Guanine-rich DNA sequences that can adopt non-Watson-Crick structures in vitro are prevalent in the human genome. Whether such structures normally exist in mammalian cells has, however, been the subject of active research for decades. Here, we show that the G-quadruplex interacting drug pyridostatin promoted growth arrest in human cancer cells via inducing replication- and transcription-dependent DNA damage. Chromatin immunoprecipitation sequence (ChIP-Seq) analysis of the DNA damage marker γH2AX provided the genome-wide distribution of pyridostatin-induced sites of damage, and revealed that pyridostatin targets gene bodies containing clusters of sequences with a propensity for G-quadruplex formation. As a result, pyridostatin modulated the expression of these genes, including the proto-oncogene SRC. We observed that pyridostatin reduced SRC protein levels and SRC-dependent cellular motility in human breast cancer cells, validating SRC as a target. Our unbiased approach to define genomic sites of action for a drug establishes a framework for discovering functional DNA-drug interactions.

DNA double-strand break (DSB) repair occurs within chromatin and can be modulated by chromatin modifying enzymes. Here we identify the related human histone deacetylases HDAC1 and HDAC2 as two participants in the DNA-damage response (DDR). We show that acetylation of histone H3 lysine 56 (H3K56) is regulated by HDAC1/2, and that HDAC1/2 are rapidly recruited to DNA-damage sites to promote H3K56 hypo-acetylation. Furthermore, we establish that HDAC1/2-depleted cells are hypersensitive to DNA-damaging agents and exhibit sustained DNA-damage signaling, phenotypes that reflect defective DSB repair, particularly by the pathway of non-homologous end-joining (NHEJ). Collectively, these results demonstrate that HDAC1 and HDAC2 function in the DDR by promoting DSB repair and thus provide important insights into the radio-sensitizing effects of HDAC inhibitors that are being developed as cancer therapies. KeywordsHDAC1; HDAC2; DNA damage; chromatin; non-homologous end-joining Because DNA damage represents a formidable challenge to the integrity of genetic material, cells have evolved multifaceted systems, collectively termed the DNA-damage response (DDR), to detect, signal and repair various types of DNA damage 1 , 2 . DNA double-strand breaks (DSBs) represent one of the most challenging forms of DNA damage which, if left unrepaired, can trigger cellular death and can contribute to human diseases, including cancer 1 . In eukaryotes, DSBs are repaired by two main pathways: non-homologous endjoining (NHEJ), which operates throughout the cell cycle, and homologous recombination (HR) which is limited to S and G2 cell-cycle phases 3 . For NHEJ, the Ku70/Ku80 complex loads onto free DNA ends where it helps recruit the DDR protein kinase DNA-PK (DNAdependent protein kinase) 4 , as well as other factors, including the nuclease Artemis and the ligase IV-XRCC4 complex, which are required for NHEJ to ensue 5 . NHEJ occurs rapidly within cells and mostly requires minimal processing of DNA ends. By contrast, HR requires extensive DNA end-resection to create stretches of single-stranded DNA (ssDNA) that bind factors such as RPA and RAD51 to promote the various steps in HR 3 . Since HR and NHEJ function together during certain phases of the cell cycle, mechanisms must exist to modulate In this study, our previous observation of a decrease of H3K56Ac upon DNA damage prompted us to evaluate the role of HDACs in the DDR. Here, we describe how human HDAC1 and HDAC2 respond to DNA damage and mediate changes in histone acetylation, including H3K56, following DNA-damage induction. Furthermore, by defining the effects of impairing HDAC1/2 function, we establish that these enzymes serve as important components of the DDR by promoting DSB signalling and repair, principally through their requirement for effective NHEJ. Europe PMC Funders Group RESULTS HDAC1 and HDAC2 localize to sites of DNA damageWe previously demonstrated that H3K56Ac levels are reduced by treatments that induce DNA damage, including the drug phleomycin that produces D...

Downregulation and mutations of the nuclear-architecture proteins Lamin A and C cause misshapen nuclei and altered chromatin organization associated with cancer and laminopathies, including the premature-aging disease Hutchinson-Gilford progeria syndrome (HGPS). Here, we identified the small molecule “Remodelin” that improved nuclear architecture, chromatin organization and fitness of both human Lamin A/C depleted cells and HGPS-derived patient cells, and decreased markers of DNA damage in these cells. Using a combination of chemical, cellular and genetic approaches, we identified the acetyl-transferase protein NAT10 as the target of Remodelin that mediated nuclear shape rescue in laminopathic cells via microtubule reorganization. These findings provide insights into how NAT10 affects nuclear architecture, and suggest alternative strategies for treating laminopathies and aging.