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G-quadruplex structures mark human regulatory chromatin

GSE76688 Homo sapiens Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other 52 samples Submitted 2016/08/05 Platform GPL18573
Summary
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.
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Direct links to NCBI, no account and no request form: the whole study as GSE76688_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 52 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA308317 and SRA study SRP068243. Searching any of these in the dataset finder brings you back here.

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