chromothripsis. Chromothripsis is an on-target toxicity that may be minimized by cell manipulation protocols or screening but cannot be completely avoided in many genome editing applications.

scholarly journals The tale of a tail: histone H4 acetylation and the repair of DNA breaks

2017 ◽  
Vol 372 (1731) ◽  
pp. 20160284 ◽  
Author(s):  
Surbhi Dhar ◽  
Ozge Gursoy-Yuzugullu ◽  
Ramya Parasuram ◽  
Brendan D. Price
Keyword(s):  
Dna Repair ◽  
Open Chromatin ◽  
Histone H4 ◽  
Dna Double Strand Breaks ◽  
Dna Breaks ◽  
Strand Breaks ◽  
Histone H4 Acetylation ◽  
Break Site ◽  
Bromodomain Proteins ◽  
Complex Architecture

The ability of cells to detect and repair DNA double-strand breaks (DSBs) within the complex architecture of the genome requires co-ordination between the DNA repair machinery and chromatin remodelling complexes. This co-ordination is essential to process damaged chromatin and create open chromatin structures which are required for repair. Initially, there is a PARP-dependent recruitment of repressors, including HP1 and several H3K9 methyltransferases, and exchange of histone H2A.Z by the NuA4-Tip60 complex. This creates repressive chromatin at the DSB in which the tail of histone H4 is bound to the acidic patch on the nucleosome surface. These repressor complexes are then removed, allowing rapid acetylation of the H4 tail by Tip60. H4 acetylation blocks interaction between the H4 tail and the acidic patch on adjacent nucleosomes, decreasing inter-nucleosomal interactions and creating open chromatin. Further, the H4 tail is now free to recruit proteins such as 53BP1 to DSBs, a process modulated by H4 acetylation, and provides binding sites for bromodomain proteins, including ZMYND8 and BRD4, which are important for DSB repair. Here, we will discuss how the H4 tail functions as a dynamic hub that can be programmed through acetylation to alter chromatin packing and recruit repair proteins to the break site. This article is part of the themed issue ‘Chromatin modifiers and remodellers in DNA repair and signalling’.

scholarly journals Mechanistic and genetic basis of single-strand templated repair at Cas12a-induced DNA breaks in Chlamydomonas reinhardtii

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Aron Ferenczi ◽  
Yen Peng Chew ◽  
Erika Kroll ◽  
Charlotte von Koppenfels ◽  
Andrew Hudson ◽  
...  
Keyword(s):  
Dna Repair ◽  
Chlamydomonas Reinhardtii ◽  
Nuclear Dna ◽  
Model Organism ◽  
Single Strand ◽  
Dna Double Strand Breaks ◽  
Dna Breaks ◽  
End Joining ◽  
Non Homologous End Joining ◽  
Underlying Mechanisms

AbstractSingle-stranded oligodeoxynucleotides (ssODNs) are widely used as DNA repair templates in CRISPR/Cas precision genome editing. However, the underlying mechanisms of single-strand templated DNA repair (SSTR) are inadequately understood, constraining rational improvements to precision editing. Here we study SSTR at CRISPR/Cas12a-induced DNA double-strand breaks (DSBs) in the eukaryotic model green microalga Chlamydomonas reinhardtii. We demonstrate that ssODNs physically incorporate into the genome during SSTR at Cas12a-induced DSBs. This process is genetically independent of the Rad51-dependent homologous recombination and Fanconi anemia pathways, is strongly antagonized by non-homologous end-joining, and is mediated almost entirely by the alternative end-joining enzyme polymerase θ. These findings suggest differences in SSTR between C. reinhardtii and animals. Our work illustrates the promising potentially of C. reinhardtii as a model organism for studying nuclear DNA repair.

scholarly journals CRISPR-Cas9 genome editing in human cells works via the Fanconi Anemia pathway

2017 ◽  
Author(s):  
Chris D Richardson ◽  
Katelynn R Kazane ◽  
Sharon J Feng ◽  
Nicholas L Bray ◽  
Axel J Schäfer ◽  
...  
Keyword(s):  
Dna Repair ◽  
Genome Editing ◽  
Fanconi Anemia ◽  
High Efficiency ◽  
Genetic Diseases ◽  
Dermal Fibroblasts ◽  
Human Cells ◽  
Individual Gene ◽  
Break Site ◽  
Repair Pathways

AbstractCRISPR-Cas9 genome editing creates targeted double strand breaks (DSBs) in eukaryotic cells that are processed by cellular DNA repair pathways. Co-administration of single stranded oligonucleotide donor DNA (ssODN) during editing can result in high-efficiency (>20%) incorporation of ssODN sequences into the break site. This process is commonly referred to as homology directed repair (HDR) and here referred to as single stranded template repair (SSTR) to distinguish it from repair using a double stranded DNA donor (dsDonor). The high efficacy of SSTR makes it a promising avenue for the treatment of genetic diseases1,2, but the genetic basis of SSTR editing is still unclear, leaving its use a mostly empiric process. To determine the pathways underlying SSTR in human cells, we developed a coupled knockdown-editing screening system capable of interrogating multiple editing outcomes in the context of thousands of individual gene knockdowns. Unexpectedly, we found that SSTR requires multiple components of the Fanconi Anemia (FA) repair pathway, but does not require Rad51-mediated homologous recombination, distinguishing SSTR from repair using dsDonors. Knockdown of FA genes impacts SSTR without altering break repair by non-homologous end joining (NHEJ) in multiple human cell lines and in neonatal dermal fibroblasts. Our results establish an unanticipated and central role for the FA pathway in templated repair from single stranded DNA by human cells. Therapeutic genome editing has been proposed to treat genetic disorders caused by deficiencies in DNA repair, including Fanconi Anemia. Our data imply that patient genotype and/or transcriptome profoundly impact the effectiveness of gene editing treatments and that adjuvant treatments to bias cells towards FA repair pathways could have considerable therapeutic value.

scholarly journals RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer

2020 ◽  
Author(s):  
Damian Wojtowicz ◽  
Jan Hoinka ◽  
Bayarbaatar Amgalan ◽  
Yoo-Ah Kim ◽  
Teresa M. Przytycka
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Mutational Signatures ◽  
Dna Damage And Repair ◽  
Therapeutic Implications ◽  
Mutational Landscape ◽  
Repair Processes ◽  
Cancer Genomes ◽  
Current Paradigm ◽  
Mutational Processes

AbstractMany mutagenic processes leave characteristic imprints on cancer genomes known as mutational signatures. These signatures have been of recent interest regarding their applicability in studying processes shaping the mutational landscape of cancer. In particular, pinpointing the presence of altered DNA repair pathways can have important therapeutic implications. However, mutational signatures of DNA repair deficiencies are often hard to infer. This challenge emerges as a result of deficient DNA repair processes acting by modifying the outcome of other mutagens. Thus, they exhibit non-additive effects that are not depicted by the current paradigm for modeling mutational processes as independent signatures. To close this gap, we present RepairSig, a method that accounts for interactions between DNA damage and repair and is able to uncover unbiased signatures of deficient DNA repair processes. In particular, RepairSig was able to replace three MMR deficiency signatures previously proposed to be active in breast cancer, with just one signature strikingly similar to the experimentally derived signature. As the first method to model interactions between mutagenic processes, RepairSig is an important step towards biologically more realistic modeling of mutational processes in cancer. The source code for RepairSig is publicly available at https://github.com/ncbi/RepairSig.

Abstract 780: Atorvastatin Activates A Novel Nbs1-dependent Mechanism Of Accelerating Dna Repair In Atherosclerosis

Circulation ◽  
2007 ◽  
Vol 116 (suppl_16) ◽  
Author(s):  
Melli M Mahmoudi ◽  
Isabelle C Gorenne ◽  
John R Mercer ◽  
Nichola L Figg ◽  
Martin R Bennett
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Oxidant Stress ◽  
Dna Breaks ◽  
Western Blots ◽  
Dna Damage And Repair ◽  
Pre Treatment ◽  
Reactive Oxidant ◽  
Sirna Knockdown ◽  
Dependent Mechanism

There is increasing evidence that reactive oxidant species (ROS) and DNA damage promote the development and complications of atherosclerosis. Although statin therapy reduces both ROS and DNA damage in atherosclerosis, the mechanism of this effect is unknown. We first examined expression of DNA damage and repair markers in vascular smooth muscle cells (VSMCs) of human atherosclerotic plaques. With increasing disease severity, there was increased VSMC expression of the DNA repair markers P-ATM/ATR substrate and P-H2AX from 2.7%±2.2 and 0.5±0.71 [mean±SEM] (AHA Grade I/II), to 21%±3.5 and 36.5±2.1 (Grade III) lesions, and 86.5%±0.7 and 69.3±7.6 (Grade IV/V). Cultured plaque VSMCs also showed a 1.5 fold increased oxidant stress; a 4.4 fold increased double-stranded DNA breaks, and expression of P-H2AX by Western blots. ROS analogues induced a robust DNA damage response in VSMCs, characterised by lengthening of tails on COMET assay, and activation of ATM and P-H2AX, with completion of repair by 6 hours. Atorvastatin pre-treatment accelerated DNA repair by approximately 2 hours without inhibiting ROS induction or DNA damage, and markedly accelerated the kinetics of nibrin (NBS-1) and P-H2AX activation, both proteins recruited to sites of DNA damage, by preventing degradation of NBS-1. Atorvastatin induced phosphorylation of HDM2, an E3 ligase and putative regulator of NBS-1 stability, and siRNA knockdown of HDM2 replicated the effect of atorvastatin on NBS-1. The ability of atorvastatin to accelerate repair was completely dependent upon NBS-1, as atorvastatin was ineffective in cells either null or expressing constitutively active NBS-I. In summary, we have demonstrated a novel NBS-1-dependent mechanism by which statins accelerate DNA repair in atherosclerosis, through HDM2 phosphorylation and stabilisation of NBS-1. We believe that both NBS-1 and HDM2 are critical to DNA repair in atherosclerosis.

scholarly journals DDX5 resolves R-loops at DNA double-strand breaks to promote DNA repair and avoid chromosomal deletions

NAR Cancer ◽  
2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Zhenbao Yu ◽  
Sofiane Y Mersaoui ◽  
Laure Guitton-Sert ◽  
Yan Coulombe ◽  
Jingwen Song ◽  
...  
Keyword(s):  
Dna Repair ◽  
Protein A ◽  
Helicase Domain ◽  
Dependent Manner ◽  
Dna Double Strand Breaks ◽  
Dna Breaks ◽  
Rna Transcripts ◽  
Chromosomal Deletions ◽  
Double Strand Dna Breaks ◽  
Dna Strand

Abstract R-loops are three-stranded structures consisting of a DNA/RNA hybrid and a displaced DNA strand. The regulatory factors required to process this fundamental genetic structure near double-strand DNA breaks (DSBs) are not well understood. We previously reported that cellular depletion of the ATP-dependent DEAD box RNA helicase DDX5 increases R-loops genome-wide causing genomic instability. In this study, we define a pivotal role for DDX5 in clearing R-loops at or near DSBs enabling proper DNA repair to avoid aberrations such as chromosomal deletions. Remarkably, using the non-homologous end joining reporter gene (EJ5-GFP), we show that DDX5-deficient U2OS cells exhibited asymmetric end deletions on the side of the DSBs where there is overlap with a transcribed gene. Cross-linking and immunoprecipitation showed that DDX5 bound RNA transcripts near DSBs and required its helicase domain and the presence of DDX5 near DSBs was also shown by chromatin immunoprecipitation. DDX5 was excluded from DSBs in a transcription- and ATM activation-dependent manner. Using DNA/RNA immunoprecipitation, we show DDX5-deficient cells had increased R-loops near DSBs. Finally, DDX5 deficiency led to delayed exonuclease 1 and replication protein A recruitment to laser irradiation-induced DNA damage sites, resulting in homologous recombination repair defects. Our findings define a role for DDX5 in facilitating the clearance of RNA transcripts overlapping DSBs to ensure proper DNA repair.

scholarly journals Double Stranded DNA Breaks and Genome Editing Trigger Ribosome Remodeling and Translational Shutdown

2018 ◽  
Author(s):  
Celeste Riepe ◽  
Elena Zelin ◽  
Stacia K. Wyman ◽  
David N. Nguyen ◽  
Jin Rui Liang ◽  
...  
Keyword(s):  
Dna Damage ◽  
Genome Editing ◽  
Ribosomal Proteins ◽  
Transcriptional Response ◽  
Strand Break ◽  
Double Strand Break ◽  
Initiation Factor ◽  
Dna Double Strand Breaks ◽  
Dna Breaks ◽  
Cellular Phenotypes

SummaryDNA damage activates a robust transcriptional stress response, but much less is known about how DNA impacts translation. The advent of genome editing via a Cas9-induced DNA double-strand break has intensified interest in understanding cellular responses to DNA damage. Here we find that DNA double-strand breaks (DSBs) induced by Cas9 or other damaging agents lead to a reduction of core ribosomal proteins, RPS27A and RPL40, and that the loss of these proteins is post-transcriptional and p53-independent. DSBs furthermore lead to the shutdown of translation through phosphorylation of eukaryotic initiation factor 2 alpha, and altering these signals affects genome editing outcomes. This DSB translational response is widespread and precedes the transcriptional response. Our results demonstrate that even a single double-strand break can lead to ribosome remodeling and reduced translational output, and suggest caution in interpreting cellular phenotypes measured immediately after genome editing.

scholarly journals CtIP-dependent nascent RNA expression flanking DNA breaks guides the choice of DNA repair pathway

2022 ◽  
Author(s):  
Daniel Gomez-Cabello ◽  
Georgios Pappas ◽  
Diana Aguilar-Morante ◽  
Christoffel Dinant ◽  
Jiri Bartek
Keyword(s):  
Dna Repair ◽  
Rna Polymerase Ii ◽  
Single Molecule ◽  
Rna World ◽  
Dna Double Strand Breaks ◽  
Dna Breaks ◽  
Nascent Rna ◽  
Rna:Dna Hybrids ◽  
Dna End Resection ◽  
Non Homologous End Joining

The RNA world is changing our views about sensing and resolution of DNA damage. Here, we developed single-molecule DNA/RNA analysis approaches to visualize how nascent RNA facilitates the repair of DNA double-strand breaks (DSBs). RNA polymerase II (RNAPII) is crucial for DSB resolution in human cells. DSB-flanking, RNAPII-generated nascent RNA forms RNA:DNA hybrids, guiding the upstream DNA repair steps towards favouring the error-free Homologous Recombination (HR) pathway over Non-Homologous End Joining. Specific RNAPII inhibitor, THZ1, impairs recruitment of essential HR proteins to DSBs, implicating nascent RNA in DNA end resection, initiation and execution of HR repair. We further propose that resection factor CtIP interacts with and re-activates RNAPII when paused by the RNA:DNA hybrids, collectively promoting faithful repair of chromosome breaks to maintain genomic integrity.

scholarly journals E2F1 Promotes Progression of Bladder Cancer by Modulating RAD54L Involved in Homologous Recombination Repair

2020 ◽  
Vol 21 (23) ◽  
pp. 9025
Author(s):  
Jeong-Yeon Mun ◽  
Seung-Woo Baek ◽  
Won Young Park ◽  
Won-Tae Kim ◽  
Seon-Kyu Kim ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Dna Repair ◽  
Homologous Recombination ◽  
Cancer Cells ◽  
Cancer Progression ◽  
Anticancer Agents ◽  
Homologous Recombination Repair ◽  
Dna Double Strand Breaks ◽  
Dna Breaks ◽  
Recombination Repair

DNA repair defects are important factors in cancer development. High DNA repair activity can affect cancer progression and chemoresistance. DNA double-strand breaks in cancer cells caused by anticancer agents can be restored by non-homologous end joining (NHEJ) and homologous recombination repair (HRR). Our previous study has identified E2F1 as a key gene in bladder cancer progression. In this study, DNA repair genes related to E2F1 were analyzed, and RAD54L involved in HRR was identified. In gene expression analysis of bladder cancer patients, the survival of patients with high RAD54L expression was shorter with cancer progression than in patients with low RAD54L expression. This study also revealed that E2F1 directly binds to the promoter region of RAD54L and regulates the transcription of RAD54L related to the HRR pathway. This study also confirmed that DNA breaks are repaired by RAD54L induced by E2F1 in bladder cancer cells treated with MMC. In summary, RAD54L was identified as a new target directly regulated by E2F1. Our results suggest that, E2F1 and RAD54L could be used as diagnostic markers for bladder cancer progression and represent potential therapeutic targets.

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