Identification of endogenous G-quadruplexes (G4s) in human, mouse, and pig (CUT&Tag)
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ABSTRACT:
PROVIDER: PRJNA901034 | ENA |
REPOSITORIES: ENA
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Project description:G-quadruplexes (G4s) are non-canonical four-stranded structures and emerge as novel genetic regulatory elements. Endogenous G4s (eG4s) can form quadruplex structures and induce double strand breaking during DNA replication, and thus contributing to genomic instability and genome evolution. Besides, eG4s are closely associated with gene expression regulation, and both their stimulative and repressive roles in the genome have been elucidated. Although functions of several specific G4s have been reported, a systematical identification and characterization of eG4s is still unconducted. Here we applied Cleavage Under Targets and Tagmentation (CUT&Tag) for mapping eG4s across human, mouse, and pig at high resolution and low background. We analyzed their genomics distribution, evolutionary conservation, dynamics, regulation, and impacts on gene expression in a single framework. CUT&Tag using G4-specific antibody, BG4
2025-08-06 | GSE217860 | GEO
Project description:G4s are non-canonical four-stranded structures and emerge as novel genetic regulatory elements. Endogenous G4s (eG4s) can form quadruplex structures and induce double strand breaking during DNA replication, and thus contributing to genomic instability and genome evolution. Besides, eG4s are closely associated with gene expression regulation, and both their stimulative and repressive roles in the genome have been elucidated. Although functions of several specific G4s have been reported, a systematical identification and characterization of eG4s is still unconducted. Here we applied Cleavage Under Targets and Tagmentation (CUT&Tag) for mapping eG4s across human, mouse, and pig at high resolution and low background. We analyzed their genomics distribution, evolutionary conservation, dynamics, regulation, and impacts on gene expression in a single framework. ATAC-seq
2025-08-06 | GSE220209 | GEO
Project description:Identification of endogenous G-quadruplexes (G4s) in human, mouse, and pig
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Project description:Identification of endogenous G-quadruplexes (G4s) in human, mouse, and pig (ATAC-Seq)
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Project description:G-quadruplexes (G4s) are noncanonical DNA secondary structures formed through the self-association of guanines. They are distributed genome-widely and participate in multiple biological processes including gene transcription, and quadruplex-targeted ligands serve as potential therapeutic agents for DNA-targeted therapies. However, the roles of G-quadruplexes in transcriptional regulation remains elusive. Here, we establish a sensitive G4-CUT&Tag method for genome-wide profiling of native G-quadruplexes with high resolution and specificity. We find that native G-quadruplex signals are cell-type specific and are associated with transcriptional regulatory elements with active epigenetic modifications. Promoter-proximal RNA polymerase II pausing promotes native G-quadruplex formation, oppositely, G-quadruplex stabilization by quadruplex-targeted ligands globally reduces RNA polymerase II occupancy at gene promoters as well as nascent RNA synthesis. Moreover, G-quadruplex stabilization modulates chromatin states and impedes transcription initiation via inhibiting the loading of general transcription factors to promoters.Together, these studies reveal a reciprocal regulation between native G-quadruplex dynamics and gene transcription in the genome, which will deepen our knowledge of G-quadruplex biology towards considering therapeutically targeting G-quadruplexes in human diseases.
2021-07-19 | GSE178668 | GEO
Project description:Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, remains a global health threat due to increasing drug resistance and high mortality rates. To combat tuberculosis effectively, novel therapeutic targets are urgently needed. G-quadruplexes (G4s) represent promising candidates for this purpose. In this study, we successfully apply the cleavage under targets and tagmentation (CUT&Tag) technique for the first time in bacteria, mapping the G4 landscape in Mtb under standard and oxidative stress conditions, the latter mimicking the environment Mtb faces within macrophages. We validate the CUT&Tag protocol using an antibody against the RNA polymerase β-subunit, confirming its association with actively transcribed genes. Employing the anti-G4 antibody BG4, we discover that Mtb G4s, unlike their eukaryotic counterparts, predominantly locate within gene coding sequences and consist of two-guanine tract motifs. Notably, oxidative stress increases G4 formation, correlating with reduced gene expression. Our findings provide the first evidence of G4 formation in Mtb cells and suggest their potential role in bacterial survival within macrophages. This study demonstrates the successful application of CUT&Tag in bacteria and unveils an unconventional G4 landscape in Mtb, offering new insights into bacterial stress response mechanisms and potential therapeutic targets.
2025-06-20 | GSE272150 | GEO
Project description:Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, remains a global health threat due to increasing drug resistance and high mortality rates. To combat tuberculosis effectively, novel therapeutic targets are urgently needed. G-quadruplexes (G4s) represent promising candidates for this purpose. In this study, we successfully apply the cleavage under targets and tagmentation (CUT&Tag) technique for the first time in bacteria, mapping the G4 landscape in Mtb under standard and oxidative stress conditions, the latter mimicking the environment Mtb faces within macrophages. We validate the CUT&Tag protocol using an antibody against the RNA polymerase β-subunit, confirming its association with actively transcribed genes. Employing the anti-G4 antibody BG4, we discover that Mtb G4s, unlike their eukaryotic counterparts, predominantly locate within gene coding sequences and consist of two-guanine tract motifs. Notably, oxidative stress increases G4 formation, correlating with reduced gene expression. Our findings provide the first evidence of G4 formation in Mtb cells and suggest their potential role in bacterial survival within macrophages. This study demonstrates the successful application of CUT&Tag in bacteria and unveils an unconventional G4 landscape in Mtb, offering new insights into bacterial stress response mechanisms and potential therapeutic targets.
2025-06-20 | GSE272149 | GEO
Project description:Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, remains a global health threat due to increasing drug resistance and high mortality rates. To combat tuberculosis effectively, novel therapeutic targets are urgently needed. G-quadruplexes (G4s) represent promising candidates for this purpose. In this study, we successfully apply the cleavage under targets and tagmentation (CUT&Tag) technique for the first time in bacteria, mapping the G4 landscape in Mtb under standard and oxidative stress conditions, the latter mimicking the environment Mtb faces within macrophages. We validate the CUT&Tag protocol using an antibody against the RNA polymerase β-subunit, confirming its association with actively transcribed genes. Employing the anti-G4 antibody BG4, we discover that Mtb G4s, unlike their eukaryotic counterparts, predominantly locate within gene coding sequences and consist of two-guanine tract motifs. Notably, oxidative stress increases G4 formation, correlating with reduced gene expression. Our findings provide the first evidence of G4 formation in Mtb cells and suggest their potential role in bacterial survival within macrophages. This study demonstrates the successful application of CUT&Tag in bacteria and unveils an unconventional G4 landscape in Mtb, offering new insights into bacterial stress response mechanisms and potential therapeutic targets.
2025-06-20 | GSE272148 | GEO
Project description: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.
2021-03-24 | GSE145090 | GEO
Project description:G-quadruplexes (G4s) are unique noncanonical nucleic acid secondary structures, which could interact with transcription factors and chromatin remodelers to regulate cell type-specific transcriptome and shape chromatin landscapes. Based on the direct interactions between G4 and natural porphyrins, we established an in situ capture sequencing approach combining synthesized biotin-PEG4-Hemin and Cleavage Under Targets and Tagmentation (CUT&Tag) strategy to profile the Hemin binding sites in the human genome. We found that a proportion of G4s overlapped with Hemin binding sites and Hemin promoted genome-wide G4 formation at Hemin binding sites. Hemin treatments impaired gene transcription initiation and altered chromatin landscape with decreased H3K27ac and H3K4me3 modifications. Interestingly, G4 was not involved in the canonic Hemin-BACH1-NRF2-mediated enhancer activation process, highlighting an unprecedented G4-dependent mechanism for metabolic regulation of transcription. Furthermore, Hemin induced specific gene expression profiles in mouse primary hepatocytes, and block of Hemin degradation in mice by Hmox1 knockdown resulted in hepatic injury, providing in vivo insights for metabolic control of gene transcription by porphyrins.
2022-11-23 | GSE198658 | GEO