GEO DataSets

(Submitter supplied) DNA structure can regulate genome function. Four-stranded DNA G-quadruplex (G4) structures have been implicated in transcriptional regulation; however, previous studies have not directly addressed the role of an individual G4 within its endogenous cellular context. Using CRISPR to genetically abrogate endogenous G4 structure folding, we directly interrogate the G4 found within the upstream regulatory region of the critical human MYC oncogene. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30173 GPL18573 GPL19057

243 Samples

Download data: BW, TXT, XLSX

(Submitter supplied) We demonstrate that there is a genome-wide correlation between endogenous AP site damages, binding of repair proteins APE1, AcAPE1 and AcOGG1 and G4 structure formation.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL16791

28 Samples

Download data: BIGWIG, BW, FA, TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL18573

52 Samples

Download data: NARROWPEAK, TXT

(Submitter supplied) Four stranded DNA G-quadruplex (G4) structures are common features of the human genome that are primarily found in active promoters associated with elevated transcription. Here, we explore the relationship between the folding of G4s in promoters, transcription and chromatin state. Transcriptional inhibition by DRB or by triptolide reveals that promoter G4 formation, as assessed G4 ChIP-seq, is not reliant on transcriptional activity. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

182 Samples

Download data: BED, NARROWPEAK

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL18460

11 Samples

Download data: BIGWIG, TXT

(Submitter supplied) G4s are nucleic acids secondary structures that form in the presence of four or more runs of gunanine. In vitro results suggested that G4s are involved in the regulation of both transcription and replication processes. In vitro results suggested that G4s are involved in the regulation of both transcription 6–10 and replication 11–13 processes allowed to demonstrate the actual folding of G4s in live cells, but also inserted them in a more biologically relevant context. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18460

6 Samples

Download data: TXT

(Submitter supplied) G4s are nucleic acids secondary structures that form in the presence of four or more runs of gunanine. In vitro results suggested that G4s are involved in the regulation of both transcription and replication processes. In vitro results suggested that G4s are involved in the regulation of both transcription 6–10 and replication 11–13 processes allowed to demonstrate the actual folding of G4s in live cells, but also inserted them in a more biologically relevant context. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18460

4 Samples

Download data: BIGWIG

(Submitter supplied) G4s are nucleic acids secondary structures that form in the presence of four or more runs of gunanine. In vitro results suggested that G4s are involved in the regulation of both transcription and replication processes. In vitro results suggested that G4s are involved in the regulation of both transcription 6–10 and replication 11–13 processes allowed to demonstrate the actual folding of G4s in live cells, but also inserted them in a more biologically relevant context. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18460

1 Sample

Download data: BIGWIG

(Submitter supplied) G-quadruplexes (G4s) are alternative DNA secondary structures of the human genome with key roles in transcription, replication and genome stability. Structure-specific small molecules and antibodies, such as BG4, have facilitated the detection of G4s in cells and chromatin. The availability of an alternative probe to BG4 would help to address some of its potential limitations in mapping G4 structures and would independently confirm and/or extend our earlier findings. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

24 Samples

Download data: BED, BW, NARROWPEAK

(Submitter supplied) G-quadruplexes (G4) are considered new drug targets for human diseases such as cancer. More than 10,000 G4s have been discovered in human chromatin, posing challenges for assessing the selectivity of a G4-interactive ligand. 3,6-bis(1-Methyl-4-vinylpyridinium) carbazole diiodide (BMVC) is the first fluorescent small molecule for G4 detection in vivo. Our previous structural study shows that BMVC binds to the MYC promoter G4 (MycG4) with high specificity. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL28372

12 Samples

Download data: TXT

(Submitter supplied) Gene expression is governed by transcription factors (TFs) that commonly recognize short DNA sequence motifs. However, TF recruitment to genomic target sites in chromatin is complex and many parameters that ultimately dictate binding-site specificity are still unknown. Here, we systematically explore the interaction of TFs with synthetic and endogenous G-quadruplexes (G4s) DNA secondary structures. Our findings reveal that certain TFs are directly recruited to promoters by endogenous G4s with binding affinities comparable to canonical B-DNA binding and that endogenous G4-TF interactions can be disrupted with synthetic small molecule ligands. G4s in promoters are bound by a large number of TFs and associated with high transcriptional activity. This discovery of structure-specific recognition expands our understanding of how TFs regulate gene transcription.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL18573

8 Samples

Download data: BED

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

15 Samples

Download data: BED, BW, NARROWPEAK, TDF