R Hänsel-Hertsch, D Beraldi, SV Lensing, G Marsico, K Zyner, A Parry, M Di Antonio, J Pike, H Kimura, M Narita, D Tannahill, S Balasubramanian
Journal name: 
Nat Genet
Citation info: 
G-quadruplex (G4) structural motifs have been linked to transcription, replication and genome instability and are implicated in cancer and other diseases. However, it is crucial to demonstrate the bona fide formation of G4 structures within an endogenous chromatin context. 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.
Research group: 
Narita Group, Balasubramanian Group
E-pub date: 
31 Oct 2016
Users with this publication listed: 
Aled Parry
Bruce Ponder
David Tannahill
Giovanni Marsico
Katie Zyner
Marco Di Antonio
Masashi Narita
Shankar Balasubramanian