Nucleotide Pool Depletion Induces G-Quadruplex-Dependent Perturbation of Gene Expression

•Hydroxyurea (HU) stochastically perturbs gene expression•G quadruplex (G4) formation potentiates HU-induced epigenetic changes•HU induces G4-dependent DNA damage and heterochromatin formation•HU and G4 helicase mutations cause similar changes in expression

SummaryNucleotide pool imbalance has been proposed to drive genetic instability in cancer. Here, we show that slowing replication forks by depleting nucleotide pools with hydroxyurea (HU) can also give rise to both transient and permanent epigenetic instability of a reporter locus, BU-1, in DT40 cells. HU induces stochastic formation of Bu-1low variants in dividing cells, which have lost the H3K4me3 present in untreated cells. This instability is potentiated by an intragenic G quadruplex, which also promotes local H2Ax phosphorylation and transient heterochromatinization. Genome-wide, gene expression changes induced by HU significantly overlap with those resulting from loss of the G4-helicases FANCJ, WRN, and BLM. Thus, the effects of global replication stress induced by nucleotide pool depletion can be focused by local replication impediments caused by G quadruplex formation to induce epigenetic instability and changes in gene expression, a mechanism that may contribute to selectable transcriptional changes in cancer.

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