scholarly journals Replication factory activation can be decoupled from the replication timing program by modulating Cdk levels

2010 ◽  
Vol 188 (2) ◽  
pp. 209-221 ◽  
Author(s):  
Alexander M. Thomson ◽  
Peter J. Gillespie ◽  
J. Julian Blow
Keyword(s):  
Replication Timing ◽  
S Phase ◽  
Replication Initiation ◽  
Cyclin Dependent Kinase ◽  
Chromosomal Dna ◽  
Replication Rate ◽  
Checkpoint Kinases ◽  
Replicative Stress ◽  
Replication Factory ◽  
Egg Extracts

In the metazoan replication timing program, clusters of replication origins located in different subchromosomal domains fire at different times during S phase. We have used Xenopus laevis egg extracts to drive an accelerated replication timing program in mammalian nuclei. Although replicative stress caused checkpoint-induced slowing of the timing program, inhibition of checkpoint kinases in an unperturbed S phase did not accelerate it. Lowering cyclin-dependent kinase (Cdk) activity slowed both replication rate and progression through the timing program, whereas raising Cdk activity increased them. Surprisingly, modest alteration of Cdk activity changed the amount of DNA synthesized during different stages of the timing program. This was associated with a change in the number of active replication factories, whereas the distribution of origins within active factories remained relatively normal. The ability of Cdks to differentially effect replication initiation, factory activation, and progression through the timing program provides new insights into the way that chromosomal DNA replication is organized during S phase.

scholarly journals Xenopus Cdc7 executes its essential function early in S phase and is counteracted by checkpoint-regulated protein phosphatase 1

Open Biology ◽  
2014 ◽  
Vol 4 (1) ◽  
pp. 130138 ◽  
Author(s):  
Wei Theng Poh ◽  
Gaganmeet Singh Chadha ◽  
Peter J. Gillespie ◽  
Philipp Kaldis ◽  
J. Julian Blow
Keyword(s):  
Protein Phosphatase ◽  
Replication Timing ◽  
S Phase ◽  
Replication Initiation ◽  
Protein Phosphatase 1 ◽  
Checkpoint Kinases ◽  
Anti Cancer ◽  
Egg Extracts ◽  
Mcm Proteins

The initiation of DNA replication requires two protein kinases: cyclin-dependent kinase (Cdk) and Cdc7. Although S phase Cdk activity has been intensively studied, relatively little is known about how Cdc7 regulates progression through S phase. We have used a Cdc7 inhibitor, PHA-767491, to dissect the role of Cdc7 in Xenopus egg extracts. We show that hyperphosphorylation of mini-chromosome maintenance (MCM) proteins by Cdc7 is required for the initiation, but not for the elongation, of replication forks. Unlike Cdks, we demonstrate that Cdc7 executes its essential functions by phosphorylating MCM proteins at virtually all replication origins early in S phase and is not limiting for progression through the Xenopus replication timing programme. We demonstrate that protein phosphatase 1 (PP1) is recruited to chromatin and rapidly reverses Cdc7-mediated MCM hyperphosphorylation. Checkpoint kinases induced by DNA damage or replication inhibition promote the association of PP1 with chromatin and increase the rate of MCM dephosphorylation, thereby counteracting the previously completed Cdc7 functions and inhibiting replication initiation. This novel mechanism for regulating Cdc7 function provides an explanation for previous contradictory results concerning the control of Cdc7 by checkpoint kinases and has implications for the use of Cdc7 inhibitors as anti-cancer agents.

scholarly journals Chk1 inhibits replication factory activation but allows dormant origin firing in existing factories

2010 ◽  
Vol 191 (7) ◽  
pp. 1285-1297 ◽  
Author(s):  
Xin Quan Ge ◽  
J. Julian Blow
Keyword(s):  
Replication Fork ◽  
S Phase ◽  
Apparent Contrast ◽  
Origin Firing ◽  
Checkpoint Kinases ◽  
Replicative Stress ◽  
Replication Fork Progression ◽  
Replication Factory ◽  
Low Levels ◽  
Fork Stalling

Replication origins are licensed by loading MCM2-7 hexamers before entry into S phase. However, only ∼10% of licensed origins are normally used in S phase, with the others remaining dormant. When fork progression is inhibited, dormant origins initiate nearby to ensure that all of the DNA is eventually replicated. In apparent contrast, replicative stress activates ataxia telangiectasia and rad-3–related (ATR) and Chk1 checkpoint kinases that inhibit origin firing. In this study, we show that at low levels of replication stress, ATR/Chk1 predominantly suppresses origin initiation by inhibiting the activation of new replication factories, thereby reducing the number of active factories. At the same time, inhibition of replication fork progression allows dormant origins to initiate within existing replication factories. The inhibition of new factory activation by ATR/Chk1 therefore redirects replication toward active factories where forks are inhibited and away from regions that have yet to start replication. This minimizes the deleterious consequences of fork stalling and prevents similar problems from arising in unreplicated regions of the genome.

scholarly journals High-throughput analysis of DNA replication in single human cells reveals constrained variability in the location and timing of replication initiation

2021 ◽  
Author(s):  
Dashiell J Massey ◽  
Amnon Koren
Keyword(s):  
Dna Replication ◽  
Replication Origin ◽  
Replication Timing ◽  
S Phase ◽  
Human Cells ◽  
Replication Initiation ◽  
High Throughput Analysis ◽  
Timing Variability ◽  
Fixed Set ◽  
Fixed Order

DNA replication occurs throughout the S phase of the cell cycle, initiating from replication origin loci that fire at different times. Debate remains about whether origins are a fixed set of loci used across all cells or a loose agglomeration of potential origins used stochastically in individual cells, and about how consistent their firing time during S phase is across cells. Here, we develop an approach for profiling DNA replication in single human cells and apply it to 2,305 replicating cells spanning the entire S phase. The resolution and scale of the data enabled us to specifically analyze initiation sites and show that these sites have confined locations that are consistently used among individual cells. Further, we find that initiation sites are activated in a similar, albeit not fixed, order across cells. Taken together, our results suggest that replication timing variability is constrained both spatially and temporally, and that the degree of variation is consistent across human cell lines.

scholarly journals Viral Cyclin–Cyclin-Dependent Kinase 6 Complexes Initiate Nuclear DNA Replication

2001 ◽  
Vol 21 (2) ◽  
pp. 624-635 ◽  
Author(s):  
Heike Laman ◽  
Dawn Coverley ◽  
Torsten Krude ◽  
Ronald Laskey ◽  
Nic Jones
Keyword(s):  
Kinase Inhibitors ◽  
Nuclear Dna ◽  
Kaposi Sarcoma ◽  
S Phase ◽  
Replication Initiation ◽  
Herpesvirus Saimiri ◽  
Cyclin Dependent Kinase ◽  
Viral Cyclin ◽  
Replication Systems

ABSTRACT The cyclins encoded by Kaposi sarcoma-associated herpesvirus and herpesvirus saimiri are homologs of human D-type cyclins. However, when complexed to cdk6, they have several activities that distinguish them from D-type cyclin-cdk6 complexes, including resistance to cyclin-dependent kinase inhibitors and an enhanced substrate range. We find that viral cyclins interact with and phosphorylate proteins involved in replication initiation. Using mammalian in vitro replication systems, we show that viral cyclin-cdk6 complexes can directly trigger the initiation of DNA synthesis in isolated late-G1-phase nuclei. Viral cyclin-cdk6 complexes share this capacity with cyclin A-cdk2, demonstrating that in addition to functioning as G1-phase cyclin-cdk complexes, they function as S-phase cyclin-cdk complexes.

scholarly journals Excess Mcm2–7 license dormant origins of replication that can be used under conditions of replicative stress

2006 ◽  
Vol 173 (5) ◽  
pp. 673-683 ◽  
Author(s):  
Anna M. Woodward ◽  
Thomas Göhler ◽  
M. Gloria Luciani ◽  
Maren Oehlmann ◽  
Xinquan Ge ◽  
...  
Keyword(s):  
Complete Genome ◽  
S Phase ◽  
Genome Replication ◽  
Replication Origins ◽  
Observable Effect ◽  
Minichromosome Maintenance ◽  
Replicative Stress ◽  
Origins Of Replication ◽  
Checkpoint Pathway ◽  
Egg Extracts

In late mitosis and early G1, replication origins are licensed for subsequent use by loading complexes of the minichromosome maintenance proteins 2–7 (Mcm2–7). The number of Mcm2–7 complexes loaded onto DNA greatly exceeds the number of replication origins used during S phase, but the function of the excess Mcm2–7 is unknown. Using Xenopus laevis egg extracts, we show that these excess Mcm2–7 complexes license additional dormant origins that do not fire during unperturbed S phases because of suppression by a caffeine-sensitive checkpoint pathway. Use of these additional origins can allow complete genome replication in the presence of replication inhibitors. These results suggest that metazoan replication origins are actually comprised of several candidate origins, most of which normally remain dormant unless cells experience replicative stress. Consistent with this model, using Caenorhabditis elegans, we show that partial RNAi-based knockdown of MCMs that has no observable effect under normal conditions causes lethality upon treatment with low, otherwise nontoxic, levels of the replication inhibitor hydroxyurea.

scholarly journals A quantitative model for cyclin-dependent kinase control of the cell cycle: revisited

2011 ◽  
Vol 366 (1584) ◽  
pp. 3572-3583 ◽  
Author(s):  
Frank Uhlmann ◽  
Céline Bouchoux ◽  
Sandra López-Avilés
Keyword(s):  
Cell Cycle ◽  
Eukaryotic Cell ◽  
Quantitative Model ◽  
S Phase ◽  
Cyclin Dependent Kinase ◽  
Genomic Integrity ◽  
Chromosomal Dna ◽  
Substrate Specificities ◽  
Daughter Cells ◽  
Molecular Events

The eukaryotic cell division cycle encompasses an ordered series of events. Chromosomal DNA is replicated during S phase of the cell cycle before being distributed to daughter cells in mitosis. Both S phase and mitosis in turn consist of an intricately ordered sequence of molecular events. How cell cycle ordering is achieved, to promote healthy cell proliferation and avert insults on genomic integrity, has been a theme of Paul Nurse's research. To explain a key aspect of cell cycle ordering, sequential S phase and mitosis, Stern & Nurse proposed ‘A quantitative model for cdc2 control of S phase and mitosis in fission yeast’. In this model, S phase and mitosis are ordered by their dependence on increasing levels of cyclin-dependent kinase (Cdk) activity. Alternative mechanisms for ordering have been proposed that rely on checkpoint controls or on sequential waves of cyclins with distinct substrate specificities. Here, we review these ideas in the light of experimental evidence that has meanwhile accumulated. Quantitative Cdk control emerges as the basis for cell cycle ordering, fine-tuned by cyclin specificity and checkpoints. We propose a molecular explanation for quantitative Cdk control, based on thresholds imposed by Cdk-counteracting phosphatases, and discuss its implications.

scholarly journals Replication timing of DNA sequences associated with human centromeres and telomeres.

1990 ◽  
Vol 10 (12) ◽  
pp. 6348-6355 ◽  
Author(s):  
K G Ten Hagen ◽  
D M Gilbert ◽  
H F Willard ◽  
S N Cohen
Keyword(s):  
Dna Sequences ◽  
Cell Sorting ◽  
Replication Timing ◽  
S Phase ◽  
Alpha Satellite ◽  
Chromosomal Dna ◽  
Telomeric Sequences ◽  
Alpha Satellite Dna ◽  
Satellite Sequences ◽  
Satellite Repeats

The timing of replication of centromere-associated human alpha satellite DNA from chromosomes X, 17, and 7 as well as of human telomeric sequences was determined by using density-labeling methods and fluorescence-activated cell sorting. Alpha satellite sequences replicated late in S phase; however, the alpha satellite sequences of the three chromosomes studied replicated at slightly different times. Human telomeres were found to replicate throughout most of S phase. These results are consistent with a model in which multiple initiations of replication occur at a characteristic time within the alpha satellite repeats of a particular chromosome, while the replication timing of telomeric sequences is determined by either telomeric origins that can initiate at different times during S phase or by replication origins within the flanking chromosomal DNA sequences.

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 Replication timing of DNA sequences associated with human centromeres and telomeres

1990 ◽  
Vol 10 (12) ◽  
pp. 6348-6355
Author(s):  
K G Ten Hagen ◽  
D M Gilbert ◽  
H F Willard ◽  
S N Cohen
Keyword(s):  
Dna Sequences ◽  
Cell Sorting ◽  
Replication Timing ◽  
S Phase ◽  
Alpha Satellite ◽  
Chromosomal Dna ◽  
Telomeric Sequences ◽  
Alpha Satellite Dna ◽  
Satellite Sequences ◽  
Satellite Repeats

The timing of replication of centromere-associated human alpha satellite DNA from chromosomes X, 17, and 7 as well as of human telomeric sequences was determined by using density-labeling methods and fluorescence-activated cell sorting. Alpha satellite sequences replicated late in S phase; however, the alpha satellite sequences of the three chromosomes studied replicated at slightly different times. Human telomeres were found to replicate throughout most of S phase. These results are consistent with a model in which multiple initiations of replication occur at a characteristic time within the alpha satellite repeats of a particular chromosome, while the replication timing of telomeric sequences is determined by either telomeric origins that can initiate at different times during S phase or by replication origins within the flanking chromosomal DNA sequences.

scholarly journals Both cyclin A and cyclin E have S-phase promoting (SPF) activity in Xenopus egg extracts

1996 ◽  
Vol 109 (6) ◽  
pp. 1555-1563 ◽  
Author(s):  
U.P. Strausfeld ◽  
M. Howell ◽  
P. Descombes ◽  
S. Chevalier ◽  
R.E. Rempel ◽  
...  
Keyword(s):  
Dna Replication ◽  
Cyclin E ◽  
Cyclin A ◽  
Early Embryo ◽  
S Phase ◽  
Chromosomal Dna ◽  
Cyclin E1 ◽  
Egg Extracts ◽  
High Concentrations ◽  
Xenopus Egg Extracts

Extracts of activated Xenopus eggs in which protein synthesis has been inhibited support a single round of chromosomal DNA replication. Affinity-depletion of cyclin dependent kinases (Cdks) from these extracts blocks the initiation of DNA replication. We define ‘S-phase promoting factor’ (SPF) as the Cdk activity required for DNA replication in these Cdk-depleted extracts. Recombinant cyclins A and E, but not cyclin B, showed significant SPF activity. High concentrations of cyclin A promoted entry into mitosis, which inhibited DNA replication. In contrast, high concentrations of cyclin E1 promoted neither nuclear envelope disassembly nor full chromosome condensation. In the early embryo cyclin E1 complexes exclusively with Cdk2 and cyclin A is complexed predominantly with Cdc2; only later in development does cyclin A associate with Cdk2. We show that baculovirus-produced complexes of cyclin A-Cd2, cyclin A-Cdk2 and cyclin E-Cdk2 could each provide SPF activity. These results suggest that although in the early Xenopus embryo cyclin E1-Cdk2 is sufficient to support entry into S-phase, cyclin A-Cdc2 provides a significant additional quantity of SPF as its levels rise during S phase.

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