G-quadruplex (G4) structural motifs have been linked to transcription1,2, replication3 and genome instability4,5 and are implicated in cancer and other diseases6,7,8. However, it is crucial to demonstrate the bona fide formation of G4 structures within an endogenous chromatin context9,10. Herein we address this through the development of G4 ChIP–seq, an antibody-based G4 chromatin immunoprecipitation and high-throughput sequencing approach. We find ∼10,000 G4 structures in human chromatin, predominantly in regulatory, nucleosome-depleted regions. G4 structures are enriched in the promoters and 5′ UTRs of highly transcribed genes, particularly in genes related to cancer and in somatic copy number amplifications, such as MYC. Strikingly, de novo and enhanced G4 formation are associated with increased transcriptional activity, as shown by HDAC inhibitor–induced chromatin relaxation and observed in immortalized as compared to normal cellular states. Our findings show that regulatory, nucleosome-depleted chromatin and elevated transcription shape the endogenous human G4 DNA landscape.
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The authors would like to thank the staff at the Genomic and Light Microscopy and Biorepository core facilities at Cancer Research UK Cambridge Institute. We are grateful to the European Molecular Biology Organization for funding R.H.-H. with the EMBO Long-Term Fellowship. We acknowledge support from University of Cambridge and Cancer Research UK program. The Balasubramanian and Narita laboratories are supported by core funding from Cancer Research UK (C14303/A17197). S.B. is a Senior Investigator of the Wellcome Trust (grant no. 099232/z/12/z).
The authors declare no competing financial interests.
Supplementary Figures 1–9. (PDF 4895 kb)
Table shows the density of HaCaT G4 ChIP–seq peaks in all cancer-related genes; see also Supplementary Figure 6 and Online Methods ‘Cancer-related genes analysis' (XLS 302 kb)
Table shows the density of HaCaT G4 ChIP–seq peaks in all SCNAs; see also Supplementary Figure 7 and Online Methods 'SCNAs analysis' (XLS 39 kb)
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Hänsel-Hertsch, R., Beraldi, D., Lensing, S. et al. G-quadruplex structures mark human regulatory chromatin. Nat Genet 48, 1267–1272 (2016). https://doi.org/10.1038/ng.3662
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