G-Quadruplex DNA suppresses Transcription during DNA Replication [PRO-Seq]
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ABSTRACT:
PROVIDER: PRJNA1310554 | ENA |
REPOSITORIES: ENA
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Project description:G-quadruplex DNA suppresses transcription during DNA replication
| PRJNA1214877 | ENA
Project description:G-quadruplex DNA (G4-DNA) structures play crucial but incompletely understood roles in coordinating DNA replication and transcription. Here, we investigate the dynamics of G4-DNA during DNA replication and its functional interplay with transcription machinery in synchronized tumor cells. Using a double-thymidine block to arrest cells in early S phase, we profile G4-DNA structures and associated transcription factors through CUT&Tag, while monitoring transcriptional changes via PRO-seq. To mechanistically dissect these relationships, we perturb the system by overexpressing G4-DNA helicases (DHX36 and BRIP1), treating with the G4-destabilizing agent PhpC, and knocking down the novel G4-binding protein RFC3. Our integrated analysis reveals how G4-DNA spatially and temporally regulates replication-transcription coupling, with important implications for understanding genome stability in cancer. These findings provide new insights into the role of G4-DNA as a regulatory nexus between DNA replication and gene expression.
2025-09-10 | GSE306387 | GEO
Project description:G-Quadruplex DNA suppresses Transcription during DNA Replication [CUT&Tag]
| PRJNA1310565 | ENA
Project description:In eukaryotic cells, although the B-form double helix is the predominant structure of DNA, various non-B-form DNA structures, including G-quadruplex DNA (G4-DNA), are also widely present. For a long time, G4-DNA has been thought to impede DNA replication due to its unique spatial conformation. However, this study demonstrates that S phase G4-DNA accumulation, far from being a passive byproduct, actively functions as a critical safeguard for genomic stability. Contrary to the traditional view of G4-DNA as a replication barrier, its physiological increase during Early S phase minimizes impact on replication itself. Instead, S phase G4-DNA specifically suppresses transcription by stabilizing the negative elongation factor (NELF) complex, thereby preventing transcription-replication conflicts (TRCs) by spatiotemporally segregating transcription and replication. Replication Factor C3 (RFC3), a component of the replication machinery, directly binds and stabilizes G4-DNA to promote its S phase accumulation. Disruption of RFC3 function or G4-DNA unwinding during S phase releases transcriptional suppression, exacerbating TRCs.
2025-01-29 | GSE287896 | GEO
Project description:G-quadruplex DNA (G4-DNA) structures play crucial but incompletely understood roles in coordinating DNA replication and transcription. Here, we investigate the dynamics of G4-DNA during DNA replication and its functional interplay with transcription machinery in synchronized tumor cells. Using a double-thymidine block to arrest cells in early S phase, we profile G4-DNA structures and associated transcription factors through CUT&Tag, while monitoring transcriptional changes via PRO-seq. To mechanistically dissect these relationships, we perturb the system by overexpressing G4-DNA helicases (DHX36 and BRIP1), treating with the G4-destabilizing agent PhpC, and knocking down the novel G4-binding protein RFC3. Our integrated analysis reveals how G4-DNA spatially and temporally regulates replication-transcription coupling, with important implications for understanding genome stability in cancer. These findings provide new insights into the role of G4-DNA as a regulatory nexus between DNA replication and gene expression.
2025-09-10 | GSE306391 | GEO
Project description:G-quadruplex (or G4) structures are non-canonical DNA structures that form in guanine-rich sequences and threaten genome stability when not properly resolved. G4 unwinding occurs during S phase via an unknown mechanism. Using Xenopus egg extracts, we define a three-step G4 unwinding mechanism that acts during DNA replication. First, the replicative helicase (CMG) stalls at a leading strand G4 structure. Second, the DHX36 helicase mediates the bypass of the CMG past the intact G4 structure, which allows approach of the leading strand to the G4. Third, G4 structure unwinding by the FANCJ helicase enables the DNA polymerase to synthesize past the G4 motif. A G4 on the lagging strand template does not stall CMG, but still requires active DNA replication for unwinding. DHX36 and FANCJ have partially redundant roles, conferring robustness to this pathway. Our data reveal a novel genome maintenance pathway that promotes faithful G4 replication thereby avoiding genome instability.
2022-02-17 | PXD027623 | Pride
Project description: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. 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.
2013-05-08 | E-GEOD-45241 | biostudies-arrayexpress
Project description:We analyze the contribution of ATRX and DAXX to G-quadruplex DNA replication in mESC
2021-05-17 | GSE151056 | GEO
Project description:Rif1 regulates replication timing and repair of double-stranded DNA breaks. Using Chromatin-immunoprecipitation-Sequencing method, we have identified 35 high-affinity Rif1 binding sites in fission yeast chromosomes. Binding sites, preferentially located to the vicinity of dormant origins, tended to contain at least two copies of a conserved motif, CNWWGTGGGGG, and base substitution within these motifs resulted in complete loss of Rif1 binding and activation of late-firing or dormant origins located as far as 50 kb away. We show that Rif1 binding sites adopt G-quadruplex-like structures in vitro in a manner dependent on the conserved sequence as well as on other G-tracts, and that the purified Rif1 preferentially binds to this structure. These results suggest that Rif1 recognizes and binds to G-quadruplex-like structures at selected intergenic regions to generate local chromatin structures that may exert a long-range suppressive effects on origin firing. ChIP-Seq profiles of Rif1 and DNA replicaiton (BrdU-incorporation) vs Input in wildt type, rap1∆, taz1∆, Rif1BS mutants and rif1∆
2015-09-10 | E-GEOD-65293 | biostudies-arrayexpress
Project description: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.
2013-05-08 | GSE45241 | GEO