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

• Published in: Nature chemical biology Vol. 8; no. 3; pp. 301 - 310
• Main Authors: Rodriguez, Raphaël, Miller, Kyle M, Forment, Josep V, Bradshaw, Charles R, Nikan, Mehran, Britton, Sébastien, Oelschlaegel, Tobias, Xhemalce, Blerta, Balasubramanian, Shankar, Jackson, Stephen P
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.03.2012; Nature Publishing Group
• Subjects: 631/337/1427; 631/92/555; 631/92/613; 692/699/67; Aminoquinolines - chemical synthesis; Aminoquinolines - chemistry; Aminoquinolines - pharmacology; Antineoplastic Agents - chemical synthesis; Antineoplastic Agents - chemistry; Antineoplastic Agents - pharmacology; Biochemical Engineering; Biochemistry; Bioorganic Chemistry; Breast cancer; Breast Neoplasms - genetics; Breast Neoplasms - pathology; Cell Biology; Cell Cycle - drug effects; Cell Proliferation - drug effects; Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Chromatin; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - drug effects; DNA - genetics; DNA Damage; DNA structure; Drug Screening Assays, Antitumor; G-Quadruplexes - drug effects; Genetics; Genomes; genomics; Humans; Immunoprecipitation; Mammalian cells; Mammals; Molecular biology; Molecular Weight; Motility; Nucleotide sequence; Oncology; Pharmacology; Picolinic Acids - chemical synthesis; Picolinic Acids - chemistry; Picolinic Acids - pharmacology; Proto-Oncogene Mas; Proto-oncogenes; Src protein; Structure-Activity Relationship; Transcription; Tumor Cells, Cultured
• ISSN: 1552-4450; 1552-4469; 1552-4469
• DOI: 10.1038/nchembio.780

Identifying DNA sequences that adopt alternative structures within the context of genomic DNA presents a major challenge. Pyridostatin, a G-quadruplex–specific chemical probe, was shown to induce DNA damage at specific genomic sites, including the proto-oncogene SRC , leading to cell cycle arrest in human cancer cells. 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.