SIRT6 is a DNA Double-Strand Break Sensor

DNA double-strand breaks (DSB) are the most deleterious type of DNA damage. In this work, we show that SIRT6 directly recognizes DNA damage through a tunnel-like structure that has high affinity for DSB. SIRT6 relocates to sites of damage independently of signaling and known sensors. It activates downstream signaling for DSB repair by triggering ATM recruitment, H2AX phosphorylation and the recruitment of proteins of the homologous recombination and non-homologous end joining pathways. Our findings indicate that SIRT6 plays a previously uncharacterized role as a DNA damage sensor, a critical factor in initiating the DNA damage response (DDR). Moreover, other Sirtuins share some DSB-binding capacity and DDR activation. SIRT6 activates the DDR before the repair pathway is chosen, and prevents genomic instability. Our findings place SIRT6 as a sensor of DSB, and pave the road to dissecting the contributions of distinct DSB sensors in downstream signaling.

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Regulation of DNA Double-Strand Break Repair by Non-Coding RNAs

10.20944/preprints201810.0500.v1 ◽

2018 ◽

Cited By ~ 1

Author(s):

Roopa Thapar

Keyword(s):

Strand Break ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

End Joining ◽

Strand Breaks ◽

Dna Double Strand Break ◽

Protein Dna Interactions ◽

Damage Response ◽

Non Coding Rnas ◽

Non Homologous End Joining

DNA double-strand breaks (DSBs) are deleterious lesions that are generated in response to ionizing radiation or replication fork collapse that can lead to genomic instability and cancer.  Eukaryotes have evolved two major pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ) to repair DSBs.  Whereas the roles of protein-DNA interactions in HR and NHEJ have been fairly well defined, the functions of small and long non-coding RNAs and RNA-DNA hybrids in the DNA damage response is just beginning to be elucidated.  This review summarizes recent discoveries on the identification of non-coding RNAs and RNA-mediated regulation of DSB repair

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Regulation of the cellular DNA double-strand break response

Biochemistry and Cell Biology ◽

10.1139/o07-135 ◽

2007 ◽

Vol 85 (6) ◽

pp. 663-674 ◽

Cited By ~ 61

Author(s):

Kendra L. Cann ◽

Geoffrey G. Hicks

Keyword(s):

Mammalian Cells ◽

Strand Break ◽

Double Strand Break ◽

Double Strand Breaks ◽

Cell Cycle Checkpoints ◽

Dna Double Strand Breaks ◽

End Joining ◽

Strand Breaks ◽

Dna Double Strand Break ◽

Cellular Dna

DNA double-strand breaks occur frequently in cycling cells, and are also induced by exogenous sources, including ionizing radiation. Cells have developed integrated double-strand break response pathways to cope with these lesions, including pathways that initiate DNA repair (either via homologous recombination or nonhomologous end joining), the cell-cycle checkpoints (G1–S, intra-S phase, and G2–M) that provide time for repair, and apoptosis. However, before any of these pathways can be activated, the damage must first be recognized. In this review, we will discuss how the response of mammalian cells to DNA double-strand breaks is regulated, beginning with the activation of ATM, the pinnacle kinase of the double-strand break signalling cascade.

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Regulation of DNA Double-Strand Break Repair by Non-Coding RNAs

Molecules ◽

10.3390/molecules23112789 ◽

2018 ◽

Vol 23 (11) ◽

pp. 2789 ◽

Cited By ~ 24

Author(s):

Roopa Thapar

Keyword(s):

Strand Break ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

End Joining ◽

Strand Breaks ◽

Dna Double Strand Break ◽

Protein Dna Interactions ◽

Damage Response ◽

Non Coding Rnas ◽

Non Homologous End Joining

DNA double-strand breaks (DSBs) are deleterious lesions that are generated in response to ionizing radiation or replication fork collapse that can lead to genomic instability and cancer. Eukaryotes have evolved two major pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ) to repair DSBs. Whereas the roles of protein-DNA interactions in HR and NHEJ have been fairly well defined, the functions of small and long non-coding RNAs and RNA-DNA hybrids in the DNA damage response is just beginning to be elucidated. This review summarizes recent discoveries on the identification of non-coding RNAs and RNA-mediated regulation of DSB repair.

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Altered DNA ligase activity in human disease

Mutagenesis ◽

10.1093/mutage/gez026 ◽

2019 ◽

Vol 35 (1) ◽

pp. 51-60 ◽

Cited By ~ 3

Author(s):

Alan E Tomkinson ◽

Tasmin Naila ◽

Seema Khattri Bhandari

Keyword(s):

Dna Damage ◽

Dna Replication ◽

Double Strand Breaks ◽

Dna Ligase ◽

Dna Double Strand Breaks ◽

End Joining ◽

Strand Breaks ◽

Dna Ligases ◽

Ligase Iv ◽

Non Homologous End Joining

Abstract The joining of interruptions in the phosphodiester backbone of DNA is critical to maintain genome stability. These breaks, which are generated as part of normal DNA transactions, such as DNA replication, V(D)J recombination and meiotic recombination as well as directly by DNA damage or due to DNA damage removal, are ultimately sealed by one of three human DNA ligases. DNA ligases I, III and IV each function in the nucleus whereas DNA ligase III is the sole enzyme in mitochondria. While the identification of specific protein partners and the phenotypes caused either by genetic or chemical inactivation have provided insights into the cellular functions of the DNA ligases and evidence for significant functional overlap in nuclear DNA replication and repair, different results have been obtained with mouse and human cells, indicating species-specific differences in the relative contributions of the DNA ligases. Inherited mutations in the human LIG1 and LIG4 genes that result in the generation of polypeptides with partial activity have been identified as the causative factors in rare DNA ligase deficiency syndromes that share a common clinical symptom, immunodeficiency. In the case of DNA ligase IV, the immunodeficiency is due to a defect in V(D)J recombination whereas the cause of the immunodeficiency due to DNA ligase I deficiency is not known. Overexpression of each of the DNA ligases has been observed in cancers. For DNA ligase I, this reflects increased proliferation. Elevated levels of DNA ligase III indicate an increased dependence on an alternative non-homologous end-joining pathway for the repair of DNA double-strand breaks whereas elevated level of DNA ligase IV confer radioresistance due to increased repair of DNA double-strand breaks by the major non-homologous end-joining pathway. Efforts to determine the potential of DNA ligase inhibitors as cancer therapeutics are on-going in preclinical cancer models.

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Regulation of DNA Double-Strand Break Repair by Non-Coding RNAs

10.20944/preprints201810.0500.v3 ◽

2018 ◽

Author(s):

Roopa Thapar

Keyword(s):

Strand Break ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

End Joining ◽

Strand Breaks ◽

Dna Double Strand Break ◽

Protein Dna Interactions ◽

Damage Response ◽

Non Coding Rnas ◽

Non Homologous End Joining

DNA double-strand breaks (DSBs) are deleterious lesions that are generated in response to ionizing radiation or replication fork collapse that can lead to genomic instability and cancer.  Eukaryotes have evolved two major pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ) to repair DSBs.  Whereas the roles of protein-DNA interactions in HR and NHEJ have been fairly well defined, the functions of small and long non-coding RNAs and RNA-DNA hybrids in the DNA damage response is just beginning to be elucidated.  This review summarizes recent discoveries on the identification of non-coding RNAs and RNA-mediated regulation of DSB repair

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Mechanistic modelling and Bayesian inference elucidates the variable dynamics of double-strand break repair

10.1101/026070 ◽

2015 ◽

Author(s):

M. Woods ◽

C.P. Barnes

Keyword(s):

Dna Repair ◽

Strand Break ◽

Double Strand Break ◽

Double Strand Breaks ◽

Data Sets ◽

End Joining ◽

Strand Breaks ◽

Alternative End Joining ◽

Intermediate Repair ◽

Non Homologous End Joining

AbstractDNA double-strand breaks are lesions that form during metabolism, DNA replication and exposure to mutagens. When a double-strand break occurs one of a number of repair mechanisms is recruited, all of which have differing propensities for mutational events. Despite DNA repair being of crucial importance, the relative contribution of these mechanisms and their regulatory interactions remain to be fully elucidated. Understanding these mutational processes will have a profound impact on our knowledge of genomic instability, with implications across health, disease and evolution. Here we present a new method to model the combined activation of non-homologous end joining, single strand annealing and alternative end joining, following exposure to ionizing radiation. We use Bayesian statistics to integrate eight biological data sets of double-strand break repair curves under varying genetic knockouts and confirm that our model is predictive by re-simulating and comparing to additional data. Analysis of the model suggests that there are at least three disjoint modes of repair, which we assign as fast, slow and intermediate. Our results show that when multiple data sets are combined, the rate for intermediate repair is variable amongst genetic knockouts. Further analysis suggests that the ratio between slow and intermediate repair depends on the presence or absence of DNA-PKcs and Ku70, which implies that non-homologous end joining and alternative end joining are not independent. Finally, we consider the proportion of double-strand breaks within each mechanism as a time series and predict activity as a function of repair rate. We outline how our insights can be directly tested using imaging and sequencing techniques and conclude that there is evidence of variable dynamics in alternative repair pathways. Our approach is an important step towards providing a unifying theoretical framework for the dynamics of DNA repair processes.

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Regulation of DNA Double-Strand Break Repair by Non-Coding RNAs

10.20944/preprints201810.0500.v2 ◽

2018 ◽

Author(s):

Roopa Thapar

Keyword(s):

Strand Break ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

End Joining ◽

Strand Breaks ◽

Dna Double Strand Break ◽

Protein Dna Interactions ◽

Damage Response ◽

Non Coding Rnas ◽

Non Homologous End Joining

DNA double-strand breaks (DSBs) are deleterious lesions that are generated in response to ionizing radiation or replication fork collapse that can lead to genomic instability and cancer.  Eukaryotes have evolved two major pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ) to repair DSBs.  Whereas the roles of protein-DNA interactions in HR and NHEJ have been fairly well defined, the functions of small and long non-coding RNAs and RNA-DNA hybrids in the DNA damage response is just beginning to be elucidated.  This review summarizes recent discoveries on the identification of non-coding RNAs and RNA-mediated regulation of DSB repair

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LC8/DYNLL1 is a 53BP1 effector and regulates checkpoint activation

Nucleic Acids Research ◽

10.1093/nar/gkz263 ◽

2019 ◽

Vol 47 (12) ◽

pp. 6236-6249 ◽

Cited By ~ 9

Author(s):

Kirk L West ◽

Jessica L Kelliher ◽

Zhanzhan Xu ◽

Liwei An ◽

Megan R Reed ◽

...

Keyword(s):

Dna Damage ◽

Double Strand Breaks ◽

Parp Inhibition ◽

Current Evidence ◽

Dependent Manner ◽

Dna Double Strand Breaks ◽

End Joining ◽

Checkpoint Activation ◽

Strand Breaks ◽

Non Homologous End Joining

Abstract The tumor suppressor protein 53BP1 plays key roles in response to DNA double-strand breaks (DSBs) by serving as a master scaffold at the damaged chromatin. Current evidence indicates that 53BP1 assembles a cohort of DNA damage response (DDR) factors to distinctly execute its repertoire of DSB responses, including checkpoint activation and non-homologous end joining (NHEJ) repair. Here, we have uncovered LC8 (a.k.a. DYNLL1) as an important 53BP1 effector. We found that LC8 accumulates at laser-induced DNA damage tracks in a 53BP1-dependent manner and requires the canonical H2AX-MDC1-RNF8-RNF168 signal transduction cascade. Accordingly, genetic inactivation of LC8 or its interaction with 53BP1 resulted in checkpoint defects. Importantly, loss of LC8 alleviated the hypersensitivity of BRCA1-depleted cells to ionizing radiation and PARP inhibition, highlighting the 53BP1-LC8 module in counteracting BRCA1-dependent functions in the DDR. Together, these data establish LC8 as an important mediator of a subset of 53BP1-dependent DSB responses.

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Recruitment of MRE-11 to complex DNA damage is modulated by meiosis-specific chromosome organization

10.1101/2020.06.26.174573 ◽

2020 ◽

Author(s):

Kailey Harrell ◽

Madison Day ◽

Sarit Smolikove

Keyword(s):

Dna Damage ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

End Joining ◽

Strand Breaks ◽

Damage Response ◽

Non Homologous End Joining ◽

Altered Form ◽

Laser Microirradiation ◽

Clustered Dna Damage

AbstractDNA double-strand breaks (DSBs) are one of the most dangerous assaults on the genome, and yet their natural and programmed production are inherent to life. When DSBs arise close together (clustered) they are particularly deleterious, and their repair may require an altered form of the DNA damage response. Our understanding of how clustered DSBs are repaired in the germline is unknown. Using UV laser microirradiation, we examine early events in the repair of clustered DSBs in germ cells within whole, live, Caenorhabditis elegans. We use precise temporal resolution to show how the recruitment of MRE-11 to complex damage is regulated, and that clustered DNA damage can recruit proteins from various repair pathways. Abrogation of non-homologous end joining or COM-1 attenuates the recruitment of MRE-11 through distinct mechanisms. The synaptonemal complex plays both positive and negative regulatory roles in these mutant contexts. These findings together indicate that MRE-11 is regulated by modifying its accessibility to chromosomes.

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