A single amino acid change in histone H4 enhances UV survival and DNA repair in yeast

Nag, Ronita; Gong, Feng; Fahy, Deirdre; Smerdon, Michael J.

doi:10.1093/nar/gkn311

Cited by 25 publications

(19 citation statements)

References 40 publications

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“…Over the course of repair, the smear returns to a HMW band indicative of repaired, full length DNA. Until now, visualization of the cleavage products has typically been via 32 P labeled probes [59], [61], [62] or ethidium bromide [63], [64]. In Figure 7A, we show an example of mock-infected samples irradiated at 50 J/m 2 and then digested with T4, run on an alkaline agarose gel and stained with SYBR Gold, a ss and dsDNA binding dye, to illustrate these gels.…”

Section: Resultsmentioning

confidence: 99%

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HCMV-Infected Cells Maintain Efficient Nucleotide Excision Repair of the Viral Genome while Abrogating Repair of the Host Genome

O’Dowd¹,

Zavala²,

Brown³

et al. 2012

PLoS Pathog

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Many viruses subvert the host cell's ability to mount and complete various DNA damage responses (DDRs) after infection. HCMV infection of permissive fibroblasts activates host DDRs at the time of viral deposition and during replication, but the DDRs remain uncompleted without arrest or apoptosis. We believe this was in part due to partitioning of the damage response and double strand break repair components. After extraction of soluble proteins, the localization of these components fell into three groups: specifically associated with the viral replication centers (RCs), diffused throughout the nucleoplasm and excluded from the RCs. Others have shown that cells are incapable of processing exogenously introduced damage after infection. We hypothesized that the inability of the cells to process damage might be due to the differential association of repair components within the RCs and, in turn, potentially preferential repair of the viral genome and compromised repair of the host genome. To test this hypothesis we used multiple strategies to examine repair of UV-induced DNA damage in mock and virus-infected fibroblasts. Comet assays indicated that repair was initiated, but was not completed in infected cells. Quantitative analysis of immunofluorescent localization of cyclobutane pyrimidine dimers (CPDs) revealed that after 24 h of repair, CPDs were significantly reduced in viral DNA, but not significantly changed in the infected host DNA. To further quantitate CPD repair, we developed a novel dual-color Southern protocol allowing visualization of host and viral DNA simultaneously. Combining this Southern methodology with a CPD-specific T4 endonuclease V alkaline agarose assay to quantitate repair of adducts, we found efficient repair of CPDs from the viral DNA but not host cellular DNA. Our data confirm that NER functions in HCMV-infected cells and almost exclusively repairs the viral genome to the detriment of the host's genome.

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Section: Resultsmentioning

confidence: 99%

“…These techniques have been used extensively to study genomic [59], [63], [64] and gene-specific [61], [62] CPD repair in a variety of organisms. However, determining repair of virus and host genomic DNA independently within HCMV-infected cells proved more challenging.…”

Section: Resultsmentioning

confidence: 99%

HCMV-Infected Cells Maintain Efficient Nucleotide Excision Repair of the Viral Genome while Abrogating Repair of the Host Genome

O’Dowd¹,

Zavala²,

Brown³

et al. 2012

PLoS Pathog

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“…The MNase accessibility was measured as previously described [47]. Briefly, 50 ml cultures of mid-log phase yeast cells (~ 1.0× 10 7 cells/ml) were pelleted, washed with PBS, suspended in yeast lytic enzyme YLE buffer containing10 mg/ml zymolaze (MP Biomedicals) in 1M sorbitol and 5 mM β-mercaptoetanol, and incubated at 30° C for 20 min.…”

Section: Methodsmentioning

confidence: 99%

Chromatin remodelling complex RSC promotes base excision repair in chromatin of Saccharomyces cerevisiae

2014

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The base excision repair (BER) pathway is a conserved DNA repair system required to maintain genomic integrity and prevent mutagenesis in all eukaryotic cells. Nevertheless, how BER operates in vivo (i.e. in the context of chromatin) is poorly understood. We have investigated the role of an essential ATP-dependent chromatin remodeling (ACR) complex RSC (Remodels the Structure of Chromatin) in BER of intact yeast cells. We show that depletion of STH1, the ATPase subunit of RSC, causes enhanced sensitivity to the DNA alkylating agent methyl methanesulfonate (MMS) and results in a substantial inhibition of BER, at the GAL1 locus and in the genome overall. Consistent with this observation, the DNA in chromatin is less accessible to micrococcal nuclease digestion in the absence of RSC. Quantitative PCR results indicate that repair deficiency in STH1 depleted cells is not due to changes in the expression of BER genes. Collectively, our data indicates the RSC complex promotes efficient BER in chromatin. These results provide, for the first time, a link between ATP-dependent chromatin remodeling and BER in living cells.

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“…Nag et al . reported that the mutation H4R45C increases the accessibility of nucleosome DNA in chromatin to exogenous nucleases and may expedite nucleosomal rearrangements during nucleotide excision repair 15 .…”

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confidence: 99%

Nucleosome alterations caused by mutations at modifiable histone residues in Saccharomyces cerevisiae

Liu

Wang

Liu

et al. 2015

Sci Rep

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Nucleosome organization exhibits dynamic properties depending on the cell state and environment. Histone proteins, fundamental components of nucleosomes, are subject to chemical modifications on particular residues. We examined the effect of substituting modifiable residues of four core histones with the non-modifiable residue alanine on nucleosome dynamics. We mapped the genome-wide nucleosomes in 22 histone mutants of Saccharomyces cerevisiae and compared the nucleosome alterations relative to the wild-type strain. Our results indicated that different types of histone mutation resulted in different phenotypes and a distinct reorganization of nucleosomes. Nucleosome occupancy was altered at telomeres, but not at centromeres. The first nucleosomes upstream (−1) and downstream (+1) of the transcription start site (TSS) were more dynamic than other nucleosomes. Mutations in histones affected the nucleosome array downstream of the TSS. Highly expressed genes, such as ribosome genes and genes involved in glycolysis, showed increased nucleosome occupancy in many types of histone mutant. In particular, the H3K56A mutant exhibited a high percentage of dynamic genomic regions, decreased nucleosome occupancy at telomeres, increased occupancy at the +1 and −1 nucleosomes, and a slow growth phenotype under stress conditions. Our findings provide insight into the influence of histone mutations on nucleosome dynamics.

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A single amino acid change in histone H4 enhances UV survival and DNA repair in yeast

Cited by 25 publications

References 40 publications

HCMV-Infected Cells Maintain Efficient Nucleotide Excision Repair of the Viral Genome while Abrogating Repair of the Host Genome

HCMV-Infected Cells Maintain Efficient Nucleotide Excision Repair of the Viral Genome while Abrogating Repair of the Host Genome

Chromatin remodelling complex RSC promotes base excision repair in chromatin of Saccharomyces cerevisiae

Nucleosome alterations caused by mutations at modifiable histone residues in Saccharomyces cerevisiae

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