Linking DNA replication checkpoint to MBF cell-cycle transcription reveals a distinct class of G1/S genes.

Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
The EMBO Journal (Impact Factor: 10.75). 02/2012; 31(7):1798-810. DOI: 10.1038/emboj.2012.27
Source: PubMed

ABSTRACT Reprogramming gene expression is crucial for DNA replication stress response. We used quantitative proteomics to establish how the transcriptional response results in changes in protein levels. We found that expression of G1/S cell-cycle targets are strongly up-regulated upon replication stress, and show that MBF, but not SBF genes, are up-regulated via Rad53-dependent inactivation of the MBF co-repressor Nrm1. A subset of G1/S genes was found to undergo an SBF-to-MBF switch at the G1/S transition, enabling replication stress-induced transcription of genes targeted by SBF during G1. This subset of G1/S genes is characterized by an overlapping Swi4/Mbp1-binding site and is enriched for genes that cause a cell cycle and/or growth defect when overexpressed. Analysis of the prototypical switch gene TOS4 (Target Of SBF 4) reveals its role as a checkpoint effector supporting the importance of this distinct class of G1/S genes for the DNA replication checkpoint response. Our results reveal that replication stress induces expression of G1/S genes via the Rad53-MBF pathway and that an SBF-to-MBF switch characterizes a new class of genes that can be induced by replication stress.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Background The coupling of cyclin dependent kinases (CDKs) to an intrinsically oscillating network of transcription factors has been proposed to control progression through the cell cycle in budding yeast, Saccharomyces cerevisiae. The transcription network regulates the temporal expression of many genes, including cyclins, and drives cell-cycle progression, in part, by generating successive waves of distinct CDK activities that trigger the ordered program of cell-cycle events. Network oscillations continue autonomously in mutant cells arrested by depletion of CDK activities, suggesting the oscillator can be uncoupled from cell-cycle progression. It is not clear what mechanisms, if any, ensure that the network oscillator is restrained when progression in normal cells is delayed or arrested. A recent proposal suggests CDK acts as a master regulator of cell-cycle processes that have the potential for autonomous oscillatory behavior.ResultsHere we find that mitotic CDK is not sufficient for fully inhibiting transcript oscillations in arrested cells. We do find that activation of the DNA replication and spindle assembly checkpoints can fully arrest the network oscillator via overlapping, but distinct mechanisms. Further, we demonstrate that the DNA replication checkpoint effector protein, Rad53, acts to arrest a portion of transcript oscillations in addition to its role in halting cell-cycle progression.Conclusions Our findings indicate that checkpoint mechanisms, likely via phosphorylation of network transcription factors, maintain coupling of the network oscillator to progression during cell-cycle arrest.
    Genome Biology 09/2014; 15(9):446. DOI:10.1186/PREACCEPT-1107846495134380 · 10.47 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Excess production of nitric oxide (NO) and reactive nitrogen intermediates (RNIs) cause nitrosative stress on cells. Schizosaccharomyces pombe was used as a model to study nitrosative stress response. This is the first report on the global gene expression profile in response to NO in S. pombe using microarray. Among 4824 genes reported for S. pombe, 818 were differentially expressed by at least 2-fold upon NO donor treatment. We previously showed that Pap1, the Activator Protein 1 transcription factor is required to combat nitrosative stress. In this study, the transcriptional response to NO in a null mutant for pap1 identified 45 genes that seem to be controlled by Pap1. Surprisingly, Pap1 regulated genes in S. pombe were distinctly different under nitrosative stress than those reported under oxidative stress. Genes of the pathways meiosis, cell cycle, spliceosome and oxidative phosphorylation were mostly affected under nitrosative stress in the fission yeast. Copyright © 2014. Published by Elsevier B.V.
    Gene 12/2014; 558(2). DOI:10.1016/j.gene.2014.12.067 · 2.20 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Checkpoints monitor critical cell cycle events such as chromosome duplication and segregation. They are highly conserved mechanisms that prevent progression into the next phase of the cell cycle when cells are unable to accomplish the previous event properly. During S phase, cells also provide a surveillance mechanism called the DNA replication checkpoint, which consists of a conserved kinase cascade that is provoked by insults that block or slow down replication forks. The DNA replication checkpoint is crucial for maintaining genome stability, because replication forks become vulnerable to collapse when they encounter obstacles such as nucleotide adducts, nicks, RNA-DNA hybrids, or stable protein-DNA complexes. These can be exogenously induced or can arise from endogenous cellular activity. Here, we summarize the initiation and transduction of the replication checkpoint as well as its targets, which coordinate cell cycle events and DNA replication fork stability.
    09/2013; 4(3):388-434. DOI:10.3390/genes4030388


Available from
Jun 3, 2014