scholarly journals Common Features of the Pericentromere and Nucleolus

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1029 ◽  
Author(s):  
Colleen J. Lawrimore ◽  
Kerry Bloom
Keyword(s):  
Liquid Phase ◽  
Replication Fork ◽  
Transfer Rna ◽  
Trna Genes ◽  
Common Features ◽  
Fork Stalling ◽  
Structural Maintenance Of Chromosome ◽  
Genomic Recombination ◽  
Segregation Stability ◽  
Smc Proteins

Both the pericentromere and the nucleolus have unique characteristics that distinguish them amongst the rest of genome. Looping of pericentromeric DNA, due to structural maintenance of chromosome (SMC) proteins condensin and cohesin, drives its ability to maintain tension during metaphase. Similar loops are formed via condensin and cohesin in nucleolar ribosomal DNA (rDNA). Condensin and cohesin are also concentrated in transfer RNA (tRNA) genes, genes which may be located within the pericentromere as well as tethered to the nucleolus. Replication fork stalling, as well as downstream consequences such as genomic recombination, are characteristic of both the pericentromere and rDNA. Furthermore, emerging evidence suggests that the pericentromere may function as a liquid–liquid phase separated domain, similar to the nucleolus. We therefore propose that the pericentromere and nucleolus, in part due to their enrichment of SMC proteins and others, contain similar domains that drive important cellular activities such as segregation, stability, and repair.

scholarly journals Saccharomyces cerevisiae Rrm3p DNA Helicase Promotes Genome Integrity by Preventing Replication Fork Stalling: Viability of rrm3 Cells Requires the Intra-S-Phase Checkpoint and Fork Restart Activities

2004 ◽  
Vol 24 (8) ◽  
pp. 3198-3212 ◽  
Author(s):  
Jorge Z. Torres ◽  
Sandra L. Schnakenberg ◽  
Virginia A. Zakian
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Damage ◽  
Replication Fork ◽  
Opportunity To Learn ◽  
Normal Growth ◽  
Dna Helicase ◽  
S Phase ◽  
Exogenous Dna ◽  
Fork Stalling ◽  
S Phase Checkpoint

ABSTRACT Rrm3p is a 5′-to-3′ DNA helicase that helps replication forks traverse protein-DNA complexes. Its absence leads to increased fork stalling and breakage at over 1,000 specific sites located throughout the Saccharomyces cerevisiae genome. To understand the mechanisms that respond to and repair rrm3-dependent lesions, we carried out a candidate gene deletion analysis to identify genes whose mutation conferred slow growth or lethality on rrm3 cells. Based on synthetic phenotypes, the intra-S-phase checkpoint, the SRS2 inhibitor of recombination, the SGS1/TOP3 replication fork restart pathway, and the MRE11/RAD50/XRS2 (MRX) complex were critical for viability of rrm3 cells. DNA damage checkpoint and homologous recombination genes were important for normal growth of rrm3 cells. However, the MUS81/MMS4 replication fork restart pathway did not affect growth of rrm3 cells. These data suggest a model in which the stalled and broken forks generated in rrm3 cells activate a checkpoint response that provides time for fork repair and restart. Stalled forks are converted by a Rad51p-mediated process to intermediates that are resolved by Sgs1p/Top3p. The rrm3 system provides a unique opportunity to learn the fate of forks whose progress is impaired by natural impediments rather than by exogenous DNA damage.

scholarly journals Mechanism for inverted-repeat recombination induced by a replication fork barrier

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Léa Marie ◽  
Lorraine S. Symington
Keyword(s):  
Replication Fork ◽  
Repetitive Sequences ◽  
Replication Stress ◽  
Yeast Genome ◽  
Physical Analysis ◽  
Srs2 Helicase ◽  
Fork Stalling ◽  
Strand Annealing ◽  
Recombination Pathway ◽  
Stalled Replication Forks

AbstractReplication stress and abundant repetitive sequences have emerged as primary conditions underlying genomic instability in eukaryotes. To gain insight into the mechanism of recombination between repeated sequences in the context of replication stress, we used a prokaryotic Tus/Ter barrier designed to induce transient replication fork stalling near inverted repeats in the budding yeast genome. Our study reveals that the replication fork block stimulates a unique recombination pathway dependent on Rad51 strand invasion and Rad52-Rad59 strand annealing activities, Mph1/Rad5 fork remodelers, Mre11/Exo1/Dna2 resection machineries, Rad1-Rad10 nuclease and DNA polymerase δ. Furthermore, we show recombination at stalled replication forks is limited by the Srs2 helicase and Mus81-Mms4/Yen1 nucleases. Physical analysis of the replication-associated recombinants revealed that half are associated with an inversion of sequence between the repeats. Based on our extensive genetic characterization, we propose a model for recombination of closely linked repeats that can robustly generate chromosome rearrangements.

scholarly journals Tracking of controlled Escherichia coli replication fork stalling and restart at repressor-bound DNA in vivo

2006 ◽  
Vol 25 (11) ◽  
pp. 2596-2604 ◽  
Author(s):  
Christophe Possoz ◽  
Sergio R Filipe ◽  
Ian Grainge ◽  
David J Sherratt
Keyword(s):  
Escherichia Coli ◽  
Replication Fork ◽  
Replication Fork Stalling ◽  
Fork Stalling

scholarly journals Single-molecule imaging reveals control of parental histone recycling by free histones during DNA replication

2020 ◽  
Vol 6 (38) ◽  
pp. eabc0330 ◽  
Author(s):  
D. T. Gruszka ◽  
S. Xie ◽  
H. Kimura ◽  
H. Yardimci
Keyword(s):  
Dna Replication ◽  
Real Time ◽  
Single Molecule ◽  
Replication Fork ◽  
Epigenetic Inheritance ◽  
Replication Forks ◽  
Replication Fork Progression ◽  
Egg Extracts ◽  
Fork Stalling ◽  
The Moment

During replication, nucleosomes are disrupted ahead of the replication fork, followed by their reassembly on daughter strands from the pool of recycled parental and new histones. However, because no previous studies have managed to capture the moment that replication forks encounter nucleosomes, the mechanism of recycling has remained unclear. Here, through real-time single-molecule visualization of replication fork progression in Xenopus egg extracts, we determine explicitly the outcome of fork collisions with nucleosomes. Most of the parental histones are evicted from the DNA, with histone recycling, nucleosome sliding, and replication fork stalling also occurring but at lower frequencies. Critically, we find that local histone recycling becomes dominant upon depletion of endogenous histones from extracts, revealing that free histone concentration is a key modulator of parental histone dynamics at the replication fork. The mechanistic details revealed by these studies have major implications for our understanding of epigenetic inheritance.

scholarly journals Genome organization via loop extrusion, insights from polymer physics models

2019 ◽  
Vol 19 (2) ◽  
pp. 119-127 ◽  
Author(s):  
Surya K Ghosh ◽  
Daniel Jost
Keyword(s):  
Genome Organization ◽  
Extrusion Process ◽  
Polymer Physics ◽  
Modern Biology ◽  
Precise Information ◽  
Multi Scale ◽  
Topologically Associated Domains ◽  
Structural Maintenance Of Chromosome ◽  
Smc Proteins

Abstract Understanding how genomes fold and organize is one of the main challenges in modern biology. Recent high-throughput techniques like Hi-C, in combination with cutting-edge polymer physics models, have provided access to precise information on 3D chromosome folding to decipher the mechanisms driving such multi-scale organization. In particular, structural maintenance of chromosome (SMC) proteins play an important role in the local structuration of chromatin, putatively via a loop extrusion process. Here, we review the different polymer physics models that investigate the role of SMCs in the formation of topologically associated domains (TADs) during interphase via the formation of dynamic loops. We describe the main physical ingredients, compare them and discuss their relevance against experimental observations.

scholarly journals Ctf18-RFC and DNA Pol ϵ form a stable leading strand polymerase/clamp loader complex required for normal and perturbed DNA replication

2020 ◽  
Vol 48 (14) ◽  
pp. 8128-8145 ◽  
Author(s):  
Katy Stokes ◽  
Alicja Winczura ◽  
Boyuan Song ◽  
Giacomo De Piccoli ◽  
Daniel B Grabarczyk
Keyword(s):  
Structural Biology ◽  
Replication Fork ◽  
Catalytic Domain ◽  
Replication Forks ◽  
Yeast Genetics ◽  
Clamp Loader ◽  
Checkpoint Signaling ◽  
Chromatid Cohesion ◽  
Leading Strand ◽  
Fork Stalling

Abstract The eukaryotic replisome must faithfully replicate DNA and cope with replication fork blocks and stalling, while simultaneously promoting sister chromatid cohesion. Ctf18-RFC is an alternative PCNA loader that links all these processes together by an unknown mechanism. Here, we use integrative structural biology combined with yeast genetics and biochemistry to highlight the specific functions that Ctf18-RFC plays within the leading strand machinery via an interaction with the catalytic domain of DNA Pol ϵ. We show that a large and unusually flexible interface enables this interaction to occur constitutively throughout the cell cycle and regardless of whether forks are replicating or stalled. We reveal that, by being anchored to the leading strand polymerase, Ctf18-RFC can rapidly signal fork stalling to activate the S phase checkpoint. Moreover, we demonstrate that, independently of checkpoint signaling or chromosome cohesion, Ctf18-RFC functions in parallel to Chl1 and Mrc1 to protect replication forks and cell viability.

scholarly journals Replication fork stalling elicits chromatin compaction for the stability of stalling replication forks

2019 ◽  
Vol 116 (29) ◽  
pp. 14563-14572 ◽  
Author(s):  
Gang Feng ◽  
Yue Yuan ◽  
Zeyang Li ◽  
Lu Wang ◽  
Bo Zhang ◽  
...  
Keyword(s):  
Replication Fork ◽  
Cellular Mechanism ◽  
Eukaryotic Cells ◽  
Replication Forks ◽  
Physical Separation ◽  
Replicative Helicase ◽  
Chromatin Compaction ◽  
Acetylation Site ◽  
Fork Stalling ◽  
The Stability

DNA replication forks in eukaryotic cells stall at a variety of replication barriers. Stalling forks require strict cellular regulations to prevent fork collapse. However, the mechanism underlying these cellular regulations is poorly understood. In this study, a cellular mechanism was uncovered that regulates chromatin structures to stabilize stalling forks. When replication forks stall, H2BK33, a newly identified acetylation site, is deacetylated and H3K9 trimethylated in the nucleosomes surrounding stalling forks, which results in chromatin compaction around forks. Acetylation-mimic H2BK33Q and its deacetylase clr6-1 mutations compromise this fork stalling-induced chromatin compaction, cause physical separation of replicative helicase and DNA polymerases, and significantly increase the frequency of stalling fork collapse. Furthermore, this fork stalling-induced H2BK33 deacetylation is independent of checkpoint. In summary, these results suggest that eukaryotic cells have developed a cellular mechanism that stabilizes stalling forks by targeting nucleosomes and inducing chromatin compaction around stalling forks. This mechanism is named the “Chromsfork” control: Chromatin Compaction Stabilizes Stalling Replication Forks.

scholarly journals Phosphorylated Rad18 directs DNA Polymerase η to sites of stalled replication

2010 ◽  
Vol 191 (5) ◽  
pp. 953-966 ◽  
Author(s):  
Tovah A. Day ◽  
Komariah Palle ◽  
Laura R. Barkley ◽  
Naoko Kakusho ◽  
Ying Zou ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Replication Fork ◽  
Genome Stability ◽  
Nuclear Antigen ◽  
Binding Motif ◽  
Polymerase Eta ◽  
Cdc7 Kinase ◽  
Replication Fork Stalling ◽  
Fork Stalling ◽  
Y Family

The E3 ubiquitin ligase Rad18 guides DNA Polymerase eta (Polη) to sites of replication fork stalling and mono-ubiquitinates proliferating cell nuclear antigen (PCNA) to facilitate binding of Y family trans-lesion synthesis (TLS) DNA polymerases during TLS. However, it is unclear exactly how Rad18 is regulated in response to DNA damage and how Rad18 activity is coordinated with progression through different phases of the cell cycle. Here we identify Rad18 as a novel substrate of the essential protein kinase Cdc7 (also termed Dbf4/Drf1-dependent Cdc7 kinase [DDK]). A serine cluster in the Polη-binding motif of Rad18 is phosphorylated by DDK. Efficient association of Rad18 with Polη is dependent on DDK and is necessary for redistribution of Polη to sites of replication fork stalling. This is the first demonstration of Rad18 regulation by direct phosphorylation and provides a novel mechanism for integration of S phase progression with postreplication DNA repair to maintain genome stability.

scholarly journals Oligodeoxynucleotide Binding to (CTG) · (CAG) Microsatellite Repeats Inhibits Replication Fork Stalling, Hairpin Formation, and Genome Instability

2012 ◽  
Vol 33 (3) ◽  
pp. 571-581 ◽  
Author(s):  
Guoqi Liu ◽  
Xiaomi Chen ◽  
Michael Leffak
Keyword(s):  
Replication Fork ◽  
Trinucleotide Repeat ◽  
Cell Model ◽  
Replication Stress ◽  
Dna Hairpin ◽  
Replication Fork Stalling ◽  
Fork Stalling ◽  
Hairpin Formation ◽  
Lagging Strand

ABSTRACT(CTG)n· (CAG)ntrinucleotide repeat (TNR) expansion in the 3′ untranslated region of the dystrophia myotonica protein kinase (DMPK) gene causes myotonic dystrophy type 1. However, a direct link between TNR instability, the formation of noncanonical (CTG)n· (CAG)nstructures, and replication stress has not been demonstrated. In a human cell model, we found that (CTG)45· (CAG)45causes local replication fork stalling, DNA hairpin formation, and TNR instability. Oligodeoxynucleotides (ODNs) complementary to the (CTG)45· (CAG)45lagging-strand template eliminated DNA hairpin formation on leading- and lagging-strand templates and relieved fork stalling. Prolonged cell culture, emetine inhibition of lagging-strand synthesis, or slowing of DNA synthesis by low-dose aphidicolin induced (CTG)45· (CAG)45expansions and contractions. ODNs targeting the lagging-strand template blocked the time-dependent or emetine-induced instability but did not eliminate aphidicolin-induced instability. These results show directly that TNR replication stalling, replication stress, hairpin formation, and instability are mechanistically linkedin vivo.

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