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Series GSE76688 Query DataSets for GSE76688
Status Public on Aug 05, 2016
Title G-quadruplex structures mark human regulatory chromatin
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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.
Overall design Two cell lines, treated with entinostat or untreated, analyzed to detect gene expression differences, presence of G-Qudruplexes and chromatin state. Each combination of conditions replicated in duplicates or triplicates.
Contributor(s) Hänsel-Hertsch R, Beraldi D, Lensing S, Marsico G, Di Antonio M, Tannahill D, Balasubramanian S
Citation(s) 27618450, 30275516
Submission date Jan 08, 2016
Last update date May 17, 2019
Contact name Dario Beraldi
Organization name Cambridge Research Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (52)
GSM2035740 Entinostat_1
GSM2035741 Entinostat_2
GSM2035742 Entinostat_3
BioProject PRJNA308317
SRA SRP068243

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Supplementary file Size Download File type/resource
GSE76688_HEKnp_Lonza_1472015_BG4.1e4_peaks.narrowPeak.gz 40.3 Kb (ftp)(http) NARROWPEAK
GSE76688_HEKnp_Lonza_1572015_BG4.1e4_peaks.narrowPeak.gz 52.0 Kb (ftp)(http) NARROWPEAK
GSE76688_diff.BG4-hacat-entinostat_vs_ctrl.txt.gz 1.8 Mb (ftp)(http) TXT
GSE76688_diff.BG4-hek_vs_hacat.txt.gz 1.0 Mb (ftp)(http) TXT
GSE76688_diff.atac-hacat-entinostat_vs_ctrl.txt.gz 3.1 Mb (ftp)(http) TXT
GSE76688_diff.atac-hek_vs_hacat.txt.gz 6.3 Mb (ftp)(http) TXT
GSE76688_expr_diff.hacat_entinostat_vs_ctrl.rnaseq.txt.gz 492.7 Kb (ftp)(http) TXT
GSE76688_expr_diff.hek_vs_hacat.rnaseq.txt.gz 497.6 Kb (ftp)(http) TXT
GSE76688_rhh145-146_K3_K4_atac_hacat_peaks.narrowPeak.gz 1.6 Mb (ftp)(http) NARROWPEAK
GSE76688_rhh147-148_untreat_14102014_atac_hacat_peaks.narrowPeak.gz 3.0 Mb (ftp)(http) NARROWPEAK
GSE76688_rhh149-150_untreat_27052014_atact_hacat_peaks.narrowPeak.gz 1.3 Mb (ftp)(http) NARROWPEAK
GSE76688_rhh175_ChIPwthacat_704_502_entst_26082015_peaks.narrowPeak.gz 270.3 Kb (ftp)(http) NARROWPEAK
GSE76688_rhh_25cyc_BG4_12082015_peaks.narrowPeak.gz 385.8 Kb (ftp)(http) NARROWPEAK
GSE76688_rhh_ATAC_entinostat_bio1_23102015_peaks.narrowPeak.gz 1.3 Mb (ftp)(http) NARROWPEAK
GSE76688_rhh_ATAC_entinostat_bio2_23102015_peaks.narrowPeak.gz 1.4 Mb (ftp)(http) NARROWPEAK
GSE76688_rhh_ChIP_entst_17082015_peaks.narrowPeak.gz 376.2 Kb (ftp)(http) NARROWPEAK
GSE76688_rhh_ChIP_entst_26082015_peaks.narrowPeak.gz 713.8 Kb (ftp)(http) NARROWPEAK
GSE76688_rhh_HEKnp_ATAC_24022015_peaks.narrowPeak.gz 4.3 Mb (ftp)(http) NARROWPEAK
GSE76688_rhh_HEKnp_ATAC_27032015_peaks.narrowPeak.gz 3.2 Mb (ftp)(http) NARROWPEAK
GSE76688_rhh_hacat_05082014_FAIRE.narrowPeak.gz 1.4 Mb (ftp)(http) NARROWPEAK
GSE76688_rhh_hacat_14062014_FAIRE.narrowPeak.gz 1.5 Mb (ftp)(http) NARROWPEAK
GSE76688_rhh_hek_09112014_FAIRE.narrowPeak.gz 579.6 Kb (ftp)(http) NARROWPEAK
GSE76688_rhh_hek_18092014_FAIRE.narrowPeak.gz 881.3 Kb (ftp)(http) NARROWPEAK
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