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Status |
Public on May 08, 2013 |
Title |
G-Quadruplex structures are stable and detectable in human genomic DNA. |
Organism |
Homo sapiens |
Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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Summary |
The G-quadruplex is an alternative DNA structural motif that is considered to be functionally important in the mammalian genome. Herein, we address the hypothesis that G-quadruplex structures can exist within double-stranded genomic DNA using a G-quadruplex-specific probe. An engineered antibody is employed to enrich for DNA containing G-quadruplex structures, followed by deep sequencing to detect and map G-quadruplexes at high resolution in genomic DNA from human breast adenocarcinoma cells. Our high sensitivity structure-based pull-down strategy enables the isolation of genomic DNA fragments bearing a single as well as multiple G-quadruplex structures. Stable G-quadruplex structures are found in sub-telomeres, gene bodies and gene regulatory regions. For a sample of identified target genes, we show that G-quadruplex stabilizing ligands can modulate transcription. These results confirm the existence of G-quadruplex structures and their persistence in human genomic DNA.
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Overall design |
Four independent libraries have been enriched in DNA G-quadruplex structures using a G-quadruplex-specific probe. One genomic input library was sequenced as control. Deep-sequencing of these libraries allowed the mapping of G-quadruplexes on the genome.
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Contributor(s) |
Lam EY, Beraldi D, Tannahill D, Balasubramanian S |
Citation(s) |
23653208 |
Submission date |
Mar 18, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Dario Beraldi |
E-mail(s) |
dario.beraldi@cruk.cam.ac.uk
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Organization name |
Cambridge Research Institute
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Street address |
Robinson Way
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City |
Cambridge |
ZIP/Postal code |
CB2 0RE |
Country |
United Kingdom |
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Platforms (3) |
GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
GPL15520 |
Illumina MiSeq (Homo sapiens) |
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Samples (5)
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Relations |
SRA |
SRP019752 |
BioProject |
PRJNA193490 |