G-Quadruplexes Are Found in Regulatory Regions of Cancer-Related Genes

In guanine-rich DNA sequences, secondary G-quadruplex (G4) structures can form that are associated with transcription, replication, and genome instability, which have been suggested to be more abundant in cancer tissue compared with normal tissue. G4 structures have been mapped to genomic DNA in vitro and have been computationally predicted to occur in replication origins and nucleosome-depleted regions, but G4 structures have not been mapped in the context of chromatin in cells. Hänsel-Hertsch and colleagues developed a G4 chromatin immunoprecipitation-sequencing (ChIP-seq) protocol to map G4 structures genome wide in spontaneously immortalized cells. In total, 10,560 G4 ChIP-seq peaks were discovered that were restricted mostly to nucleosome-depleted regions in transcriptionally active euchromatin. Genes with promoters containing a G4 structure exhibited elevated transcription, even when compared with other nucleosome-depleted promoters that contained underlying primary DNA sequences associated with G4 formation. Consistent with previous findings, G4 structures were found in MYC and SRC regulatory elements, and G4 structures were found to also be enriched in other cancer-associated genes including TP53, JUN, HOXA9, FOXA1, and RAC1 and in regions with somatic copy-number alterations. Using a histone deacetylase (HDAC) inhibitor to induce chromatin relaxation led to the formation of new G4 structures in some nucleosome-depleted regulatory regions and increased expression of proximal genes. Further, gene transcription increased in regions where HDAC inhibition induced G4 structures but did not alter chromatin accessibility, demonstrating that G4 structures promote transcription independent of chromatin accessibility. In less proliferative cells, the number of G4 structures was lower, suggesting a possible role for G4 structures in enhancing proliferation, and accordingly such cells exhibited reduced sensitivity to a G4-targeting small molecule. These findings reveal a role for G4 structures in promoting gene transcription in the context of chromatin, and suggest the possibility of targeting G4 structures in cancer.

Hänsel-Hertsch R, Beraldi D, Lensing SV, Marsico G, Zyner K, Parry A, et al. G-quadruplex structures mark human regulatory chromatin. Nat Genet 2016 Sep 12 [Epub ahead of print].