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.

Figure 1. Loss of Hdac3 alters histone acetylation

Western blot analysis of nuclear extracts prepared from Ad-Cre infected Hdac3^FL/+ and Hdac3^FL/− MEFs for changes in post-translational modifications of histone H3 and H4. Two independent western analyses were done using two different isolates of MEFs. A representative blot from one analysis is shown. The levels of H3 and H4 served as a loading control. The numbers above each lane indicate the time in hr after the initiation of Ad-Cre infection (Hr PI).

Figure 2. Inactivation of Hdac3 affects gene expression

(A) Classification of genes that were up- regulated at least 1.5-fold in both tamoxifen-treated Hdac3^FL/− ERCre+ and in Ad-Cre treated Hdac3^FL/−MEF at the 72hr time point. The data were analyzed using Gene Spring software to obtain the gene list and then these genes were categorized based on their different biological functions such as development (Dev.), signal transduction (Signal Trans.), cell cycle, and metabolism, using the Panther Gene Classification software. (B) Total RNA was isolated 72 hr after addition of tamoxifen to Cre-ER containing MEFs and real time PCR (Q-PCR) analysis was performed to validate the genes that were up regulated in both Ad-Cre and tamoxifen (64hr and 72hr) treated MEFs. Real time PCR was done in duplicate with the RNA isolate that was used for the microarray and with a different isolate of RNA (biological replicate) obtained from tamoxifen- and ethanol-treated Hdac3^FL/−/ERCre+ MEFs. The values represent the average fold-increase ± S.E. of duplicate samples. (C) MEFs (Hdac3 ^FL/+ and Hdac3 ^FL/−) were infected with Ad-Cre and ChIP analysis was performed 50hr post infection and the data was quantified by real-time PCR analysis. The level of acetylated histone H3 obtained in uninfected and infected samples was normalized to the total histone H3 occupancy. The fold-increase in the acetylated H3 level was then calculated for the Ad-Cre infected Hdac3^FL/− and Hdac3^FL/+ MEFs after normalization to the values obtained from the uninfected cells as the control. The relative fold-increase in Ad-Cre infected Hdac3^FL/− MEFs, denoted as Hdac3^−/− in the figure, was calculated by normalizing the values to those obtained from infected Hdac3^FL/+ MEFs denoted as Con. For Cyp51, primers 2 Kbp upstream of the transcriptional start site, at the transcriptional start site, and in Exon 5 were used. The data shown are the average fold-increase ± S.E. obtained from two different MEF preparations, each done in duplicate.

Figure 3. Examination of H3Ser10 phosphorylation in Hdac3^−/− MEFs and restoration of H3Ser10 phosphorylation by caffeine treatment in Hdac3^−/− NIH 3T3 cells

(A) Immunofluorescence analysis of mock infected or Ad-Cre infected Hdac3^FL/−MEFs using anti-phospho-H3Ser10 at 90hr post-infection. Cells were stained with Hoechst 33258 to visualize the nucleus. (B) Immunofluorescence analysis using anti-Hdac3 shows the localization of Hdac3 with chromatin in interphase and prophase stages of the cell cycle. The wild type MEFs were counterstained with Hoechst 33258 to visualize the DNA. (C) Caffeine restores histone H3Ser10 phosphorylation in Hdac3^−/−NIH 3T3 cells. Immunofluoresence staining of untreated and caffeine-treated cells using anti-phospho H3Ser10 on Hdac3^FL/− and Hdac3^−/− NIH 3T3 cells. Cells were treated with 2mM caffeine for 30 min prior to fixation. Hoechst staining of the cells was performed to visualize the nucleus. Two independent experiments were performed and the images shown are from a representative experiment. (D) Quantification of Phospho-H3Ser10 positive metaphase cells in Hdac3^FL/− and Hdac3^−/− NIH 3T3 cells in the absence and presence of caffeine. The values represent average percentage ± S.E. obtained from two independent experiments.

Figure 4. Deletion of Hdac3 results in a cell cycle delay

(A) Flow cytometry analysis of BrdU incorporation versus DNA content performed for Hdac3^FL/+ and Hdac3^FL/− MEFs at 90 hr following Ad-Cre infection. The experiment was done two times and a representative profile is shown as BrdU incorporation versus propidium iodide staining. (B) Ad-Cre infected Hdac3^FL/+ and Hdac3^FL/− MEFs were incubated with 10 μM BrdU for 45min, washed, and cultured in the absence of BrdU for the indicated times. BrdU/PI flow cytometry analysis of a representative experiment is shown. (C) Histogram representation of BrdU⁺ cells from (B) progressing through the cell cycle over a 10 hr time course.

Figure 5. Inactivation of Hdac3 causes DNA damage

(A) Immunofluoresence analysis of γH2AX 90 hr after Ad-Cre infection of Hdac3^FL/+ and Hdac3^FL/− MEFs. The experiment was done three times and images from a representative experiment are shown. (B) To obtain quantitative data of the H2AX foci distribution, the number of foci in 100–150 cells were manually counted and the percentage of cells containing 0, 1–10, 10–20, and greater than 20 foci per cell was calculated. Data represent the average percentage ± S.E. of three independent experiments. Student’s t-test demonstrated that the percentage of cells with greater than 20 foci in Hdac3^FL/− MEFs is statistically significant with a p value of 0.017. (C) Detection of KAP1 phosphorylation at Ser824 in Ad-Cre infected Hdac3^FL/+ and Hdac3^FL/− MEFs was performed by immunofluoresence. The data shown are representative of two experiments performed with two different isolates of MEF. (D) The percentage of the infected Hdac3^FL/+ and Hdac3^FL/− cells that are positive for KAP1 phosphorylation was determined after counting approximately 100 cells in each experiment. The data represent the average percentage ± S.E. of 2 independent experiments. (E) Western analysis for phospho MCM2 (S108) and for p53 levels of Hdac3^FL/+ and Hdac3^FL/− MEFs infected with Ad-Cre. Extracts prepared from doxorubicin (2μg/ml)- treated NIH 3T3 cells were used as a positive control. The level of total histone H3 was used as a loading control. (F) MEFs (Hdac3^FL/+) were treated either with increasing doses of SAHA (0.5–4μM) or with DMSO for 24hr. Immunofluoresence analysis of γH2AX in treated MEFs was performed and quantification of the γH2AX foci was calculated as the average percentage of cells with 20 or more foci in two different MEF isolates, and approximately 50 cells were counted in each isolate. The each point on the graph is the mean of the percentages ± S.E. obtained with two different MEF isolates.

Figure 6. DNA damage in Hdac3^−/− MEFs is cell cycle dependent

(A) MEFs (Hdac3^FL/+ and Hdac3^FL/−) were mock infected or infected with Ad-Cre for 3 hr and 45 hr later the cells were cultured in media containing 0.5% serum for 60 hr prior to immunofluorescence using anti-γH2AX or p-KAP1. (B) Quantification of the γH2AX foci or p-Kap1 positive cells in serum starved Hdac3^FL/+, Hdac3^FL/−, Hdac3^+/−, and Hdac3^−/− MEFs. Shown are the averages of 2 independent experiments with the standard error. Student’s t-test indicated that the differences in cell with 20 γH2AX foci were significant (p = 0.007).

Figure 7. Inactivation of Hdac3 sensitizes MEFs to irradiation

(A) Hdac3^FL/+ and Hdac3^FL/− MEFs infected with Ad-Cre were serum starved for 60 hr and irradiated with 1Gy of IR and γH2AX immunofluoresence was performed at 0 hr, 2 hr, and 24 hr following irradiation. (B) Quantitative analysis of γH2AX foci distribution following irradiation. (C) Immunofluoresence analysis of infected and serum starved Hdac3^FL/+ and Hdac3^FL/− MEFs at 0, 2, and 24 hr following 1Gy irradiation using anti-phospho-KAP-1. (D) Quantitative analysis of the data shown in C. The experiment was performed using two different preparations of MEFs and representative data are shown. (E) Quantification of the “comet” assays shown in Fig. S12. The DNA damage is expressed as the “tail moment” at the time of IR treatment (upper panel) and 4 hr later (lower panel). Tail moments of at least 25 comets in each treatment were calculated using the Comet Score software and the percentage of cells with different categories of tail moments was calculated. The experiment was done with two different MEF preparations and representative data from one experiment is shown.