scholarly journals Replication in Hydroxyurea: It's a Matter of Time

2007 ◽  
Vol 27 (18) ◽  
pp. 6396-6406 ◽  
Author(s):  
Gina M. Alvino ◽  
David Collingwood ◽  
John M. Murphy ◽  
Jeffrey Delrow ◽  
Bonita J. Brewer ◽  
...  
Keyword(s):  
Specific Effect ◽  
Slow Motion ◽  
S Phase ◽  
Short Exposure ◽  
Microarray Experiments ◽  
Checkpoint Response ◽  
Origin Activation ◽  
Genome Wide ◽  
Time Frames ◽  
Extended Exposure

ABSTRACT Hydroxyurea (HU) is a DNA replication inhibitor that negatively affects both the elongation and initiation phases of replication and triggers the “intra-S phase checkpoint.” Previous work with budding yeast has shown that, during a short exposure to HU, MEC1/RAD53 prevent initiation at some late S phase origins. In this study, we have performed microarray experiments to follow the fate of all origins over an extended exposure to HU. We show that the genome-wide progression of DNA synthesis, including origin activation, follows the same pattern in the presence of HU as in its absence, although the time frames are very different. We find no evidence for a specific effect that excludes initiation from late origins. Rather, HU causes S phase to proceed in slow motion; all temporal classes of origins are affected, but the order in which they become active is maintained. We propose a revised model for the checkpoint response to HU that accounts for the continued but slowed pace of the temporal program of origin activation.

scholarly journals Developmental differences in genome replication program and origin activation

2020 ◽  
Vol 48 (22) ◽  
pp. 12751-12777
Author(s):  
Cathia Rausch ◽  
Patrick Weber ◽  
Paulina Prorok ◽  
David Hörl ◽  
Andreas Maiser ◽  
...  
Keyword(s):  
Dna Replication ◽  
Single Molecule ◽  
Embryonic Stem ◽  
S Phase ◽  
Developmental Differences ◽  
Centromeric Heterochromatin ◽  
Genome Replication ◽  
Origin Activation ◽  
Spatio Temporal ◽  
Mes Cells

Abstract To ensure error-free duplication of all (epi)genetic information once per cell cycle, DNA replication follows a cell type and developmental stage specific spatio-temporal program. Here, we analyze the spatio-temporal DNA replication progression in (un)differentiated mouse embryonic stem (mES) cells. Whereas telomeres replicate throughout S-phase, we observe mid S-phase replication of (peri)centromeric heterochromatin in mES cells, which switches to late S-phase replication upon differentiation. This replication timing reversal correlates with and depends on an increase in condensation and a decrease in acetylation of chromatin. We further find synchronous duplication of the Y chromosome, marking the end of S-phase, irrespectively of the pluripotency state. Using a combination of single-molecule and super-resolution microscopy, we measure molecular properties of the mES cell replicon, the number of replication foci active in parallel and their spatial clustering. We conclude that each replication nanofocus in mES cells corresponds to an individual replicon, with up to one quarter representing unidirectional forks. Furthermore, with molecular combing and genome-wide origin mapping analyses, we find that mES cells activate twice as many origins spaced at half the distance than somatic cells. Altogether, our results highlight fundamental developmental differences on progression of genome replication and origin activation in pluripotent cells.

scholarly journals Replication fork rate and origin activation during the S phase of Saccharomyces cerevisiae.

1980 ◽  
Vol 85 (1) ◽  
pp. 108-115 ◽  
Author(s):  
C J Rivin ◽  
W L Fangman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Cycle ◽  
Cycle Length ◽  
Replication Fork ◽  
Nitrogen Sources ◽  
S Phase ◽  
Phase Duration ◽  
Yeast Saccharomyces Cerevisiae ◽  
Origin Activation ◽  
Cell Cycle Length

When the growth rate of the yeast Saccharomyces cerevisiae is limited with various nitrogen sources, the duration of the S phase is proportional to cell cycle length over a fourfold range of growth rates (C.J. Rivin and W. L. Fangman, 1980, J. Cell Biol. 85:96-107). Molecular parameters of the S phases of these cells were examined by DNA fiber autoradiography. Changes in replication fork rate account completely for the changes in S-phase duration. No changes in origin-to-origin distances were detected. In addition, it was found that while most adjacent replication origins are activated within a few minutes of each other, new activations occur throughout the S phase.

Review: In-Water Systems to Reactively Manage Biofouling in Sea Chests and Internal Pipework

2017 ◽  
Vol 51 (2) ◽  
pp. 89-104 ◽  
Author(s):  
Abraham Growcott ◽  
Daniel Kluza ◽  
Eugene Georgiades
Keyword(s):  
Structural Complexity ◽  
Marine Species ◽  
Short Exposure ◽  
Thermal Treatments ◽  
Thermal Systems ◽  
Major Pathway ◽  
Chemical Treatments ◽  
Regulatory Constraints ◽  
Time Frames ◽  
Temperature Water

AbstractSea chests are cavities built into a vessel's hull to aid the efficiency of pumping seawater into internal pipework systems. Sea chests and internal pipework are known hotspots for the accumulation of biofouling, and vessel biofouling is a major pathway for the introduction and spread of nonindigenous marine species. The use of preventive strategies to minimize biofouling within sea chests and internal pipework is difficult due to their structural complexity; therefore, reactive methods to manage the associated biosecurity risk are required. This review examines the efficacy, environmental considerations, and cost of different systems to reactively manage sea chest and internal pipework biofouling within operationally realistic time frames (<3 days) and identifies those that warrant further investigation. Physical removal systems with recapture capability should be developed for accessible areas (e.g., grates), as such systems provide an operational benefit to the vessel. For internal and inaccessible surfaces, the development of thermal systems, particularly steam systems, is encouraged as they offer broad-spectrum efficacy at obtainable temperatures and require relatively short exposure periods. Compared to chemical treatments, thermal treatments are less influenced by environmental variables (e.g., temperature, water chemistry) and regulatory constraints.

scholarly journals Assembly of a Complex Containing Cdc45p, Replication Protein A, and Mcm2p at Replication Origins Controlled by S-Phase Cyclin-Dependent Kinases and Cdc7p-Dbf4p Kinase

2000 ◽  
Vol 20 (9) ◽  
pp. 3086-3096 ◽  
Author(s):  
Lee Zou ◽  
Bruce Stillman
Keyword(s):  
Dna Polymerase ◽  
Origin Recognition Complex ◽  
Protein A ◽  
Replication Protein A ◽  
S Phase ◽  
Replication Protein ◽  
Dependent Manner ◽  
Replication Origins ◽  
Cyclin Dependent Kinases ◽  
Origin Activation

ABSTRACT In Saccharomyces cerevisiae, replication origins are activated with characteristic timing during S phase. S-phase cyclin-dependent kinases (S-CDKs) and Cdc7p-Dbf4p kinase are required for origin activation throughout S phase. The activation of S-CDKs leads to association of Cdc45p with chromatin, raising the possibility that Cdc45p defines the assembly of a new complex at each origin. Here we show that both Cdc45p and replication protein A (RPA) bind to Mcm2p at the G1-S transition in an S-CDK-dependent manner. During S phase, Cdc45p associates with different replication origins at specific times. The origin associations of Cdc45p and RPA are mutually dependent, and both S-CDKs and Cdc7p-Dbf4p are required for efficient binding of Cdc45p to origins. These findings suggest that S-CDKs and Cdc7p-Dbf4p promote loading of Cdc45p and RPA onto a preformed prereplication complex at each origin with preprogrammed timing. TheARS1 association of Mcm2p, but not that of the origin recognition complex, is diminished by disruption of the B2 element ofARS1, a potential origin DNA-unwinding element. Cdc45p is required for recruiting DNA polymerase α onto chromatin, and it associates with Mcm2p, RPA, and DNA polymerase ɛ only during S phase. These results suggest that the complex containing Cdc45p, RPA, and MCMs is involved in origin unwinding and assembly of replication forks at each origin.

scholarly journals Genome-wide copy number profiling of single cells in S-phase reveals DNA-replication domains

2013 ◽  
Vol 41 (6) ◽  
pp. e66-e66 ◽  
Author(s):  
Niels Van der Aa ◽  
Jiqiu Cheng ◽  
Ligia Mateiu ◽  
Masoud Zamani Esteki ◽  
Parveen Kumar ◽  
...  
Keyword(s):  
Dna Replication ◽  
Copy Number ◽  
Single Cells ◽  
S Phase ◽  
Genome Wide

scholarly journals G2 phase chromatin lacks determinants of replication timing

2010 ◽  
Vol 189 (6) ◽  
pp. 967-980 ◽  
Author(s):  
Junjie Lu ◽  
Feng Li ◽  
Christopher S. Murphy ◽  
Michael W. Davidson ◽  
David M. Gilbert
Keyword(s):  
Spatial Organization ◽  
Replication Timing ◽  
S Phase ◽  
Decision Point ◽  
Genome Wide Analysis ◽  
Quiescent Cells ◽  
Egg Extract ◽  
Genome Wide ◽  
G2 Phase

DNA replication in all eukaryotes follows a defined replication timing program, the molecular mechanism of which remains elusive. Using a Xenopus laevis egg extract replication system, we previously demonstrated that replication timing is established during early G1 phase of the cell cycle (timing decision point [TDP]), which is coincident with the repositioning and anchorage of chromatin in the newly formed nucleus. In this study, we use this same system to show that G2 phase chromatin lacks determinants of replication timing but maintains the overall spatial organization of chromatin domains, and we confirm this finding by genome-wide analysis of rereplication in vivo. In contrast, chromatin from quiescent cells retains replication timing but exhibits disrupted spatial organization. These data support a model in which events at the TDP, facilitated by chromatin spatial organization, establish determinants of replication timing that persist independent of spatial organization until the process of chromatin replication during S phase erases those determinants.

scholarly journals Transcription-mediated organization of the replication initiation program across large genes sets up common fragile sites genome-wide

2019 ◽  
Author(s):  
Olivier Brison ◽  
Sami EL-Hilali ◽  
Dana Azar ◽  
Stéphane Koundrioukoff ◽  
Mélanie Schmidt ◽  
...  
Keyword(s):  
Replication Timing ◽  
S Phase ◽  
Fragile Sites ◽  
Replication Initiation ◽  
Common Fragile Sites ◽  
Large Gene ◽  
Genome Wide ◽  
Underlying Mechanisms ◽  
Large Genes ◽  
Nascent Transcripts

ABSTRACTCommon Fragile Sites (CFSs) are chromosome regions prone to breakage under replication stress, known to drive chromosome rearrangements during oncogenesis. Most CFSs nest in large expressed genes, suggesting that transcription elicits their instability but the underlying mechanisms remained elusive. Analyses of genome-wide replication timing of human lymphoblasts here show that stress-induced delayed/under-replication is the hallmark of CFSs. Extensive genome-wide analyses of nascent transcripts, replication origin positioning and fork directionality reveal that 80% of CFSs nest in large transcribed domains poor in initiation events, thus replicated by long-traveling forks. In contrast to formation of sequence-dependent fork barriers or head-on transcription-replication conflicts, traveling-long in late S phase explains CFS replication features. We further show that transcription inhibition during the S phase, which excludes the setting of new replication origins, fails to rescue CFS stability. Altogether, results show that transcription-dependent suppression of initiation events delays replication of large gene body, committing them to instability.

scholarly journals Genome-wide identification of CCT genes in wheat (Triticum aestivum L.) and their expression analysis during vernalization

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0262147
Author(s):  
HongWei Zhang ◽  
Bo Jiao ◽  
FuShuang Dong ◽  
XinXia Liang ◽  
Shuo Zhou ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Low Temperature ◽  
Winter Wheat ◽  
Expression Analysis ◽  
Gene Clusters ◽  
Triticum Aestivum L ◽  
Whole Wheat ◽  
Genome Wide ◽  
Leaf Tissues ◽  
Extended Exposure

Numerous CCT genes are known to regulate various biological processes, such as circadian rhythm regulation, flowering, light signaling, plant development, and stress resistance. The CCT gene family has been characterized in many plants but remains unknown in the major cereal wheat (Triticum aestivum L.). Extended exposure to low temperature (vernalization) is necessary for winter wheat to flower successfully. VERNALIZATION2 (VRN2), a specific CCT-containing gene, has been proved to be strongly associated with vernalization in winter wheat. Mutation of all VRN2 copies in three subgenomes results in the eliminated demands of low temperature in flowering. However, no other CCT genes have been reported to be associated with vernalization to date. The present study screened CCT genes in the whole wheat genome, and preliminarily identified the vernalization related CCT genes through expression analysis. 127 CCT genes were identified in three subgenomes of common wheat through a hidden Markov model-based method. Based on multiple alignment, these genes were grouped into 40 gene clusters, including the duplicated gene clusters TaCMF6 and TaCMF8, each tandemly arranged near the telomere. The phylogenetic analysis classified these genes into eight groups. The transcriptome analysis using leaf tissues collected before, during, and after vernalization revealed 49 upregulated and 31 downregulated CCT genes during vernalization, further validated by quantitative real-time PCR. Among the differentially expressed and well-investigated CCT gene clusters analyzed in this study, TaCMF11, TaCO18, TaPRR95, TaCMF6, and TaCO16 were induced during vernalization but decreased immediately after vernalization, while TaCO1, TaCO15, TaCO2, TaCMF8, and TaPPD1 were stably suppressed during and after vernalization. These data imply that some vernalization related CCT genes other than VRN2 may exist in wheat. This study improves our understanding of CCT genes and provides a foundation for further research on CCT genes related to vernalization in wheat.

scholarly journals CRL4 ubiquitin ligase stimulates Fanconi anemia pathway-induced single-stranded DNA-RPA signaling

BMC Cancer ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Tamara Codilupi ◽  
Doreen Taube ◽  
Hanspeter Naegeli
Keyword(s):  
Cancer Cells ◽  
Ubiquitin Ligase ◽  
Fanconi Anemia ◽  
S Phase ◽  
Single Stranded Dna ◽  
Anticancer Efficacy ◽  
Checkpoint Response ◽  
Checkpoint Kinases ◽  
Interfering Rna ◽  
Crosslinking Agents

Abstract Background DNA-crosslinking agents like cisplatin and mitomycin C (MMC) are indispensible for the treatment of many solid malignancies. These anticancer drugs generate DNA interstrand crosslinks (ICLs) that cause cell death by blocking replication forks. Many factors counteracting ICL-induced DNA replication stress, including the Fanconi anemia (FA) pathway, are regulated by ubiquitination and, therefore, ubiquitin ligases are potential targets for the sensitization of cancer cells to crosslinking agents. In this study, we investigated the function of the CRL4 ubiquitin ligase in modulating the response of cancer cells to ICL induction. Methods The two cullin paralogs CUL4A and CUL4B, which form the CRL4 ligase scaffold, were depleted in cancer cells by small interfering RNA followed by analysis of the cellular and biochemical responses to ICLs elicited upon cisplatin or MMC treatment. Results We report that the combined depletion of CUL4A and CUL4B weakens an FA pathway-dependent S phase checkpoint response. CRL4 positively stimulates the monoubiquitination of FANCD2 required for the recruitment of XPF-ERCC1, a structure-specific endonuclease that, in turn, contributes to the display of single-stranded DNA (ssDNA) at ICLs. After CRL4 down regulation, the missing ssDNA results in reduced recruitment of RPA, thereby dampening activation of ATR and CHK1 checkpoint kinases and allowing for S phase progression despite ICL induction. Conclusion Our findings indicate that CRL4 promotes cell survival by potentiating an FA pathway-dependent ssDNA-RPA signaling platform installed at ICLs. The anticancer efficacy of crosslinking agents may, therefore, be enhanced by down regulating CRL4 activity.

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