Abstract
BackgroundHistone deacetylases (HDACs) play a critical role in the maintenance of genome stability. Class I HDACs, histone deacetylase 1 and 2 (Hdac1 and Hdac2) are recruited to the replication fork by virtue of their interactions with the replication machinery. However, functions for Hdac1 and Hdac2 (Hdacs1,2) in DNA replication are not fully understood.ResultsUsing genetic knockdown systems and novel Hdacs1,2-selective inhibitors, we found that loss of Hdacs1,2 leads to a reduction in the replication fork velocity, and an increase in replication stress response culminating in DNA damage. These observed defects are due to a direct role for Hdacs1,2 in DNA replication, as transcription of genes involved in replication was not affected in the absence of Hdacs1,2. We found that loss of Hdacs1,2 functions increases histone acetylation (ac) on chromatin in S-phase cells and affects nascent chromatin structure, as evidenced by the altered sensitivity of newly synthesized DNA to nuclease digestion. Specifically, H4K16ac, a histone modification involved in chromatin decompaction, is increased on nascent chromatin upon abolishing Hdacs1,2 activities. It was previously shown that H4K16ac interferes with the functions of SMARCA5, an ATP-dependent ISWI family chromatin remodeler. We found SMARCA5 also associates with nascent DNA and loss of SMARCA5 decreases replication fork velocity similar to the loss or inhibition of Hdacs1,2.ConclusionsOur studies reveal important roles for Hdacs1,2 in nascent chromatin structure maintenance and regulation of SMARCA5 chromatin-remodeler function, which together are required for proper replication fork progression and genome stability in S-phase.
Highlights
Histone deacetylases (HDACs) play a critical role in the maintenance of genome stability
We examined whether Hdacs1,2 associate with replication origins in cells synchronized in Sphase
Using chromatin immunoprecipitation (ChIP) assays, we found that Hdac1 and Hdac2 are enriched at candidate early (α-globin), mid-late and late (β-globin) replicating loci in cells synchronized in Sphase [17] (Figure 1B and Additional file 1: Figures S1A and S1B)
Summary
Histone deacetylases (HDACs) play a critical role in the maintenance of genome stability. Several broad-spectrum inhibitors are in various stages of clinical trials for both solid tumors and hematopoietic malignancies [1] Two of these compounds (SAHA/Vorinostat and Depsipeptide/Romidepsin) have gained FDA approval for their use against T-cell cutaneous lymphomas. Knockout of either Hdac or Hdac had minimal effect on hematopoiesis and on the cell cycle, likely due to compensation for one by the other, as they are highly similar proteins. Deletion of both genes dramatically impaired proliferation in multiple cell types by blocking cells at the G1 to S phase transition [6,7]. While a role for HDACs in transcription is well established [9,10,11], these enzymes function in DNA replication
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