The realization that G-quadruplex (G4) DNA structures are involved in transcriptional regulation1 and the maintenance of genome integrity2 has led to growing interest in their potential as cancer therapeutic targets3–7. Although numerous small molecules with high affinity for G4s have been reported and the molecular mechanisms of their G4-binding activity investigated, there is a need for greater understanding of the endogenous effects of these ligands within a cellular context. Herein, the chromatin remodeling activity of three G4-stabilizing small molecules, GTC-365 and GTC-260 shown to have high specificity for the hTERT G48 and GQC-05 shown to have high specificity for the cMYC G49, will be measured. Having established the IC50 of each of these compounds in MCF7 breast cancer cell lines using an MTS assay, cells were treated with each compound independently. The assay for transposase-accessible chromatin with sequencing (ATAC-Seq)10 was used to generate a library of tagmented gDNA following compound treatment in order to produce genome-wide maps of nucleosome depleted regions. By comparing the data from treated and untreated cells, it will be possible to assess whether the cellular activity of these compounds leads to alterations in the chromatin landscape and if these changes are concordant with G4-forming regions. Given that nucleosome positioning determines the ability of transcriptional machinery to access DNA11, any chromatin remodelling activity by these small molecules could alter the transcriptional output of genes. An understanding of the chromatin-level changes induced by G4-ligands is therefore crucial if G4s are to be pursued as clinically relevant anticancer targets.