scholarly journals Histone dynamics during DNA replication stress

2021 ◽  
Vol 28 (1) ◽  
Author(s):  
Chia-Ling Hsu ◽  
Shin Yen Chong ◽  
Chia-Yeh Lin ◽  
Cheng-Fu Kao
Keyword(s):  
Stress Responses ◽  
Genome Stability ◽  
Genome Instability ◽  
Replication Stress ◽  
Dna Lesions ◽  
Protective Mechanisms ◽  
Replication Process ◽  
Dna Replication Stress ◽  
External Sources

AbstractAccurate and complete replication of the genome is essential not only for genome stability but also for cell viability. However, cells face constant threats to the replication process, such as spontaneous DNA modifications and DNA lesions from endogenous and external sources. Any obstacle that slows down replication forks or perturbs replication dynamics is generally considered to be a form of replication stress, and the past decade has seen numerous advances in our understanding of how cells respond to and resolve such challenges. Furthermore, recent studies have also uncovered links between defects in replication stress responses and genome instability or various diseases, such as cancer. Because replication stress takes place in the context of chromatin, histone dynamics play key roles in modulating fork progression and replication stress responses. Here, we summarize the current understanding of histone dynamics in replication stress, highlighting recent advances in the characterization of fork-protective mechanisms.

scholarly journals Multi-BRCT Domain Protein Brc1 Links Rhp18/Rad18 and γH2A To Maintain Genome Stability during S Phase

2017 ◽  
Vol 37 (22) ◽  
Author(s):  
Michael C. Reubens ◽  
Sophie Rozenzhak ◽  
Paul Russell
Keyword(s):  
Genome Stability ◽  
Genome Instability ◽  
Replication Stress ◽  
S Phase ◽  
Dna Lesions ◽  
Brct Domain ◽  
Replication Forks ◽  
Content Type ◽  
Domain Protein ◽  
Chromosome Integrity

ABSTRACT DNA replication involves the inherent risk of genome instability, since replisomes invariably encounter DNA lesions or other structures that stall or collapse replication forks during the S phase. In the fission yeast Schizosaccharomyces pombe, the multi-BRCT domain protein Brc1, which is related to budding yeast Rtt107 and mammalian PTIP, plays an important role in maintaining genome integrity and cell viability when cells experience replication stress. The C-terminal pair of BRCT domains in Brc1 were previously shown to bind phosphohistone H2A (γH2A) formed by Rad3/ATR checkpoint kinase at DNA lesions; however, the putative scaffold interactions involving the N-terminal BRCT domains 1 to 4 of Brc1 have remained obscure. Here, we show that these domains bind Rhp18/Rad18, which is an E3 ubiquitin protein ligase that has crucial functions in postreplication repair. A missense allele in BRCT domain 4 of Brc1 disrupts binding to Rhp18 and causes sensitivity to replication stress. Brc1 binding to Rhp18 and γH2A are required for the Brc1 overexpression suppression of smc6-74, a mutation that impairs the Smc5/6 structural maintenance of chromosomes complex required for chromosome integrity and repair of collapsed replication forks. From these findings, we propose that Brc1 provides scaffolding functions linking γH2A, Rhp18, and Smc5/6 complex at damaged replication forks.

scholarly journals Multi-BRCT domain protein Brc1 links Rhp18/Rad18 and γH2A to maintain genome stability during S-phase

2017 ◽  
Author(s):  
Michael C. Reubens ◽  
Sophie Rozenzhak ◽  
Paul Russell
Keyword(s):  
Genome Stability ◽  
Genome Instability ◽  
Replication Stress ◽  
S Phase ◽  
Dna Lesions ◽  
Brct Domain ◽  
Replication Forks ◽  
Histone H2a ◽  
Domain Protein ◽  
Chromosome Integrity

ABSTRACTDNA replication involves the inherent risk of genome instability, as replisomes invariably encounter DNA lesions or other structures that stall or collapse replication forks during S-phase. In the fission yeast Schizosaccharomyces pombe, the multi-BRCT domain protein Brc1, which is related to budding yeast Rtt107 and mammalian PTIP, plays an important role in maintaining genome integrity and cell viability when cells experience replication stress. The C-terminal pair of BRCT domains in Brc1 were previously shown to bind phospho-histone H2A (γH2A) formed by Rad3/ATR checkpoint kinase at DNA lesions; however, the putative scaffold interactions involving the N-terminal BRCT domains 1-4 of Brc1 have remained obscure. Here we show that these domains bind Rhp18/Rad18, which is an E3 ubiquitin protein ligase that has crucial functions in postreplication repair. A missense allele in BRCT domain 4 of Brc1 disrupts binding to Rhp18 and causes sensitivity to replication stress. Brc1 binding to Rhp18 and γH2A are required for the Brc1-overexpression suppression of smc6-74, which impairs the Smc5/6 structural maintenance of chromosomes complex required for chromosome integrity and repair of collapsed replication forks. From these findings we propose that Brc1 provides scaffolding functions linking γH2A, Rhp18, and Smc5/6 complex at damaged replication forks.

scholarly journals FBH1 promotes DNA double-strand breakage and apoptosis in response to DNA replication stress

2013 ◽  
Vol 200 (2) ◽  
pp. 141-149 ◽  
Author(s):  
Yeon-Tae Jeong ◽  
Mario Rossi ◽  
Lukas Cermak ◽  
Anita Saraf ◽  
Laurence Florens ◽  
...  
Keyword(s):  
Dna Replication ◽  
Genome Stability ◽  
Protein A ◽  
Replication Stress ◽  
Genotoxic Stress ◽  
Dna Helicase ◽  
Dna Lesions ◽  
Physical Interaction ◽  
Helicase Activity ◽  
Dna Replication Stress

Proper resolution of stalled replication forks is essential for genome stability. Purification of FBH1, a UvrD DNA helicase, identified a physical interaction with replication protein A (RPA), the major cellular single-stranded DNA (ssDNA)–binding protein complex. Compared with control cells, FBH1-depleted cells responded to replication stress with considerably fewer double-strand breaks (DSBs), a dramatic reduction in the activation of ATM and DNA-PK and phosphorylation of RPA2 and p53, and a significantly increased rate of survival. A minor decrease in ssDNA levels was also observed. All these phenotypes were rescued by wild-type FBH1, but not a FBH1 mutant lacking helicase activity. FBH1 depletion had no effect on other forms of genotoxic stress in which DSBs form by means that do not require ssDNA intermediates. In response to catastrophic genotoxic stress, apoptosis prevents the persistence and propagation of DNA lesions. Our findings show that FBH1 helicase activity is required for the efficient induction of DSBs and apoptosis specifically in response to DNA replication stress.

scholarly journals Regulation of ETAA1-mediated ATR activation couples DNA replication fidelity and genome stability

2019 ◽  
Vol 218 (12) ◽  
pp. 3943-3953 ◽  
Author(s):  
Divya Achuthankutty ◽  
Roshan Singh Thakur ◽  
Peter Haahr ◽  
Saskia Hoffmann ◽  
Alexandros P. Drainas ◽  
...  
Keyword(s):  
Dna Replication ◽  
Cellular Response ◽  
Genome Stability ◽  
Genome Instability ◽  
Replication Stress ◽  
Regulatory Control ◽  
Replicative Stress ◽  
Dna Replication Stress ◽  
Stress Dependent ◽  
Atr Kinase

The ATR kinase is a master regulator of the cellular response to DNA replication stress. Activation of ATR relies on dual pathways involving the TopBP1 and ETAA1 proteins, both of which harbor ATR-activating domains (AADs). However, the exact contribution of the recently discovered ETAA1 pathway to ATR signaling in different contexts remains poorly understood. Here, using an unbiased CRISPR-Cas9–based genome-scale screen, we show that the ATR-stimulating function of ETAA1 becomes indispensable for cell fitness and chromosome stability when the fidelity of DNA replication is compromised. We demonstrate that the ATR-activating potential of ETAA1 is controlled by cell cycle– and replication stress–dependent phosphorylation of highly conserved residues within its AAD, and that the stimulatory impact of these modifications is required for the ability of ETAA1 to prevent mitotic chromosome abnormalities following replicative stress. Our findings suggest an important role of ETAA1 in protecting against genome instability arising from incompletely duplicated DNA via regulatory control of its ATR-stimulating potential.

scholarly journals MRE11-RAD50-NBS1 activates Fanconi Anemia R-loop suppression at transcription-replication conflicts

2018 ◽  
Author(s):  
Emily Yun-chia Chang ◽  
James P. Wells ◽  
Shu-Huei Tsai ◽  
Yan Coulombe ◽  
Yujia A. Chan ◽  
...  
Keyword(s):  
Dna Replication ◽  
Fanconi Anemia ◽  
Replication Fork ◽  
Genome Instability ◽  
Human Cancer ◽  
Replication Stress ◽  
Maintenance Factors ◽  
Genome Wide ◽  
A Genome ◽  
Dna Replication Stress

SUMMARYEctopic R-loop accumulation causes DNA replication stress and genome instability. To avoid these outcomes, cells possess a range of anti-R-loop mechanisms, including RNaseH that degrades the RNA moiety in R-loops. To comprehensively identify anti-R-loop mechanisms, we performed a genome-wide trigenic interaction screen in yeast lacking RNH1 and RNH201. We identified >100 genes critical for fitness in the absence of RNaseH, which were enriched for DNA replication fork maintenance factors such as RAD50. We show in yeast and human cells that R-loops accumulate during RAD50 depletion. In human cancer cell models, we find that RAD50 and its partners in the MRE11-RAD50-NBS1 complex regulate R-loop-associated DNA damage and replication stress. We show that a non-nucleolytic function of MRE11 is important for R-loop suppression via activation of PCNA-ubiquitination by RAD18 and recruiting anti-R-loop helicases in the Fanconi Anemia pathway. This work establishes a novel role for MRE11-RAD50-NBS1 in directing tolerance mechanisms of transcription-replication conflicts.

scholarly journals ARID1A regulates R-loop associated DNA replication stress

2020 ◽  
Author(s):  
Shuhe Tsai ◽  
Emily Yun-chia Chang ◽  
Louis-Alexandre Fournier ◽  
James P. Wells ◽  
Sean W. Minaker ◽  
...  
Keyword(s):  
Dna Replication ◽  
Genome Stability ◽  
Clear Cell ◽  
Replication Stress ◽  
Clear Cell Ovarian Carcinoma ◽  
Dna Replication Stress ◽  
Cancer Types ◽  
The Impact ◽  
Oncogenic Gene ◽  
Transcription And Replication

ABSTRACTARID1A is lost in up to 7% of all cancers, and this frequency increases in certain cancer types, such as clear cell ovarian carcinoma where ARID1A protein is lost in about 50% of cases. While the impact of ARID1A loss on the function of the BAF chromatin remodeller complexes is likely to drive oncogenic gene expression programs in specific contexts, ARID1A also binds genome stability regulators such as ATR and TOP2. Here we show that ARID1A loss leads to DNA replication stress associated with R-loops and transcription-replication conflicts in human cells. These effects correlate with altered transcription and replication dynamics in ARID1A knockout cells and to reduced TOP2A binding at R-loop sites. Together this work extends mechanisms of replication stress in ARID1A deficient cells with implications for targeting ARID1A deficient cancers.

scholarly journals Distinct roles of structure-specific endonucleases EEPD1 and Metnase in replication stress responses

NAR Cancer ◽  
2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Neelam Sharma ◽  
Michael C Speed ◽  
Christopher P Allen ◽  
David G Maranon ◽  
Elizabeth Williamson ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Cell Lines ◽  
Stress Responses ◽  
Genome Instability ◽  
Replication Stress ◽  
Cancer Etiology ◽  
Double Knockout ◽  
Damage Response ◽  
Stalled Replication Forks ◽  
Single Knockout

Abstract Accurate DNA replication and segregation are critical for maintaining genome integrity and suppressing cancer. Metnase and EEPD1 are DNA damage response (DDR) proteins frequently dysregulated in cancer and implicated in cancer etiology and tumor response to genotoxic chemo- and radiotherapy. Here, we examine the DDR in human cell lines with CRISPR/Cas9 knockout of Metnase or EEPD1. The knockout cell lines exhibit slightly slower growth rates, significant hypersensitivity to replication stress, increased genome instability and distinct alterations in DDR signaling. Metnase and EEPD1 are structure-specific nucleases. EEPD1 is recruited to and cleaves stalled forks to initiate fork restart by homologous recombination. Here, we demonstrate that Metnase is also recruited to stalled forks where it appears to dimethylate histone H3 lysine 36 (H3K36me2), raising the possibility that H3K36me2 promotes DDR factor recruitment or limits nucleosome eviction to protect forks from nucleolytic attack. We show that stalled forks are cleaved normally in the absence of Metnase, an important and novel result because a prior study indicated that Metnase nuclease is important for timely fork restart. A double knockout was as sensitive to etoposide as either single knockout, suggesting a degree of epistasis between Metnase and EEPD1. We propose that EEPD1 initiates fork restart by cleaving stalled forks, and that Metnase may promote fork restart by processing homologous recombination intermediates and/or inducing H3K36me2 to recruit DDR factors. By accelerating fork restart, Metnase and EEPD1 reduce the chance that stalled replication forks will adopt toxic or genome-destabilizing structures, preventing genome instability and cancer. Metnase and EEPD1 are overexpressed in some cancers and thus may also promote resistance to genotoxic therapeutics.

scholarly journals The impact of transcription-mediated replication stress on genome instability and human disease

2020 ◽  
Vol 1 (5) ◽  
pp. 207-234
Author(s):  
Stefano Gnan ◽  
Yaqun Liu ◽  
Manuela Spagnuolo ◽  
Chun-Long Chen
Keyword(s):  
Dna Replication ◽  
Gene Transcription ◽  
Human Disease ◽  
Genome Stability ◽  
Genome Instability ◽  
Current Knowledge ◽  
Replication Stress ◽  
Genome Replication ◽  
Living Organisms ◽  
The Impact

Abstract DNA replication is a vital process in all living organisms. At each cell division, > 30,000 replication origins are activated in a coordinated manner to ensure the duplication of > 6 billion base pairs of the human genome. During differentiation and development, this program must adapt to changes in chromatin organization and gene transcription: its deregulation can challenge genome stability, which is a leading cause of many diseases including cancers and neurological disorders. Over the past decade, great progress has been made to better understand the mechanisms of DNA replication regulation and how its deregulation challenges genome integrity and leads to human disease. Growing evidence shows that gene transcription has an essential role in shaping the landscape of genome replication, while it is also a major source of endogenous replication stress inducing genome instability. In this review, we discuss the current knowledge on the various mechanisms by which gene transcription can impact on DNA replication, leading to genome instability and human disease.

scholarly journals Global analysis of genomic instability caused by DNA replication stress in Saccharomyces cerevisiae

2016 ◽  
Vol 113 (50) ◽  
pp. E8114-E8121 ◽  
Author(s):  
Dao-Qiong Zheng ◽  
Ke Zhang ◽  
Xue-Chang Wu ◽  
Piotr A. Mieczkowski ◽  
Thomas D. Petes
Keyword(s):  
Dna Replication ◽  
Genomic Instability ◽  
Dna Polymerase ◽  
Replication Stress ◽  
Dna Lesions ◽  
Chromosome Loss ◽  
Dna Breaks ◽  
Dna Polymerase Δ ◽  
Dna Replication Stress ◽  
Low Levels

DNA replication stress (DRS)-induced genomic instability is an important factor driving cancer development. To understand the mechanisms of DRS-associated genomic instability, we measured the rates of genomic alterations throughout the genome in a yeast strain with lowered expression of the replicative DNA polymerase δ. By a genetic test, we showed that most recombinogenic DNA lesions were introduced during S or G2 phase, presumably as a consequence of broken replication forks. We observed a high rate of chromosome loss, likely reflecting a reduced capacity of the low-polymerase strains to repair double-stranded DNA breaks (DSBs). We also observed a high frequency of deletion events within tandemly repeated genes such as the ribosomal RNA genes. By whole-genome sequencing, we found that low levels of DNA polymerase δ elevated mutation rates, both single-base mutations and small insertions/deletions. Finally, we showed that cells with low levels of DNA polymerase δ tended to accumulate small promoter mutations that increased the expression of this polymerase. These deletions conferred a selective growth advantage to cells, demonstrating that DRS can be one factor driving phenotypic evolution.

scholarly journals Treacle and TOPBP1 control replication stress response in the nucleolus

2021 ◽  
Vol 220 (8) ◽  
Author(s):  
Artem K. Velichko ◽  
Natalia Ovsyannikova ◽  
Nadezhda V. Petrova ◽  
Artem V. Luzhin ◽  
Maria Vorobjeva ◽  
...  
Keyword(s):  
Stress Response ◽  
Genome Instability ◽  
Replication Stress ◽  
Low Complexity ◽  
Drug Induced ◽  
Response Factors ◽  
Checkpoint Activation ◽  
Stalled Replication Forks

Replication stress is one of the main sources of genome instability. Although the replication stress response in eukaryotic cells has been extensively studied, almost nothing is known about the replication stress response in nucleoli. Here, we demonstrate that initial replication stress–response factors, such as RPA, TOPBP1, and ATR, are recruited inside the nucleolus in response to drug-induced replication stress. The role of TOPBP1 goes beyond the typical replication stress response; it interacts with the low-complexity nucleolar protein Treacle (also referred to as TCOF1) and forms large Treacle–TOPBP1 foci inside the nucleolus. In response to replication stress, Treacle and TOPBP1 facilitate ATR signaling at stalled replication forks, reinforce ATR-mediated checkpoint activation inside the nucleolus, and promote the recruitment of downstream replication stress response proteins inside the nucleolus without forming nucleolar caps. Characterization of the Treacle–TOPBP1 interaction mode leads us to propose that these factors can form a molecular platform for efficient stress response in the nucleolus.

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