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DNA G-quadruplexes modulate highly transcribed genes in human chromatin [ChIPseq]

ABSTRACT: 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. . In the present work we mapped G4s in the chromatin of a WD-LPS cell line (93T449), we integrated the information of G4 folding with their chromatin context, the transcriptional level of the associated genes and compared the results with data obtained in a cell line of different origin (HaCaT).

ORGANISM(S): Homo sapiens

PROVIDER: GSE145535 | GEO | 2021/04/26

REPOSITORIES: GEO

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DNA G-quadruplexes modulate highly transcribed genes in human chromatin [RNA-seq]

Project description: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. . In the present work we mapped G4s in the chromatin of a WD-LPS cell line (93T449), we integrated the information of G4 folding with their chromatin context, the transcriptional level of the associated genes and compared the results with data obtained in a cell line of different origin (HaCaT).

2021-04-26 | GSE145537 | GEO

DNA G-quadruplexes modulate highly transcribed genes in human chromatin [ATAC-seq]

2021-04-26 | GSE145532 | GEO

Parallel G-quadruplexes recruit the HSV-1 transcription factor ICP4 to promote viral transcription in herpes virus-infected human cells

Project description:G-quadruplexes (G4s) are four-stranded nucleic acid structures abundant at gene promoters. They can adopt several distinctive conformations. G4s have been shown to form in the herpes simplex virus-1 (HSV-1) genome during its viral cycle. Here by cross-linking/pull-down assay we identified ICP4, the major HSV-1 transcription factor, as the protein that most efficiently interacts with viral G4s during infection. ICP4 specific and direct binding and unfolding of parallel G4s, including those present in HSV-1 immediate early gene promoters, induced transcription in vitro and in infected cells. This mechanism was also exploited by ICP4 to promote its own transcription. Proximity ligation assay allowed visualization of G4-protein interaction at the single selected G4 in cells. G4 ligands inhibited ICP4 binding to G4s. Our results indicate the existence of a well-defined G4-viral protein network that regulates the productive HSV-1 cycle. They also point to G4s as elements that recruit transcription factors to activate transcription in cells.

2021-09-10 | PXD024743 | Pride

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

Project description: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.

2023-04-14 | GSE187007 | GEO

DNA G-quadruplexes contribute to CTCF and cohesin recruitment

Project description:G-quadruplex (G4) sites in the human genome frequently colocalize with CCCTC-binding factor (CTCF)-bound sites within topologically associating domains (TADs) or at TAD boundaries. We investigated three mechanisms by which G4s may contribute to CTCF recruitment. One involved direct interactions between CTCF and G4s that persisted in the G0/G1 phase of the cell cycle. Synthetic G4s from CpG islands (CGIs) formed complexes with CTCF in vitro, and CTCF occupancy at the respective sites in the genome was modulated by a G4-stabilizing ligand. Another possible mechanism was through G4 interference with DNA methyltransferase activity in CGIs. Bioinformatics analysis confirmed that G4s underlie the association between CTCF and CGIs, but did not support a critical role for methylation in CTCF recruitment to G4-harboring CGIs. The third mechanism was through attracting additional protein factors. We found that G4s are recognized by the nucleosome density modulating high-mobility group (HMG) proteins and the cohesin-interacting protein additional sex combs-like 1. The affinity for these proteins is the basis for indirect G4 contributions to CTCF positioning and TAD demarcation.

2021-04-23 | GSE173074 | GEO

Detection of genomic G-quadruplexes in living cells using a small artificial protein

Project description:G-quadruplex (G4) structures formed by guanine-rich nucleic acids are implicated in essential physiological and pathological processes and serve as important drug targets. The genome-wide detection of G4s in living cells is important for exploring the functional role of G4s but has not yet been achieved due to the lack of a suitable G4 probe. Here we report an artificial 6.7 kDa G4 probe (G4P) protein that binds G4s with high affinity and specificity. We used it to capture G4s in living human, mouse, and chicken cells with the ChIP-Seq technique, yielding genome-wide landscape as well as details on the positions, frequencies, and sequence identities of G4 formation in these cells. Our results indicate that transcription is accompanied by a robust formation of G4s in genes. In human cells, we detected up to >123,000 G4P peaks, of which >1/3 had a fold increase of ≥5 and were present in >60% promoters and ~70% genes. Being much smaller than a scFv antibody (27 kDa) or even a nanobody (12-15 kDa), we expect that the G4P may find diverse applications in biology, medicine, and molecular devices as a G4 affinity agent.

2020-10-13 | GSE133379 | GEO

Whole genome mapping of DNA G-quadruplexes in multiple species by G4-seq

Project description:The identification of DNA G-quadruplexes (G4s) in the genome is important to study different biological processes in which these structures play a role, such as genome rearrangement, transcriptional regulation and DNA replication. G4-seq allowed the high-throughput experimental mapping of G-quadruplexes in the human genome. We developed here an improved version of this method, named G4-seq2, which we applied to generate G-quadruplexes genomic maps for 12 species, selected as important models organism to study development or as pathogens of clinical relevance. Those multi-species maps, publicly available for the community, will allow to further understand the design principle of G-quadruplex formation in genomic context, to study G-quadruplex biology in those model organisms, to predict ligand targeting for therapeutic usage and to design G-quadruplex computational predictors based on genome-wide experimental measurements.

2018-08-01 | GSE110582 | GEO

Stress promotes RNA G-quadruplex folding in human cells

Project description:Guanine (G)-rich nucleic acids can fold into G-quadruplex (G4) structures under permissive conditions. Although many RNAs contain sequences that fold into RNA G4s (rG4s) in vitro, their folding and functions in vivo are not well understood. Here, we showed that the folding of putative rG4s in human cells into rG4 structures was dynamically induced by stress. By using high-throughput dimethylsulfate probing, we identified hundreds of endogenous stress-induced rG4s. Our results demonstrated that stress-induced rG4s were enriched in mRNA 3′-untranslated regions and enhanced mRNA stability. Furthermore, stress-induced rG4 folding was readily reversible upon stress removal. In summary, our study revealed the dynamic regulation of rG4 folding in living human cells and suggests suggested that widespread rG4 motifs may have a global regulatory impact on mRNA stability and cellular stress response.

2022-12-15 | GSE200706 | GEO

DNA G-quadruplexes in human stem cells and during differentiation

Project description:The establishment of cell identity involves the activation of developmental gene expression programs and is underpinned by epigenetic factors including DNA methylation and histone modifications. G-quadruplex DNA secondary structures (G4) are genomic elements implicated in transcriptional regulation, genome instability and cancer. We reasoned that G4s might be central features that influence development. In human embryonic stem cells G4s are highly abundant and progressively lost during differentiation. They are prevalent in enhancers and promoters and their inheritance is linked to transcriptional stabilisation of key homeostasis genes and to transitions in the histone modification landscape. Interventional G4 stabilisation by a small molecule leads to developmental delay. Our findings suggest that G4s are epigenetic marks involved in stem cell pluripotency and differentiation.

2021-11-10 | GSE161531 | GEO

DNA G-quadruplexes are transcription factor binding hot spots in human chromatin

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

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