Small-molecule-induced DNA damage identifies alternative DNA structures in human genes.

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Rodriguez, Raphaël 
Miller, Kyle M 
Forment, Josep V 
Bradshaw, Charles R 
Nikan, Mehran 

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 promotes growth arrest in human cancer cells by inducing replication- and transcription-dependent DNA damage. A chromatin immunoprecipitation sequencing 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 abundance and SRC-dependent cellular motility in human breast cancer cells, validating SRC as a target of this drug. Our unbiased approach to define genomic sites of action for a drug establishes a framework for discovering functional DNA-drug interactions.

Aminoquinolines, Antineoplastic Agents, Breast Neoplasms, Cell Cycle, Cell Proliferation, DNA, DNA Damage, Drug Screening Assays, Antitumor, G-Quadruplexes, Humans, Molecular Weight, Picolinic Acids, Proto-Oncogene Mas, Structure-Activity Relationship, Tumor Cells, Cultured
Journal Title
Nat Chem Biol
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Springer Science and Business Media LLC
Wellcome Trust (086861/Z/08/Z)
Cancer Research Uk (None)
Biotechnology and Biological Sciences Research Council (BB/G008337/1)
Wellcome Trust (092096/Z/10/Z)