Involvement of the DNA damage response kinase Rad53 and core histones in the transcriptional response to carbon source switch in budding yeast
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PROVIDER: PRJNA564533 | ENA |
REPOSITORIES: ENA
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Project description:We applied RNA-Seq analysis to investigate the involvement of the DNA damage response kinase Rad53 and core histones in the transcriptional response to a carbon source switch from 2% glucose to 3% ethanol. Cells were cultured in synthetic complete medium with 2% glucose and switched to 3% ethanol. Samples were collleted in log phase in glucose, 1 hour after the switch (acute response) or 20 hours after the switch (adaptation). The data show that subtelomeric genes are repressed in sml1 rad53 mutants irrespective of the carbon source, in a histone-dependent manner. The data further show that Rad53 is not involved in the global carbon source switch response, but specifically in the expression of switch-inducible subtelomeric genes.
2020-07-09 | GSE137091 | GEO
Project description:In budding yeast, DNA lesions and stalled replication forks are sensed by the apical checkpoint kinase Mec1/ATR, which leads to the downstream activation of the effector kinase Rad53/CHK1. This activation depends on Rad9 and Mrc1, two checkpoint mediators that integrate the nature of the challenge in different phases of the cell cycle. Rad9 mediates the activation of the DNA damage checkpoint throughout the cell cycle, while the function of Mrc1 is restricted to the S phase of the cell cycle, when it travels with the replication fork and activates the DNA replication checkpoint in response to a variety of replication impediments. In this scenario, the role of Rad9 in S phase has been largely disregarded since the discovery of Mrc1, because Rad9 is dispensable for the timely activation of Rad53 in response to the drug hydroxyurea, which halts forks, and is only recruited to those stalled forks when Mrc1 is absent. Thus, Rad9 is simply believed to act as a backup pathway for Mrc1 during replication. We have re-evaluated the role of Rad9 when DNA damage arises during replication and characterized its functional interplay with Mrc1. To this end, we have used genome-wide approaches, single-molecule analysis, pulsed-field and 2D gel electrophoresis, as well as a careful combination of different replication-challenging drugs. We have found that both Mrc1 and Rad9 play distinct but complementary functions in the replication stress response during S phase, for they coordinate the early and late functions of Rad53, respectively. While Mrc1 is responsible for the fast activation of Rad53 in response to fork-halting drugs in order to repress late origins, Rad9 maintains Rad53 in an active state during prolonged fork arrest and is necessary to sustain this response for long periods. Remarkably, we also have found that Rad9 possesses the unprecedented activity of slowing down replication fork progression in response to DNA damage. This work thus restores the legitimate role of Rad9 as a central actor in the maintenance of genome integrity during replication. This has important implications for our understanding of the management of the checkpoint during perturbed replication in human cells, for Rad9 has three orthologues, 53BP1, BRCA1 and MDC1, whose contribution to this aspect of genome integrity remains largely unexplored.
2018-08-27 | GSE109654 | GEO
Project description:We show that synthesising histones with different chemical modifications can induce a transcriptional response that alters the phenotype of those cells.
2023-02-01 | GSE166493 | GEO
Project description:We identified lysine 37 of histone H2B as a novel site of histone lysine methylation in budding yeast. Microarray analysis was performed to determine global changes in gene expression upon mutation of this lysine residue to a unmodifiable form. Histones were acid-extracted from asynchronously grown yeast expressing wild-type H2B or H2B harboring a K37A mutation.
2010-09-26 | E-GEOD-24380 | biostudies-arrayexpress
Project description:Across eukaryotes, inhibition of the progression of the DNA replication machinery causes an S-phase checkpoint response. This response regulates multiple processes, including inhibition of replication initiation and fork stabilisation. How these events are coordinated remains poorly understood. Here we show that the replicative helicase component Cdc45 targets the checkpoint kinase Rad53 to distinct replication complexes in the budding yeast Saccharomyces cerevisiae. Rad53 binds to FHA-interaction motifs in an unstructured loop region of Cdc45, which is phosphorylated by Rad53 itself, and this interaction is necessary for the inhibition of origin firing through Sld3. In addition to regulating replication initiation, Cdc45 also recruits Rad53 to stalled replication forks, which we demonstrate is important for the response to replication stress. Finally we show that a Cdc45 mutation that is orthologous to an allele found in patients with Meier-Gorlin Syndrome disrupts the functional interaction with Rad53. Together we present a single mechanism by which Rad53 targets replication initiation and elongation complexes, which may be relevant to human disease.
2019-02-26 | GSE122110 | GEO
Project description:The nucleosome plays a central role in genome regulation. Traditional methods for mapping nucleosomes depend on the resistance of the nucleosome core to micrococcal nuclease (MNase). However, the lengths of the protected DNA fragments are heterogeneous, limiting the accuracy of nucleosome position information. To resolve this problem, we removed residual linker DNA by simultaneous digestion of yeast chromatin with MNase and exonuclease III (ExoIII). Paired-end sequencing of mono-nucleosomes revealed not only core particles (145-147 bp), but also intermediate particles in which ~8 bp project from one side (154 bp) or both sides (161 bp) of the nucleosome core. We term these particles "pseudo-chromatosomes" because they are present in yeast lacking linker histone. They are also observed after MNase-ExoIII digestion of chromatin reconstituted using recombinant core histones. We propose that the pseudo-chromatosome provides a DNA framework to facilitate H1 binding. Comparison of budding yeast nucleosome sequences obtained using micrococcal nuclease (MNase-seq) and MNase + exonuclease III (ExoIII) (MNase-ExoIII-seq): wild type cells and hho1-null cells. Nucleosome sequences from native chromatin and H1-depleted chromatin from mouse liver. Nucleosome sequences from a plasmid reconstituted into nucleosomes using recombinant yeast histones or native chicken erythrocyte histones.
2015-09-23 | E-GEOD-65889 | biostudies-arrayexpress
Project description:This study investigates the ability of tumor budding to identify prognosis in different MMR states and different levels of tumor lymphocyte infiltration. Tumor budding is usually defined as an isolated single cancer cell or a cluster of up to four cancer cells located at the front of an infiltrating tumor.
| 2760877 | ecrin-mdr-crc
Project description:Recycling of parental histones is an important step in epigenetic inheritance. During DNA replication, DNA polymerase epsilon subunit DPB3/DPB4 and DNA replication helicase subunit MCM2 are involved in the transfer of parental histones to the leading and lagging DNA strands, respectively. Single Dpb3 deletion (dpb3[DELTA]) or Mcm2 mutation (mcm2-3A), which each disrupt one parental histone transfer pathway, leads to the other[prime]s predominance. However, the impact of the two histone transfer pathways on chromatin structure and DNA repair remains elusive. In this study, we used budding yeast Saccharomyces cerevisiae to determine the genetic and epigenetic outcomes from disruption of parental histone H3-H4 tetramer transfer. We found that a dpb3[DELTA]/mcm2-3A double mutant did not exhibit the single dpb3[DELTA] and mcm2-3A mutants[prime] asymmetric parental histone patterns, suggesting that the processes by which parental histones are transferred to the leading and lagging strands are independent. Surprisingly, the frequency of homologous recombination was significantly lower in dpb3[DELTA], mcm2-3A, and dpb3[DELTA]/mcm2-3A mutants relative to the wild-type strain, likely due to the elevated levels of free histones detected in the mutant cells. Together, these findings indicate that proper transfer of parental histones to the leading and lagging strands during DNA replication is essential for maintaining chromatin structure and that high levels of free histones due to parental histone transfer defects are detrimental to cells.
2024-04-24 | GSE240331 | GEO
