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Series GSE107690 Query DataSets for GSE107690
Status Public on Jul 16, 2018
Title G-quadruplex structures moulds the DNA methylome
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Control of DNA methylation level is critical for gene regulation, and the factors that govern hypomethylation at CpG islands (CGIs) are still being uncovered. Here, we provide evidence that G-quadruplex (G4) DNA secondary structures are genomic features that influence methylation at CGIs. We show that the presence of G4 structure is tightly associated with CGI hypomethylation. Surprisingly, we find that these G4 sites are enriched for DNA methyltransferase 1 (DNMT1) occupancy, which is consistent with our biophysical observations that DNMT1 exhibits higher binding affinity for G4s as compared to duplex, hemi-methylated or single-stranded DNA. The biochemical assays also show that the G4 structure itself, rather than sequence, inhibits DNMT1 enzymatic activity. Based on these data, we propose that G4 formation sequesters DNMT1 thereby protecting certain CGIs from methylation and inhibiting local methylation.
 
Overall design G4 ChIP-seq perform on asynchronous K562 cells to detect the presence of DNA G-Quadruplexes. Experiment performed in 2 biological replicatest with 2 and 3 technical replicates, respectively. WGBS was done in entinostat treated HaCaT cells and control cells.
 
Contributor(s) Spiegel J, Ghanbarian A, Marsico G, Beraldi D, Hänsel-Hertsch R, Mao S, Tannahill D, Balasubramanian S
Citation(s) 30275516
Submission date Dec 05, 2017
Last update date May 17, 2019
Contact name Avazeh T Ghanbarian
Organization name University of Cambridge
Department Cancer Research UK, Cambridge Inst
Lab Balasubramanian
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (15)
GSM2876090 K562_BG4-ChIP-rep_1a
GSM2876091 K562_BG4-ChIP-rep_1c
GSM2876092 K562_BG4-ChIP-rep_1_input
Relations
BioProject PRJNA421087
SRA SRP126139

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE107690_K562_High_confidence_peaks.bed.gz 73.9 Kb (ftp)(http) BED
GSE107690_RAW.tar 3.2 Gb (http)(custom) TAR (of BW, NARROWPEAK, TDF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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