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Deletion of histone deacetylase 3 reveals critical roles in S phase progression and DNA damage control.

ABSTRACT: Histone deacetylases (HDACs) are enzymes that modify key residues in histones to regulate chromatin architecture, and they play a vital role in cell survival, cell-cycle progression, and tumorigenesis. To understand the function of Hdac3, a critical component of the N-CoR/SMRT repression complex, a conditional allele of Hdac3 was engineered. Cre-recombinase-mediated inactivation of Hdac3 led to a delay in cell-cycle progression, cell-cycle-dependent DNA damage, and apoptosis in mouse embryonic fibroblasts (MEFs). While no overt defects in mitosis were observed in Hdac3-/- MEFs, including normal H3Ser10 phosphorylation, DNA damage was observed in Hdac3-/- interphase cells, which appears to be associated with defective DNA double-strand break repair. Moreover, we noted that Hdac3-/- MEFs were protected from DNA damage when quiescent, which may provide a mechanistic basis for the action of HDAC inhibitors on cycling tumor cells.

SUBMITTER: Bhaskara S

PROVIDER: S-EPMC2373760 | biostudies-literature | 2008 Apr

REPOSITORIES: biostudies-literature

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Deletion of histone deacetylase 3 reveals critical roles in S phase progression and DNA damage control.

Bhaskara Srividya S Chyla Brenda J BJ Amann Joseph M JM Knutson Sarah K SK Cortez David D Sun Zu-Wen ZW Hiebert Scott W SW

Molecular cell 20080401 1

Histone deacetylases (HDACs) are enzymes that modify key residues in histones to regulate chromatin architecture, and they play a vital role in cell survival, cell-cycle progression, and tumorigenesis. To understand the function of Hdac3, a critical component of the N-CoR/SMRT repression complex, a conditional allele of Hdac3 was engineered. Cre-recombinase-mediated inactivation of Hdac3 led to a delay in cell-cycle progression, cell-cycle-dependent DNA damage, and apoptosis in mouse embryonic f ...[more]

PMID: 18406327

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Project description:Histone deacetylases (HDAC) are enzymes that modify key residues in histones to regulate chromatin architecture, and play a vital role in cell survival, cell cycle progression, and tumorigenesis. To understand the function of Hdac3, a critical component of the N-CoR/SMRT repression complex, a conditional allele of Hdac3 was engineered. Given the vital role of HDAC3 in normal cells and in the generation and treatment of various cancers, a conditional deletion of Hdac3 was engineered in mice. The deletion of Hdac3 in the germ line yielded very early embryonic lethality. Therefore, mouse embryonic-derived fibroblasts (MEFs) containing the Hdac3 conditional allele were used to examine the function of Hdac3 in cell viability and in cell cycle control. Given the links between Hdac3 and transcriptional repression, we used oligonucleotide micro arrays to examine RNA isolated from control and Cre recombinase expressing MEFs to define the changes in gene expression upon inactivation of Hdac3. Initially, we compared RNA from Ad-Cre infected Hdac3FL/+ and Hdac3FL/- MEFs and then we extended the analysis to Hdac3FL/- MEFs expressing Cre-ER (tamoxifen responsive Cre-estrogen receptor fusion protein). When the gene expression of ethanol-treated (vehicle) and tamoxifen-treated MEFs was compared at 72 hr post-induction, 83 genes were induced and 111 genes were down-regulated at least 1.5-fold upon inactivation of Hdac3. Approximately, 48 genes were up-regulated in both Ad-Cre and tamoxifen-treated MEFs at the 72 hr time point. The majority of the affected genes were associated with signal transduction and metabolism. Overall, few of the up-regulated genes at the 72hr time point in Ad-Cre and tamoxifen-treated MEFs are associated with apoptosis or with cell cycle control. Thus, these metabolic regulatory genes may be “core” Hdac3-regulated genes, and alterations in gene expression are unlikely to trigger apoptosis. Keywords: Conditional knock out analysis, genetic modification

Project description:Dynamic acetylation of metabolic proteins has emerged as a ubiquitous post-translational modification of human metabolic proteins. However, the corresponding modifying enzymes and the functions of the modification await exploration. Using a genome-wide synthetic lethality screen, we constructed a genetic interaction network of human histone deacetylases (HDACs) and discovered many metabolic substrates of these enzymes. We further confirmed that the adenosine monophosphate-activated protein kinase (AMPK) catalytic subunit is acetylated and deacetylated by EP300 and HDAC1, respectively. Deacetylation of AMPK catalytic subunit enhances physical interaction with the upstream kinase LKB1, and leads to AMPK phosphorylation and activation. These findings highlight the importance of genetic interaction profiling to identify specific substrates of individual HDACs and elucidate how cells use protein (de)acetylation to coordinate nutrient availability and cellular energy status. To study the functional specificity of individual HDAC, we developed a genome-wide genetic interaction profiling technology in cultured human cells by RNAi using pooled TRC (The RNAi Consortium) 75k human shRNA library and complexity deconvolution by high-density microarray with a half-hairpin barcode design. The HCT116 colon cancer cell line was chosen as the screen platform because of its quasinormal diploid karyotype. The performance of the customized microarray we designed was first evaluated by the receiver operating characteristic (ROC) curve showing high sensitivity (89%), specificity (94%) and area under curve (0.95), as well as a control hybridization without DNA sample showing low background signal. Both results suggest that the fluorescent signals were generated by specific hybridization reactions. The high correlation of signal between Cy5 and Cy3 channel as well as dye-swap experiments indicated that biases between the two labeling fluorophores during competitive hybridization were negligible. Moreover, correlation between technical and biological replicates confirmed the high reproducibility of the methodology. In the screen, we used stable polyclonal cells expressing shRNA constructs targeting firefly luciferase (shLuciferase) as control. We checked the knockdown efficiency in protein or RNA level of individual shRNA constructs for 12 human HDAC genes (HDAC1~4, HDAC6~9, SIRT1~3 and SIRT5) by immunoblotting or quantitative PCR, and generated stable polyclonal query cell lines expressing two shRNA constructs with the highest knockdown efficiency for each HDAC gene. After transduction by TRC shRNA lentiviral pools, benchmark samples were harvested prior to puromycin selection, and the remaining cells were propagated under selection and harvested again after 18 population doublings as the end samples. Half-hairpin barcode library of the benchmark and end samples was recovered from genomic DNA respectively by PCR with Cy5 and Cy3-labeled primers, gel purified, and hybridized to the microarray. For each shRNA construct, the Z-score of the log2(Cy5/Cy3) was computed, and Z-score difference was calculated by subtracting the Z-score of the control sample from that of the query sample. Z-score differences larger than 1.5 and less than -1.5 were used as arbitrary thresholds to define candidate negative and positive genetic interactions, respectively.

Dataset Information

Deletion of histone deacetylase 3 reveals critical roles in S phase progression and DNA damage control.

Publications

Deletion of histone deacetylase 3 reveals critical roles in S phase progression and DNA damage control.

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