Replication in Hydroxyurea: It's a Matter of Time

Alvino, Gina M.; Collingwood, David H.; Murphy, John M.; Delrow, Jeffrey J.; Brewer, Bonita J.; Raghuraman, M. K.

doi:10.1128/mcb.00719-07

Cited by 212 publications

(276 citation statements)

References 41 publications

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“…Moreover, in a given population of cells, each origin has a distinct probability of activation, which is defined as origin efficiency. Although population studies have demonstrated that each origin has distinct timing and efficiency properties (Raghuraman et al 2001;Yabuki et al 2002;Alvino et al 2007;McCune et al 2008;McGuffee et al 2013;Müller et al 2014), DNA combing experiments have shown that DNA replication occurs stochastically in individual cells and, therefore, is not as deterministic as population analyses suggest (Patel et al 2006;Czajkowsky et al 2008). These findings can be reconciled by averaging the heterogeneous replication kinetics of a large number of cells, which recapitulates the observed data from population studies (Czajkowsky et al 2008).…”

supporting

confidence: 66%

Nucleosome occupancy as a novel chromatin parameter for replication origin functions

et al. 2016

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Eukaryotic DNA replication initiates from multiple discrete sites in the genome, termed origins of replication (origins). Prior to S phase, multiple origins are poised to initiate replication by recruitment of the pre-replicative complex (pre-RC). For proper replication to occur, origin activation must be tightly regulated. At the population level, each origin has a distinct firing time and frequency of activation within S phase. Many studies have shown that chromatin can strongly influence initiation of DNA replication. However, the chromatin parameters that affect properties of origins have not been thoroughly established. We found that nucleosome occupancy in G1 varies greatly around origins across the S. cerevisiae genome, and nucleosome occupancy around origins significantly correlates with the activation time and efficiency of origins, as well as pre-RC formation. We further demonstrate that nucleosome occupancy around origins in G1 is established during transition from G2/M to G1 in a pre-RC-dependent manner. Importantly, the diminished cell-cycle changes in nucleosome occupancy around origins in the orc1-161 mutant are associated with an abnormal global origin usage profile, suggesting that proper establishment of nucleosome occupancy around origins is a critical step for regulation of global origin activities. Our work thus establishes nucleosome occupancy as a novel and key chromatin parameter for proper origin regulation.

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confidence: 66%

Nucleosome occupancy as a novel chromatin parameter for replication origin functions

et al. 2016

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“…However, previous genomewide studies of HU-treated cells (Feng et al 2006;Alvino et al 2007), of an rrm3D mutant (Azvolinsky et al 2009), and of a clb5D mutant (McCune et al 2008) do not support this idea. Thus, some aspect of impaired DNA replication that is yet to be elucidated likely accounts for the greatly enhanced frequency of Ty1-Ty1 recombination that forms the HTA2-HTB2 amplification.…”

Section: Discussionmentioning

confidence: 49%

“…Therefore, we measured the amplification frequency after treatment with MMS, a DNA-damaging agent, or HU, which slows DNA replication (Feng et al 2006;Alvino et al 2007). To measure the amplification frequency in wild-type cells, we adapted a previously described method that can detect two copies of the amplified region in a wild-type background, the coq1THIS3 reporter (Figure 2A; Chan and Botstein 1993;Libuda and Winston 2006; see materials and methods for details).…”

Section: Resultsmentioning

confidence: 99%

Alterations in DNA Replication and Histone Levels Promote Histone Gene Amplification in Saccharomyces cerevisiae

Libuda¹,

Winston

2010

Genetics

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Gene amplification, a process that increases the copy number of a gene or a genomic region to two or more, is utilized by many organisms in response to environmental stress or decreased levels of a gene product. Our previous studies in Saccharomyces cerevisiae identified the amplification of a histone H2A-H2B gene pair, HTA2-HTB2, in response to the deletion of the other H2A-H2B gene pair, HTA1-HTB1. This amplification arises from a recombination event between two flanking Ty1 elements to form a new, stable circular chromosome and occurs at a frequency higher than has been observed for other Ty1-Ty1 recombination events. To understand the regulation of this amplification event, we screened the S. cerevisiae nonessential deletion set for mutations that alter the amplification frequency. Among the deletions that increase HTA2-HTB2 amplification frequency, we identified those that either decrease DNA replication fork progression (rrm3D, dpb3D, dpb4D, and clb5D) or that reduce histone H3-H4 levels (hht2-hhf2D). These two classes are related because reduced histone H3-H4 levels increase replication fork pauses, and impaired replication forks cause a reduction in histone levels. Consistent with our mutant screen, we found that the introduction of DNA replication stress by hydroxyurea induces the HTA2-HTB2 amplification event. Taken together, our results suggest that either reduced histone levels or slowed replication forks stimulate the HTA2-HTB2 amplification event, contributing to the restoration of normal chromatin structure.

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“…We therefore tested whether, in the cdc7-1 rif1D strain, replication depends on deregulated telomere-proximal origins or genome-wide initiation events. To distinguish between these possibilities, we used an isotopic labeling method (Alvino et al 2007) to monitor the appearance of replicated DNA in the cdc7-1 rif1D strain released from a-factor at 37°C (Fig. 1D, top panel; Supplemental Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Genomewide percent replication values were normalized, and the data were smoothed as described (Alvino et al 2007;Feng et al 2009). …”

Section: Microarray Analysis Of Genomic Dna Replication Profilesmentioning

confidence: 99%

Rif1 controls DNA replication by directing Protein Phosphatase 1 to reverse Cdc7-mediated phosphorylation of the MCM complex

et al. 2014

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Initiation of eukaryotic DNA replication requires phosphorylation of the MCM complex by Dbf4-dependent kinase (DDK), composed of Cdc7 kinase and its activator, Dbf4. We report here that budding yeast Rif1 (Rap1-interacting factor 1) controls DNA replication genome-wide and describe how Rif1 opposes DDK function by directing Protein Phosphatase 1 (PP1)-mediated dephosphorylation of the MCM complex. Deleting RIF1 partially compensates for the limited DDK activity in a cdc7-1 mutant strain by allowing increased, premature phosphorylation of Mcm4. PP1 interaction motifs within the Rif1 N-terminal domain are critical for its repressive effect on replication. We confirm that Rif1 interacts with PP1 and that PP1 prevents premature Mcm4 phosphorylation. Remarkably, our results suggest that replication repression by Rif1 is itself also DDK-regulated through phosphorylation near the PP1-interacting motifs. Based on our findings, we propose that Rif1 is a novel PP1 substrate targeting subunit that counteracts DDK-mediated phosphorylation during replication. Fission yeast and mammalian Rif1 proteins have also been implicated in regulating DNA replication. Since PP1 interaction sites are evolutionarily conserved within the Rif1 sequence, it is likely that replication control by Rif1 through PP1 is a conserved mechanism.

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Replication in Hydroxyurea: It's a Matter of Time

Cited by 212 publications

References 41 publications

Nucleosome occupancy as a novel chromatin parameter for replication origin functions

Nucleosome occupancy as a novel chromatin parameter for replication origin functions

Alterations in DNA Replication and Histone Levels Promote Histone Gene Amplification in Saccharomyces cerevisiae

Rif1 controls DNA replication by directing Protein Phosphatase 1 to reverse Cdc7-mediated phosphorylation of the MCM complex

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