ADAR2-mediated RNA editing of DNA:RNA hybrids is required for DNA double strand break repair

The maintenance of genomic stability requires the coordination of multiple cellular tasks upon the appearance of DNA lesions. RNA editing, the post-transcriptional sequence alteration of RNA, has a profound effect on cell homeostasis, but its implication in the response to DNA damage was not previously explored. Here we show that, in response to DNA breaks, an overall change of the Adenosine-to-Inosine RNA editing is observed, a phenomenon we call the RNA Editing DAmage Response (REDAR). REDAR relies on the checkpoint kinase ATR and the recombination factor CtIP. Moreover, depletion of the RNA editing enzyme ADAR2 renders cells hypersensitive to genotoxic agents, increases genomic instability and hampers homologous recombination by impairing DNA resection. Such a role of ADAR2 in DNA repair goes beyond the recoding of specific transcripts, but depends on ADAR2 editing DNA:RNA hybrids to ease their dissolution.

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ADAR-mediated RNA editing of DNA:RNA hybrids is required for DNA double strand break repair

Nature Communications ◽

10.1038/s41467-021-25790-2 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Sonia Jimeno ◽

Rosario Prados-Carvajal ◽

María Jesús Fernández-Ávila ◽

Sonia Silva ◽

Domenico Alessandro Silvestris ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Rna Editing ◽

Genomic Stability ◽

Strand Break ◽

Dna Lesions ◽

Dna Breaks ◽

Dna Double Strand Break ◽

Editing Enzyme

AbstractThe maintenance of genomic stability requires the coordination of multiple cellular tasks upon the appearance of DNA lesions. RNA editing, the post-transcriptional sequence alteration of RNA, has a profound effect on cell homeostasis, but its implication in the response to DNA damage was not previously explored. Here we show that, in response to DNA breaks, an overall change of the Adenosine-to-Inosine RNA editing is observed, a phenomenon we call the RNA Editing DAmage Response (REDAR). REDAR relies on the checkpoint kinase ATR and the recombination factor CtIP. Moreover, depletion of the RNA editing enzyme ADAR2 renders cells hypersensitive to genotoxic agents, increases genomic instability and hampers homologous recombination by impairing DNA resection. Such a role of ADAR2 in DNA repair goes beyond the recoding of specific transcripts, but depends on ADAR2 editing DNA:RNA hybrids to ease their dissolution.

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A Degenerate PCNA-Interacting Peptide (DPIP) box targets RNF168 to replicating DNA to limit 53BP1 signaling

10.1101/2021.03.17.435897 ◽

2021 ◽

Author(s):

Yang Yang ◽

Deepika Jayaprakash ◽

Robert Hollingworth ◽

Steven Chen ◽

Amy Jablonski ◽

...

Keyword(s):

Dna Damage ◽

Dna Replication ◽

Replication Fork ◽

Strand Break ◽

S Phase ◽

C Terminus ◽

Dna Double Strand Break ◽

Damage Response ◽

Phase Functions

The E3 ligase RNF168 has been suggested to have roles at DNA replication forks in addition to its canonical functions in DNA double-strand break (DSB) signaling. However, the precise role of RNF168 in DNA replication remains unclear. Here we demonstrate that RNF168 is recruited to DNA replication factories independent of the canonical DSB response pathway regulators and identify a degenerate PCNA-Interacting Peptide (DPIP) motif in the C-terminus of RNF168 which mediates its binding to PCNA. An RNF168 mutant harboring substitutions in the DPIP box fails to interact with PCNA and is not recruited to sites of DNA synthesis, yet fully retains its ability to promote DSB-induced 53BP1 foci. Surprisingly, the RNF168 DPIP mutant also retains the ability to support ongoing DNA replication fork movement, demonstrating that PCNA-binding is dispensable for normal S-phase functions. However, replisome-associated RNF168 functions to suppress the DSB-induced 53BP1 DNA damage response during S-phase. Moreover, we show that WT RNF168 can perform PCNA ubiquitylation independently of RAD18 and also synergizes with RAD18 to amplify PCNA ubiquitylation. Taken together, our results identify non-canonical functions of RNF168 at the replication fork and demonstrate new mechanisms of cross talk between the DNA damage and replication stress response pathways.

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Schizosaccharomyces pombe KAT5 contributes to resection and repair of a DNA double strand break

Genetics ◽

10.1093/genetics/iyab042 ◽

2021 ◽

Author(s):

Tingting Li ◽

Ruben C Petreaca ◽

Susan L Forsburg

Keyword(s):

Dna Damage ◽

Homologous Recombination ◽

Chromatin Remodeling ◽

Dna Damage Response ◽

Histone Acetyltransferase ◽

Strand Break ◽

Double Strand Break ◽

Dna Damage Checkpoint ◽

Dna Double Strand Break ◽

Damage Response

Abstract Chromatin remodeling is essential for effective repair of a DNA double strand break. KAT5 (S. pombe Mst1, human TIP60) is a MYST family histone acetyltransferase conserved from yeast to humans that coordinates various DNA damage response activities at a DNA double strand break (DSB), including histone remodeling and activation of the DNA damage checkpoint. In S. pombe, mutations in mst1+ causes sensitivity to DNA damaging drugs. Here we show that Mst1 is recruited to DSBs. Mutation of mst1+ disrupts recruitment of repair proteins and delays resection. These defects are partially rescued by deletion of pku70, which has been previously shown to antagonize repair by homologous recombination. These phenotypes of mst1 are similar to pht1-4KR, a non-acetylatable form of histone variant H2A.Z, which has been proposed to affect resection. Our data suggest that Mst1 functions to direct repair of DSBs towards homologous recombination pathways by modulating resection at the double strand break.

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DNA Damage-Induced Phosphorylation of TRF2 Is Required for the Fast Pathway of DNA Double-Strand Break Repair

Molecular and Cellular Biology ◽

10.1128/mcb.00944-08 ◽

2009 ◽

Vol 29 (13) ◽

pp. 3597-3604 ◽

Cited By ~ 29

Author(s):

Nazmul Huda ◽

Hiromi Tanaka ◽

Marc S. Mendonca ◽

David Gilley

Keyword(s):

Dna Damage ◽

Dna Damage Response ◽

Functional Role ◽

Strand Break ◽

Telomere Maintenance ◽

Telomeric Dna ◽

Dsb Repair ◽

Dna Double Strand Break ◽

Damage Response ◽

Fast Pathway

ABSTRACT Protein kinases of the phosphatidylinositol 3-kinase-like kinase family, originally known to act in maintaining genomic integrity via DNA repair pathways, have been shown to also function in telomere maintenance. Here we focus on the functional role of DNA damage-induced phosphorylation of the essential mammalian telomeric DNA binding protein TRF2, which coordinates the assembly of the proteinaceous cap to disguise the chromosome end from being recognized as a double-stand break (DSB). Previous results suggested a link between the transient induction of human TRF2 phosphorylation at threonine 188 (T188) by the ataxia telangiectasia mutated protein kinase (ATM) and the DNA damage response. Here, we report evidence that X-ray-induced phosphorylation of TRF2 at T188 plays a role in the fast pathway of DNA DSB repair. These results connect the highly transient induction of human TRF2 phosphorylation to the DNA damage response machinery. Thus, we find that a protein known to function in telomere maintenance, TRF2, also plays a functional role in DNA DSB repair.

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The complex matter of DNA double-strand break detection

Biochemical Society Transactions ◽

10.1042/bst0310040 ◽

2003 ◽

Vol 31 (1) ◽

pp. 40-44 ◽

Cited By ~ 26

Author(s):

J.M. Bradbury ◽

S.P. Jackson

Keyword(s):

Dna Damage ◽

Genome Stability ◽

Strand Break ◽

Damage Sensing ◽

Dna Double Strand Break ◽

Mre11 Complex ◽

Damage Response ◽

Radiation Induced ◽

Dna Damage Signalling ◽

Complex Matter

To maintain genomic stability, despite constant exposure to agents that damage DNA, eukaryotic cells have developed elaborate and highly conserved pathways of DNA damage sensing, signalling and repair. In this review, we concentrate mainly on what we know about DNA damage sensing with particular reference to Lcd1p, a yeast protein that functions early in DNA damage signalling, and MDC1 (mediator of DNA damage checkpoint 1), a recently identified human protein that may be involved in recruiting the MRE11 complex to radiation-induced nuclear foci. We describe a model for the DNA damage response in which factors are recruited sequentially to sites of DNA damage to form complexes that can amplify the original signal and propagate it to the multitude of response pathways necessary for genome stability.

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Role of Base Excision Repair Pathway in the Processing of Complex DNA Damage Generated by Oxidative Stress and Anticancer Drugs

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2020.617884 ◽

2021 ◽

Vol 8 ◽

Author(s):

Yeldar Baiken ◽

Damira Kanayeva ◽

Sabira Taipakova ◽

Regina Groisman ◽

Alexander A. Ishchenko ◽

...

Keyword(s):

Dna Damage ◽

Base Excision Repair ◽

Genome Instability ◽

Excision Repair ◽

Chromosomal Rearrangements ◽

Strand Break ◽

Dna Lesions ◽

Complex Nature ◽

Base Excision

Chemical alterations in DNA induced by genotoxic factors can have a complex nature such as bulky DNA adducts, interstrand DNA cross-links (ICLs), and clustered DNA lesions (including double-strand breaks, DSB). Complex DNA damage (CDD) has a complex character/structure as compared to singular lesions like randomly distributed abasic sites, deaminated, alkylated, and oxidized DNA bases. CDD is thought to be critical since they are more challenging to repair than singular lesions. Although CDD naturally constitutes a relatively minor fraction of the overall DNA damage induced by free radicals, DNA cross-linking agents, and ionizing radiation, if left unrepaired, these lesions cause a number of serious consequences, such as gross chromosomal rearrangements and genome instability. If not tightly controlled, the repair of ICLs and clustered bi-stranded oxidized bases via DNA excision repair will either inhibit initial steps of repair or produce persistent chromosomal breaks and consequently be lethal for the cells. Biochemical and genetic evidences indicate that the removal of CDD requires concurrent involvement of a number of distinct DNA repair pathways including poly(ADP-ribose) polymerase (PARP)-mediated DNA strand break repair, base excision repair (BER), nucleotide incision repair (NIR), global genome and transcription coupled nucleotide excision repair (GG-NER and TC-NER, respectively), mismatch repair (MMR), homologous recombination (HR), non-homologous end joining (NHEJ), and translesion DNA synthesis (TLS) pathways. In this review, we describe the role of DNA glycosylase-mediated BER pathway in the removal of complex DNA lesions.

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53BP1 mediated recruitment of RASSF1A at ribosomal DNA breaks facilitates local ATM signal amplification

10.1101/2021.11.17.469058 ◽

2021 ◽

Author(s):

Stavroula Tsaridou ◽

Georgia Velimezi ◽

Frances Willenbrock ◽

Maria Chatzifrangkeskou ◽

Andreas Panagopoulos ◽

...

Keyword(s):

Dna Damage ◽

Cell Viability ◽

Copy Number ◽

Adaptor Proteins ◽

Fragile Sites ◽

Dna Lesions ◽

Dna Breaks ◽

Damage Response ◽

Rdna Copy ◽

Rdna Copy Number

DNA lesions occur across the genome and constitute a threat to cell viability; however, damage at specific genomic loci has a disproportionally greater impact on the overall genome stability. The ribosomal RNA gene repeats (rDNA) are emerging fragile sites due to repetitive nature, clustering and high transcriptional activity. Recent progress in understanding how the rDNA damage response is organized has highlighted the key role of adaptor proteins in the response. Here we identify that the scaffold and tumor suppressor, RASSF1A is recruited at sites of damage and enriched at rDNA breaks. Employing targeted nucleolar DNA damage, we find that RASSF1A recruitment requires ATM activity and depends on 53BP1. At sites of damage RASSF1A facilitates local ATM signal establishment and rDNA break repair. RASSF1A silencing, a common epigenetic event during malignant transformation, results in persistent breaks, rDNA copy number alterations and decreased cell viability. Meta-analysis of a lung adenocarcinoma cohort showed that RASSF1A epigenetic silencing leads in rDNA copy number discrepancies. Overall, we present evidence that RASSF1A acts as a DNA repair factor and offer mechanistic insight in how the nucleolar DNA damage response is organized.

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SETD2 is required for DNA double-strand break repair and activation of the p53-mediated checkpoint

eLife ◽

10.7554/elife.02482 ◽

2014 ◽

Vol 3 ◽

Cited By ~ 121

Author(s):

Sílvia Carvalho ◽

Alexandra C Vítor ◽

Sreerama C Sridhara ◽

Filipa B Martins ◽

Ana C Raposo ◽

...

Keyword(s):

Dna Damage ◽

Strand Break ◽

Dna Lesions ◽

Alternative Mechanism ◽

Dna Double Strand Breaks ◽

Cell Renal Cell Carcinoma ◽

Strand Breaks ◽

Dna Damage Signaling ◽

Dna Double Strand Break ◽

Recombination Repair

Histone modifications establish the chromatin states that coordinate the DNA damage response. In this study, we show that SETD2, the enzyme that trimethylates histone H3 lysine 36 (H3K36me3), is required for ATM activation upon DNA double-strand breaks (DSBs). Moreover, we find that SETD2 is necessary for homologous recombination repair of DSBs by promoting the formation of RAD51 presynaptic filaments. In agreement, SETD2-mutant clear cell renal cell carcinoma (ccRCC) cells displayed impaired DNA damage signaling. However, despite the persistence of DNA lesions, SETD2-deficient cells failed to activate p53, a master guardian of the genome rarely mutated in ccRCC and showed decreased cell survival after DNA damage. We propose that this novel SETD2-dependent role provides a chromatin bookmarking instrument that facilitates signaling and repair of DSBs. In ccRCC, loss of SETD2 may afford an alternative mechanism for the inactivation of the p53-mediated checkpoint without the need for additional genetic mutations in TP53.

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The Role of Small Noncoding RNA in DNA Double-Strand Break Repair

International Journal of Molecular Sciences ◽

10.3390/ijms21218039 ◽

2020 ◽

Vol 21 (21) ◽

pp. 8039

Author(s):

Iwona Rzeszutek ◽

Gabriela Betlej

Keyword(s):

Dna Damage ◽

Dna Damage Response ◽

Noncoding Rna ◽

Rna Binding ◽

Rna Binding Proteins ◽

Strand Break ◽

Double Strand Break ◽

Wide Range ◽

Damage Response

DNA damage is a common phenomenon promoted through a variety of exogenous and endogenous factors. The DNA damage response (DDR) pathway involves a wide range of proteins, and as was indicated, small noncoding RNAs (sncRNAs). These are double-strand break-induced RNAs (diRNAs) and DNA damage response small RNA (DDRNA). Moreover, RNA binding proteins (RBPs) and RNA modifications have also been identified to modulate diRNA and DDRNA function in the DDR process. Several theories have been formulated regarding the synthesis and function of these sncRNAs during DNA repair; nevertheless, these pathways’ molecular details remain unclear. Here, we review the current knowledge regarding the mechanisms of diRNA and DDRNA biosynthesis and discuss the role of sncRNAs in maintaining genome stability.

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