RIF1 acts in DNA repair through phosphopeptide recognition of 53BP1

SummaryThe chromatin-binding protein 53BP1 promotes DNA repair by orchestrating the recruitment of downstream effectors including PTIP, RIF1 and shieldin to DNA double-strand break sites. While how PTIP recognizes 53BP1 is known, the molecular details of RIF1 recruitment to DNA damage sites remains undefined. Here, we report that RIF1 is a phosphopeptide-binding protein that directly interacts with three phosphorylated 53BP1 epitopes. The RIF1-binding sites on 53BP1 share an essential LxL motif followed by two closely apposed phosphorylated residues. Simultaneous mutation of these sites on 53BP1 abrogates RIF1 accumulation into ionizing radiation-induced foci, but surprisingly only fully compromises 53BP1-dependent DNA repair when an alternative mode of shieldin recruitment to DNA damage sites is also disabled. Intriguingly, this alternative mode of recruitment still depends on RIF1 but does not require its interaction with 53BP1. RIF1 therefore employs phosphopeptide recognition to promote DNA repair but also modifies shieldin action independently of 53BP1 binding.

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Akt/PKB suppresses DNA damage processing and checkpoint activation in late G2

The Journal of Cell Biology ◽

10.1083/jcb.201003004 ◽

2010 ◽

Vol 190 (3) ◽

pp. 297-305 ◽

Cited By ~ 53

Author(s):

Naihan Xu ◽

Nadia Hegarat ◽

Elizabeth J. Black ◽

Mary T. Scott ◽

Helfrid Hochegger ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Protein A ◽

Strand Break ◽

Checkpoint Activation ◽

Interacting Protein ◽

Dna Double Strand Break ◽

Radiation Induced ◽

G2 Cells ◽

Tumor Types

Using chemical genetics to reversibly inhibit Cdk1, we find that cells arrested in late G2 are unable to delay mitotic entry after irradiation. Late G2 cells detect DNA damage lesions and form γ-H2AX foci but fail to activate Chk1. This reflects a lack of DNA double-strand break processing because late G2 cells fail to recruit RPA (replication protein A), ATR (ataxia telangiectasia and Rad3 related), Rad51, or CtIP (C-terminal interacting protein) to sites of radiation-induced damage, events essential for both checkpoint activation and initiation of DNA repair by homologous recombination. Remarkably, inhibition of Akt/PKB (protein kinase B) restores DNA damage processing and Chk1 activation after irradiation in late G2. These data demonstrate a previously unrecognized role for Akt in cell cycle regulation of DNA repair and checkpoint activation. Because Akt/PKB is frequently activated in many tumor types, these findings have important implications for the evolution and therapy of such cancers.

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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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Perfecting DNA double-strand break repair on transcribed chromatin

Essays in Biochemistry ◽

10.1042/ebc20190094 ◽

2020 ◽

Vol 64 (5) ◽

pp. 705-719 ◽

Cited By ~ 5

Author(s):

Xin Yi Tan ◽

Michael S.Y. Huen

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Chromosomal Aberrations ◽

Chromatin Structure ◽

Genome Stability ◽

Transcriptional Control ◽

Strand Break ◽

Double Strand Break ◽

Dna Double Strand Break ◽

Molecular Bases

Abstract Timely repair of DNA double-strand break (DSB) entails coordination with the local higher order chromatin structure and its transaction activities, including transcription. Recent studies are uncovering how DSBs trigger transient suppression of nearby transcription to permit faithful DNA repair, failing of which leads to elevated chromosomal aberrations and cell hypersensitivity to DNA damage. Here, we summarize the molecular bases for transcriptional control during DSB metabolism, and discuss how the exquisite coordination between the two DNA-templated processes may underlie maintenance of genome stability and cell homeostasis.

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Poly(ADP-ribosyl)ation temporally confines SUMO-dependent ataxin-3 recruitment to control DNA double-strand break repair

Journal of Cell Science ◽

10.1242/jcs.247809 ◽

2021 ◽

pp. jcs.247809

Author(s):

Annika Pfeiffer ◽

Laura K. Herzog ◽

Martijn S. Luijsterburg ◽

Rashmi G. Shah ◽

Magdalena B. Rother ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Time Window ◽

Strand Break ◽

Dna Double Strand Breaks ◽

Strand Breaks ◽

Dna Double Strand Break ◽

Dna Repair Proteins ◽

Short Time Window ◽

Short Time

DNA damage-induced SUMOylation serves as a signal for two antagonizing proteins that both stimulate repair of DNA double strand breaks (DSBs). Here, we demonstrate that the SUMO-dependent recruitment of the deubiquitylating enzyme ataxin-3 to DSBs, unlike recruitment of the ubiquitin ligase RNF4, additionally depends on PARP1-mediated poly(ADP-ribosyl)ation (PARylation). The co-dependence of ataxin-3 recruitment on PARylation and SUMOylation temporally confines its presence at DSBs to a short time window directly following detection of the DNA damage. We propose that this mechanism ensures that ataxin-3 prevents the premature removal of DNA repair proteins only during the early phase of the DSB response and does not interfere with the subsequent timely displacement of DNA repair proteins by RNF4. Thus, our data show that PARylation differentially regulates SUMO-dependent recruitment of ataxin-3 and RNF4 to DSBs, explaining how both proteins can play a stimulatory role at DSBs despite their opposing activities.

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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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Nuclear localization of Beclin 1 promotes radiation-induced DNA damage repair independent of autophagy

Scientific Reports ◽

10.1038/srep45385 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 13

Author(s):

Fei Xu ◽

Yixuan Fang ◽

Lili Yan ◽

Lan Xu ◽

Suping Zhang ◽

...

Keyword(s):

Dna Damage ◽

Dna Damage Repair ◽

Strand Break ◽

Beclin 1 ◽

Dsb Repair ◽

Dna Topoisomerase ◽

Damage Repair ◽

Dna Double Strand Break ◽

Radiation Induced

Abstract Beclin 1 is a well-established core mammalian autophagy protein that is embryonically indispensable and has been presumed to suppress oncogenesis via an autophagy-mediated mechanism. Here, we show that Beclin 1 is a prenatal primary cytoplasmic protein but rapidly relocated into the nucleus during postnatal development in mice. Surprisingly, deletion of beclin1 in in vitro human cells did not block an autophagy response, but attenuated the expression of several DNA double-strand break (DSB) repair proteins and formation of repair complexes, and reduced an ability to repair DNA in the cells exposed to ionizing radiation (IR). Overexpressing Beclin 1 improved the repair of IR-induced DSB, but did not restore an autophagy response in cells lacking autophagy gene Atg7, suggesting that Beclin 1 may regulate DSB repair independent of autophagy in the cells exposed to IR. Indeed, we found that Beclin 1 could directly interact with DNA topoisomerase IIβ and was recruited to the DSB sites by the interaction. These findings reveal a novel function of Beclin 1 in regulation of DNA damage repair independent of its role in autophagy particularly when the cells are under radiation insult.

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DNA Damage Repair and DNA Methylation in the Kidney

American Journal of Nephrology ◽

10.1159/000501356 ◽

2019 ◽

Vol 50 (2) ◽

pp. 81-91 ◽

Cited By ~ 4

Author(s):

Kaori Hayashi ◽

Akihito Hishikawa ◽

Hiroshi Itoh

Keyword(s):

Dna Methylation ◽

Dna Damage ◽

Dna Repair ◽

Methylation Status ◽

Dna Damage Repair ◽

Strand Break ◽

Repair System ◽

Damage Repair ◽

Dna Double Strand Break ◽

Cell Type Specific

The DNA repair system is essential for the maintenance of genome integrity and is mainly investigated in the areas of aging and cancer. The DNA repair system is strikingly cell-type specific, depending on the expression of DNA repair factors; therefore, different DNA repair systems may exist in each type of kidney cell. Importance of DNA repair in the kidney is suggested by renal phenotypes caused by both genetic mutations in the DNA repair pathway and increased stimuli of DNA damage. Recently, we reported the importance of DNA double-strand break repair in glomerular podocytes and its involvement in the alteration of DNA methylation status, which regulates podocyte phenotypes. In this review, we summarize the roles of the DNA repair system in the kidneys and possible associations with altered kidney DNA methylation, which have been infrequently reported together. Investigations of DNA damage repair and epigenetic changes in the kidneys may achieve a profound understanding of kidney aging and diseases.

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The Role of Polycomb Group Protein BMI1 in DNA Repair and Genomic Stability

International Journal of Molecular Sciences ◽

10.3390/ijms22062976 ◽

2021 ◽

Vol 22 (6) ◽

pp. 2976

Author(s):

Amira Fitieh ◽

Andrew J. Locke ◽

Mobina Motamedi ◽

Ismail Hassan Ismail

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Gene Silencing ◽

Strand Break ◽

Polycomb Group ◽

Polycomb Group Protein ◽

Post Translational Modifications ◽

Dna Damage Signaling ◽

Dna Double Strand Break ◽

Group Protein

The polycomb group (PcG) proteins are a class of transcriptional repressors that mediate gene silencing through histone post-translational modifications. They are involved in the maintenance of stem cell self-renewal and proliferation, processes that are often dysregulated in cancer. Apart from their canonical functions in epigenetic gene silencing, several studies have uncovered a function for PcG proteins in DNA damage signaling and repair. In particular, members of the poly-comb group complexes (PRC) 1 and 2 have been shown to recruit to sites of DNA damage and mediate DNA double-strand break repair. Here, we review current understanding of the PRCs and their roles in cancer development. We then focus on the PRC1 member BMI1, discussing the current state of knowledge of its role in DNA repair and genome integrity, and outline how it can be targeted pharmacologically.

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Fanconi Anemia Protein FANCD2 Promotes Immunoglobulin Gene Conversion and DNA Repair through a Mechanism Related to Homologous Recombination

Molecular and Cellular Biology ◽

10.1128/mcb.25.1.34-43.2005 ◽

2005 ◽

Vol 25 (1) ◽

pp. 34-43 ◽

Cited By ~ 98

Author(s):

Kazuhiko Yamamoto ◽

Seiki Hirano ◽

Masamichi Ishiai ◽

Kenichi Morishima ◽

Hiroyuki Kitao ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Homologous Recombination ◽

Gene Conversion ◽

Fanconi Anemia ◽

Strand Break ◽

Immunoglobulin Gene ◽

Dna Double Strand Break ◽

Mutant Cells ◽

Light Chain Locus

ABSTRACT Recent studies show overlap between Fanconi anemia (FA) proteins and those involved in DNA repair mediated by homologous recombination (HR). However, the mechanism by which FA proteins affect HR is unclear. FA proteins (FancA/C/E/F/G/L) form a multiprotein complex, which is responsible for DNA damage-induced FancD2 monoubiquitination, a key event for cellular resistance to DNA damage. Here, we show that FANCD2-disrupted DT40 chicken B-cell line is defective in HR-mediated DNA double-strand break (DSB) repair, as well as gene conversion at the immunoglobulin light-chain locus, an event also mediated by HR. Gene conversions occurring in mutant cells were associated with decreased nontemplated mutations. In contrast to these defects, we also found increased spontaneous sister chromatid exchange (SCE) and intact Rad51 foci formation after DNA damage. Thus, we propose that FancD2 promotes a subpathway of HR that normally mediates gene conversion by a mechanism that avoids crossing over and hence SCEs.

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DNA Double Strand Break Repair Pathways in Response to Different Types of Ionizing Radiation

Frontiers in Genetics ◽

10.3389/fgene.2021.738230 ◽

2021 ◽

Vol 12 ◽

Author(s):

Gerarda van de Kamp ◽

Tim Heemskerk ◽

Roland Kanaar ◽

Jeroen Essers

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Spatial Configuration ◽

Strand Break ◽

Dna Lesions ◽

Particle Therapy ◽

Photon Radiation ◽

Particle Radiation ◽

Dna Double Strand Break ◽

Repair Mechanisms

The superior dose distribution of particle radiation compared to photon radiation makes it a promising therapy for the treatment of tumors. However, the cellular responses to particle therapy and especially the DNA damage response (DDR) is not well characterized. Compared to photons, particles are thought to induce more closely spaced DNA lesions instead of isolated lesions. How this different spatial configuration of the DNA damage directs DNA repair pathway usage, is subject of current investigations. In this review, we describe recent insights into induction of DNA damage by particle radiation and how this shapes DNA end processing and subsequent DNA repair mechanisms. Additionally, we give an overview of promising DDR targets to improve particle therapy.

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