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| Status |
Public on Apr 14, 2023 |
| Title |
G4access identifies G-quadruplexes and their associations with open chromatin and imprinting control regions. Nat Genet (2023). https://doi.org/10.1038/s41588-023-01437-4 |
| Organisms |
Saccharomyces cerevisiae; Drosophila melanogaster; Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
Expression profiling by high throughput sequencing
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| Summary |
Metazoan promoters are highly enriched in secondary structure forming motifs, among which G-quadruplexes (G4s). We describe G4access, a novel approach to isolate and sequence G4s when associated to open chromatin, based on their resistance to Micrococcal nuclease. G4access is an antibody- and crosslink-independent procedure that allows for high enrichment of predicted G4s (PG4s) motifs, most of which can be confirmed in vitro. Using this technique in several human and mouse cell lines, we were able to show a cell-specific enrichment that both relates to apparent nucleosome depletion and transcription at promoters. G4access allows scoring for PG4 pattern variation linked to nucleosome positioning changes that occur following treatment with a G4 ligand. It also reveals an unexpected role of G4s in hybrid mouse ES cells in the context of imprinting control regions, in which we propose that they will hallmark allelic active loci. Finally, we extended our procedure to non-mammalian species showing less annotated G4s in their genome. We found a decreased but still substantial G4 enrichment and confirmed their association to open and transcriptionally active regions of the yeast genome. Overall, our study not only provides a novel tool for studying G4 forming sequences in the cellular context but also indicates their essential roles as promoter elements, in chromatin opening and nucleosome positioning.
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| Overall design |
We developed G4access, a novel, efficient and Ab and crosslinking-independent method coupled to high-throughput sequencing, that enriches for G4 forming sequences associated to open chromatin in cells. Taking advantage of the sequence preference of the Micrococcal nuclease. G4access signals were then compared to RNA Polymerase II signals upon KM05283 and Tryptolid (Two transcription inhibitors) and Pyridostatin (a G4 ligand).
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| Web link |
https://doi.org/10.1038/s41588-023-01437-4
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| Contributor(s) |
Garcia-Oliver E, Esnault C, El Aabidine AZ, Magat T, Cucchiarini A, Lleres D, Goerke L, Luo Y, Verga D, Lacroix L, Feil R, Spicuglia S, Mergny JL, Andrau JC |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Nov 02, 2021 |
| Last update date |
Jul 24, 2023 |
| Contact name |
Amal Makrini |
| E-mail(s) |
amal.makrini@igmm.cnrs.fr
|
| Organization name |
IGMM
|
| Street address |
1919 route de mende
|
| City |
Montpellier |
| ZIP/Postal code |
34000 |
| Country |
France |
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| Platforms (8)
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| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL25244 |
Illumina NovaSeq 6000 (Drosophila melanogaster) |
| GPL27812 |
Illumina NovaSeq 6000 (Saccharomyces cerevisiae) |
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| Samples (63)
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| Relations |
| BioProject |
PRJNA777258 |
| SRA |
SRP344238 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE187007_ES_B6xJF1_G4acces_bin10.wig.gz |
241.3 Mb |
(ftp)(http) |
WIG |
| GSE187007_ES_JF1xB6_G4acces_bin10.wig.gz |
338.1 Mb |
(ftp)(http) |
WIG |
| GSE187007_GSE187007_Raji_PDS_chRNA_negative_NormalizedERCC.wig.gz |
20.6 Mb |
(ftp)(http) |
WIG |
| GSE187007_GSE187007_Raji_PDS_chRNA_positive_NormalizedERCC.wig.gz |
21.4 Mb |
(ftp)(http) |
WIG |
| GSE187007_HaCaT_G4acces_bin10.wig.gz |
154.6 Mb |
(ftp)(http) |
WIG |
| GSE187007_Hela_H9_siDHX36_rep1_rep2.wig.gz |
308.7 Mb |
(ftp)(http) |
WIG |
| GSE187007_Hela_H9_siNT_rep1_rep2.wig.gz |
344.7 Mb |
(ftp)(http) |
WIG |
| GSE187007_Hela_H9_siWRN_rep1_rep2.wig.gz |
207.6 Mb |
(ftp)(http) |
WIG |
| GSE187007_K562_G4acces_bin10.wig.gz |
250.9 Mb |
(ftp)(http) |
WIG |
| GSE187007_K562_input_bin10.wig.gz |
142.4 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_DMSO_control_TSA_G4access_merge_bin10.wig.gz |
525.8 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_DMSO_control_TSA_mnase_Midpoint_merge_bin10_smoothed5.wig.gz |
994.2 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_DMSO_control_TSA_mnase_merge_bin10_smoothed5.wig.gz |
1.6 Gb |
(ftp)(http) |
WIG |
| GSE187007_Raji_G4acces_DMSO_bin10.wig.gz |
34.6 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_G4acces_KM_bin10.wig.gz |
13.7 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_G4acces_PDS_24h_bin10.wig.gz |
145.2 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_G4acces_PDS_30min_bin10.wig.gz |
115.0 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_G4acces_PDS_60min_bin10.wig.gz |
164.3 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_G4acces_Triptolide_bin10.wig.gz |
19.9 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_G4acces_bin10.wig.gz |
78.0 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_Mnase-seq_untreated1_bin10_Scaled_Smooth5.wig.gz |
842.4 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_Mnase-seq_untreated2_bin10_Scaled_Smooth5.wig.gz |
751.7 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_PolII_untreated1_bin50_Scaled.wig.gz |
106.7 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_PolII_untreated2_bin50_Scaled.wig.gz |
95.8 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_Pol_II_DMSO_bin10_NormalisedDroso_Smoothed5.wig.gz |
494.2 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_Pol_II_KM_bin10_NormalisedDroso_Smoothed5.wig.gz |
620.0 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_Pol_II_Triptolide_bin10_NormalisedDroso_Smoothed5.wig.gz |
656.3 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_TSA_G4access_merge_bin10.wig.gz |
444.1 Mb |
(ftp)(http) |
WIG |
| GSE187007_Raji_TSA_mnase_merge_bin10_smoothed5.wig.gz |
1.6 Gb |
(ftp)(http) |
WIG |
| GSE187007_Raji_TSA_mnase_midpoint_merge_bin10_smoothed5.wig.gz |
977.4 Mb |
(ftp)(http) |
WIG |
| GSE187007_dm6_G4H1.2.bed.gz |
1.0 Mb |
(ftp)(http) |
BED |
| GSE187007_dm6_G4H1.5.bed.gz |
419.5 Kb |
(ftp)(http) |
BED |
| GSE187007_dm6_G4H2.0.bed.gz |
110.9 Kb |
(ftp)(http) |
BED |
| GSE187007_dm6_G4acces_bin10.wig.gz |
1.5 Mb |
(ftp)(http) |
WIG |
| GSE187007_hg19_G4H1.2.bed.gz |
31.4 Mb |
(ftp)(http) |
BED |
| GSE187007_hg19_G4H1.52.bed.gz |
12.5 Mb |
(ftp)(http) |
BED |
| GSE187007_hg19_G4H2.0.bed.gz |
3.0 Mb |
(ftp)(http) |
BED |
| GSE187007_mm9_G4H1.2.bed.gz |
28.7 Mb |
(ftp)(http) |
BED |
| GSE187007_mm9_G4H1.5.bed.gz |
13.3 Mb |
(ftp)(http) |
BED |
| GSE187007_mm9_G4H2.0.bed.gz |
5.1 Mb |
(ftp)(http) |
BED |
| GSE187007_sc3_G4H1.2.bed.gz |
26.4 Kb |
(ftp)(http) |
BED |
| GSE187007_sc3_G4H1.5.bed.gz |
4.9 Kb |
(ftp)(http) |
BED |
| GSE187007_sc3_G4H2.0.bed.gz |
641 b |
(ftp)(http) |
BED |
| GSE187007_sc3_G4acces_bin10.wig.gz |
3.8 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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