scholarly journals Polycomb Repression without Bristles: Facultative Heterochromatin and Genome Stability in Fungi

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 638 ◽  
Author(s):  
John B. Ridenour ◽  
Mareike Möller ◽  
Michael Freitag
Keyword(s):  
Transcriptional Repression ◽  
Genome Stability ◽  
Genome Instability ◽  
Future Research ◽  
Genome Maintenance ◽  
Facultative Heterochromatin ◽  
H3k27 Methylation ◽  
Polycomb Repression ◽  
Fungal Genomes ◽  
And Function

Genome integrity is essential to maintain cellular function and viability. Consequently, genome instability is frequently associated with dysfunction in cells and associated with plant, animal, and human diseases. One consequence of relaxed genome maintenance that may be less appreciated is an increased potential for rapid adaptation to changing environments in all organisms. Here, we discuss evidence for the control and function of facultative heterochromatin, which is delineated by methylation of histone H3 lysine 27 (H3K27me) in many fungi. Aside from its relatively well understood role in transcriptional repression, accumulating evidence suggests that H3K27 methylation has an important role in controlling the balance between maintenance and generation of novelty in fungal genomes. We present a working model for a minimal repressive network mediated by H3K27 methylation in fungi and outline challenges for future research.

scholarly journals Replisome bypass of a protein-based R-loop block by Pif1

2020 ◽  
Vol 117 (48) ◽  
pp. 30354-30361
Author(s):  
Grant D. Schauer ◽  
Lisanne M. Spenkelink ◽  
Jacob S. Lewis ◽  
Olga Yurieva ◽  
Stefan H. Mueller ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Stability ◽  
Genome Instability ◽  
Multiprotein Complex ◽  
Genome Maintenance ◽  
Visualization Technique ◽  
General Displacement ◽  
Maintain Genome Stability ◽  
Protein Blocks

Efficient and faithful replication of the genome is essential to maintain genome stability. Replication is carried out by a multiprotein complex called the replisome, which encounters numerous obstacles to its progression. Failure to bypass these obstacles results in genome instability and may facilitate errors leading to disease. Cells use accessory helicases that help the replisome bypass difficult barriers. All eukaryotes contain the accessory helicase Pif1, which tracks in a 5′–3′ direction on single-stranded DNA and plays a role in genome maintenance processes. Here, we reveal a previously unknown role for Pif1 in replication barrier bypass. We use an in vitro reconstitutedSaccharomyces cerevisiaereplisome to demonstrate that Pif1 enables the replisome to bypass an inactive (i.e., dead) Cas9 (dCas9) R-loop barrier. Interestingly, dCas9 R-loops targeted to either strand are bypassed with similar efficiency. Furthermore, we employed a single-molecule fluorescence visualization technique to show that Pif1 facilitates this bypass by enabling the simultaneous removal of the dCas9 protein and the R-loop. We propose that Pif1 is a general displacement helicase for replication bypass of both R-loops and protein blocks.

scholarly journals The yeast core spliceosome maintains genome integrity through R-loop prevention and α-tubulin expression

2018 ◽  
Author(s):  
Annie S. Tam ◽  
Veena Mathew ◽  
Tianna S. Sihota ◽  
Anni Zhang ◽  
Peter C. Stirling
Keyword(s):  
Gene Expression ◽  
Dna Replication ◽  
Chromosome Segregation ◽  
Genome Stability ◽  
Spindle Assembly Checkpoint ◽  
Genome Instability ◽  
Genome Integrity ◽  
Genome Maintenance ◽  
Maintenance Factors ◽  
Spindle Assembly Checkpoint Protein

To achieve genome stability cells must coordinate the action of various DNA transactions including DNA replication, repair, transcription and chromosome segregation. How transcription and RNA processing enable genome stability is only partly understood. Two predominant models have emerged: one involving changes in gene expression that perturb other genome maintenance factors, and another in which genotoxic DNA:RNA hybrids, called R-loops, impair DNA replication. Here we characterize genome instability phenotypes in a panel yeast splicing factor mutants and find that mitotic defects, and in some cases R-loop accumulation, are causes of genome instability. Genome instability in splicing mutants is exacerbated by loss of the spindle-assembly checkpoint protein Mad1. Moreover, removal of the intron from the α-tubulin gene TUB1 restores genome integrity. Thus, while R-loops contribute in some settings, defects in yeast splicing predominantly lead to genome instability through effects on gene expression.

scholarly journals A genome-wide screen identifies genes that suppress the accumulation of spontaneous mutations in young and aged yeast cells

2018 ◽  
Author(s):  
Daniele Novarina ◽  
Georges Janssens ◽  
Koen Bokern ◽  
Tim Schut ◽  
Noor van Oerle ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Genome Stability ◽  
Genome Instability ◽  
Spontaneous Mutation ◽  
Yeast Cells ◽  
Spontaneous Mutations ◽  
Genome Maintenance ◽  
Spontaneous Mutation Rate ◽  
Genome Wide ◽  
A Genome

To ensure proper transmission of genetic information, cells need to preserve and faithfully replicate their genome, and failure to do so leads to genome instability, a hallmark of both cancer and aging. Defects in genes involved in guarding genome stability cause several human progeroid syndromes, and an age-dependent accumulation of mutations has been observed in different organisms, from yeast to mammals. However, it is unclear if the spontaneous mutation rate changes during aging, and if specific pathways are important for genome maintenance in old cells. We developed a high-throughput replica-pinning approach to screen for genes important to suppress the accumulation of spontaneous mutations during yeast replicative aging. We found 13 known mutation suppression genes, and 31 genes that had no previous link to spontaneous mutagenesis, and all acted independently of age. Importantly, we identified PEX19, encoding an evolutionarily conserved peroxisome biogenesis factor, as an age-specific mutation suppression gene. While wild-type and pex19Δ young cells have similar spontaneous mutation rates, aged cells lacking PEX19 display an elevated mutation rate. This finding suggests that functional peroxisomes are important to preserve genome integrity specifically in old cells, possibly due to their role in reactive oxygen species metabolism.

scholarly journals Multistep mechanism of DNA replication-coupled G-quadruplex resolution

2020 ◽  
Author(s):  
Koichi Sato ◽  
Nerea Martin-Pintado ◽  
Harm Post ◽  
Maarten Altelaar ◽  
Puck Knipscheer
Keyword(s):  
Dna Replication ◽  
Genome Stability ◽  
Genome Instability ◽  
Genome Maintenance ◽  
Replicative Helicase ◽  
Dna Structures ◽  
G Quadruplex ◽  
Egg Extracts ◽  
Leading Strand ◽  
Lagging Strand

SummaryG-quadruplex (or G4) structures are non-canonical DNA structures that form in guanine-rich sequences and threaten genome stability when not properly resolved. G4 unwinding occurs during S phase via an unknown mechanism. Using Xenopus egg extracts, we define a three-step G4 unwinding mechanism that is coupled to DNA replication. First, the replicative helicase (CMG) stalls at a leading strand G4 structure. Second, the DHX36 helicase mediates the bypass of the CMG past the intact G4 structure, which allows approach of the leading strand to the G4. Third, G4 structure unwinding by the FANCJ helicase enables the DNA polymerase to synthesize past the G4 motif. A G4 on the lagging strand template does not stall CMG, but still requires DNA replication for unwinding. DHX36 and FANCJ have partially redundant roles, conferring robustness to this pathway. Our data reveal a novel genome maintenance pathway that promotes faithful G4 replication thereby avoiding genome instability.

scholarly journals Molecular connections between circadian rhythm and genome maintenance pathways

2020 ◽  
Author(s):  
Arun Mouli Kolinjivadi ◽  
Siao Ting Chong ◽  
Joanne Ngeow
Keyword(s):  
Cell Cycle ◽  
Dna Repair ◽  
Dna Replication ◽  
Circadian Clock ◽  
Genome Stability ◽  
Genome Instability ◽  
Model Systems ◽  
Genome Maintenance ◽  
Replication Fork Progression ◽  
Repair Efficiency

Co-ordinated oscillation of mammalian circadian clock and cell cycle is essential for cellular and organismal homeostasis. Existing preclinical, epidemiological, molecular and biochemical evidence reveal a robust interplay between circadian clock, genome instability and cancer. Furthermore, recent investigations have demonstrated that the alterations in circadian clock perturb genome stability by modulating the cell cycle timing, altering DNA replication fork progression, influencing DNA Damage Response (DDR) and DNA repair efficiency. In this review, we examine the most recent findings from different eukaryotic model systems and discuss the functional interaction between circadian factors with key DNA replication, DDR and DNA repair genes.

scholarly journals DDB1 Maintains Genome Integrity through Regulation of Cdt1

2006 ◽  
Vol 26 (21) ◽  
pp. 7977-7990 ◽  
Author(s):  
Courtney A. Lovejoy ◽  
Kimberli Lock ◽  
Ashwini Yenamandra ◽  
David Cortez
Keyword(s):  
Dna Damage ◽  
Genome Stability ◽  
Genome Instability ◽  
Excision Repair ◽  
Dna Lesions ◽  
Cell Cycle Checkpoints ◽  
Dna Double Strand Breaks ◽  
Genome Maintenance ◽  
Strand Breaks ◽  
Ubiquitin Ligase Complex

ABSTRACT DDB1, a component of a Cul4A ubiquitin ligase complex, promotes nucleotide excision repair (NER) and regulates DNA replication. We have investigated the role of human DDB1 in maintaining genome stability. DDB1-depleted cells accumulate DNA double-strand breaks in widely dispersed regions throughout the genome and have activated ATM and ATR cell cycle checkpoints. Depletion of Cul4A yields similar phenotypes, indicating that an E3 ligase function of DDB1 is important for genome maintenance. In contrast, depletion of DDB2, XPA, or XPC does not cause activation of DNA damage checkpoints, indicating that defects in NER are not involved. One substrate of DDB1-Cul4A that is crucial for preventing genome instability is Cdt1. DDB1-depleted cells exhibit increased levels of Cdt1 protein and rereplication, despite containing other Cdt1 regulatory mechanisms. The rereplication, accumulation of DNA damage, and activation of checkpoint responses in DDB1-depleted cells require entry into S phase and are partially, but not completely, suppressed by codepletion of Cdt1. Therefore, DDB1 prevents DNA lesions from accumulating in replicating human cells, in part by regulating Cdt1 degradation.

scholarly journals Exploring the Structures and Functions of Macromolecular SLX4-Nuclease Complexes in Genome Stability

2021 ◽  
Vol 12 ◽  
Author(s):  
Brandon J. Payliss ◽  
Ayushi Patel ◽  
Anneka C. Sheppard ◽  
Haley D. M. Wyatt
Keyword(s):  
Dna Repair ◽  
Homologous Recombination ◽  
Genome Stability ◽  
Genome Instability ◽  
Strand Break ◽  
Biochemical Properties ◽  
Strand Breaks ◽  
Dna Double Strand Break ◽  
Recent Developments ◽  
And Function

All organisms depend on the ability of cells to accurately duplicate and segregate DNA into progeny. However, DNA is frequently damaged by factors in the environment and from within cells. One of the most dangerous lesions is a DNA double-strand break. Unrepaired breaks are a major driving force for genome instability. Cells contain sophisticated DNA repair networks to counteract the harmful effects of genotoxic agents, thus safeguarding genome integrity. Homologous recombination is a high-fidelity, template-dependent DNA repair pathway essential for the accurate repair of DNA nicks, gaps and double-strand breaks. Accurate homologous recombination depends on the ability of cells to remove branched DNA structures that form during repair, which is achieved through the opposing actions of helicases and structure-selective endonucleases. This review focuses on a structure-selective endonuclease called SLX1-SLX4 and the macromolecular endonuclease complexes that assemble on the SLX4 scaffold. First, we discuss recent developments that illuminate the structure and biochemical properties of this somewhat atypical structure-selective endonuclease. We then summarize the multifaceted roles that are fulfilled by human SLX1-SLX4 and its associated endonucleases in homologous recombination and genome stability. Finally, we discuss recent work on SLX4-binding proteins that may represent integral components of these macromolecular nuclease complexes, emphasizing the structure and function of a protein called SLX4IP.

scholarly journals S. pombe DNA translocases Rrp1 and Rrp2 have distinct roles at centromeres and telomeres that ensure genome stability

2019 ◽  
Author(s):  
Anna Barg-Wojas ◽  
Kamila Schirmeisen ◽  
Jakub Muraszko ◽  
Karol Kramarz ◽  
Gabriela Baranowska ◽  
...  
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Genome Stability ◽  
Genome Instability ◽  
Chromosome Instability ◽  
Telomere Maintenance ◽  
Nucleosome Dynamics ◽  
Dna Translocases ◽  
Telomere Function ◽  
And Function ◽  
Dna Translocase

ABSTRACTHomologous recombination (HR) is a DNA repair mechanism that ensures, together with heterochromatin machinery, the proper replication, structure and function of telomeres and centromeres that is essential for the maintenance of genome integrity. Schizosaccharomyces pombe Rrp1 and Rrp2 participate in HR and are orthologues of Saccharomyces cerevisiae Uls1, a SWI2/SNF2 DNA translocase and SUMO-Targeted Ubiquitin Ligase. We show that Rrp1 or Rrp2 upregulation leads to chromosome instability and growth defects. These phenotypes depend on putative DNA translocase activities of Rrp1 and Rrp2. Either Rrp1 or Rrp2 overproduction results in a reduction in global histone levels, suggesting that Rrp1 and Rrp2 may modulate nucleosome dynamics. In addition we show that Rrp2, but not Rrp1, acts at telomeres. We propose that this role depends on the previously described interaction between Rrp2 and Top2. We conclude that Rrp1 and Rrp2 have important roles for centromere and telomere function and maintenance, contributing to the preservation of genome stability during vegetative cell growth.SUMMARY STATEMENTSchizosaccharomyces pombe DNA translocases Rrp1 and Rrp2 modulate centromere and telomere maintenance pathways and dysregulation of their activity leads to genome instability.

scholarly journals PUMILIO, but not RBMX, binding is required for regulation of genomic stability by noncoding RNA NORAD

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Mahmoud M Elguindy ◽  
Florian Kopp ◽  
Mohammad Goodarzi ◽  
Frederick Rehfeld ◽  
Anu Thomas ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Genome Stability ◽  
Rna Binding ◽  
Genome Instability ◽  
Genomic Stability ◽  
Premature Aging ◽  
Negative Regulator ◽  
Genome Maintenance ◽  
Genetic Rescue ◽  
Rna Fish

NORAD is a conserved long noncoding RNA (lncRNA) that is required for genome stability in mammals. NORAD acts as a negative regulator of PUMILIO (PUM) proteins in the cytoplasm, and we previously showed that loss of NORAD or PUM hyperactivity results in genome instability and premature aging in mice (Kopp et al., 2019). Recently, however, it was reported that NORAD regulates genome stability through an interaction with the RNA binding protein RBMX in the nucleus. Here, we addressed the contributions of NORAD:PUM and NORAD:RBMX interactions to genome maintenance by this lncRNA in human cells. Extensive RNA FISH and fractionation experiments established that NORAD localizes predominantly to the cytoplasm with or without DNA damage. Moreover, genetic rescue experiments demonstrated that PUM binding is required for maintenance of genomic stability by NORAD whereas binding of RBMX is dispensable for this function. These data provide an important foundation for further mechanistic dissection of the NORAD-PUMILIO axis in genome maintenance.

scholarly journals Selective defects in gene expression control genome instability in yeast splicing mutants

2019 ◽  
Vol 30 (2) ◽  
pp. 191-200 ◽  
Author(s):  
Annie S. Tam ◽  
Tianna S. Sihota ◽  
Karissa L. Milbury ◽  
Anni Zhang ◽  
Veena Mathew ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Stability ◽  
Spindle Assembly Checkpoint ◽  
Genome Instability ◽  
Genome Maintenance ◽  
Expression Control ◽  
Maintenance Factors ◽  
Gene Expression Control ◽  
Multiple Routes ◽  
Spindle Assembly Checkpoint Protein

RNA processing mutants have been broadly implicated in genome stability, but mechanistic links are often unclear. Two predominant models have emerged: one involving changes in gene expression that perturb other genome maintenance factors and another in which genotoxic DNA:RNA hybrids, called R-loops, impair DNA replication. Here we characterize genome instability phenotypes in yeast splicing factor mutants and find that mitotic defects, and in some cases R-loop accumulation, are causes of genome instability. In both cases, alterations in gene expression, rather than direct cis effects, are likely to contribute to instability. Genome instability in splicing mutants is exacerbated by loss of the spindle-assembly checkpoint protein Mad1. Moreover, removal of the intron from the α-tubulin gene TUB1 restores genome integrity. Thus, differing penetrance and selective effects on the transcriptome can lead to a range of phenotypes in conditional mutants of the spliceosome, including multiple routes to genome instability.

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