G-Quadruplex structural motifs modulate protein-RNA interactions within the transcriptome
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PROVIDER: PRJNA1198313 | ENA |
REPOSITORIES: ENA
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Project description:RNA secondary structures, including G-quadruplexes (G4s), have emerged as vital players in protein–RNA interactions. The RNA-binding protein Fused in Sarcoma (FUS), which is strongly implicated in both neurodegenerative disease and cancer, is known to interact with RNA molecules through a variety of GU-rich sequences. However, a definitive consensus motif for FUS–RNA recognition and binding has not yet been determined. Here, we hypothesize that G4 structures, which are inherently G-rich, may play a key role in FUS binding. We examine the role of G4s in FUS–RNA binding by developing an RNA immunoprecipitation sequencing (RIP-seq) protocol under G4-stabilising and non-stabilising conditions. We find that G4s regulate the binding of FUS to target RNAs, providing new information on protein–RNA binding motifs, while reinforcing the importance of RNA secondary structures as pivotal regulators of protein interactions. These insights advance our understanding of FUS-RNA binding dynamics and future potential for identifying new therapeutic targets for neurodegenerative disease and other FUS-related pathologies.
2025-09-06 | GSE284272 | GEO
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: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
Project description:G-quadruplex structures in the 5’ UTR of mRNAs are widely considered to suppress translation without affecting transcription. The current study describes the comprehensive analysis of proteins binding to four different G-quadruplex motifs located in mRNAs of the cancer-related genes Bcl-2, NRAS, MMP16, and ARPC2. Following metabolic labeling (Stable Isotope Labeling with Amino acids in Cell culture, SILAC) of proteins in the human cell line HEK293, G-quadruplex binding proteins were enriched by pull-down assays and identified by LC-orbitrap mass spectrometry. We found different patterns of interactions for the G-quadruplex motifs under investigation. While the G-quadruplexes in the mRNAs of NRAS and MMP16 specifically interacted with a small number of proteins, the Bcl-2 and ARPC2 G-quadruplexes exhibited a broad range of proteinaceous interaction partners with 99 and 82 candidate proteins identified in at least two replicates, respectively. Among the interaction partners were many proteins known to bind to RNA, including multiple heterogenous nuclear ribonucleoproteins (hnRNPs). The identified ribosomal proteins are likely to reflect stalling of the ribosome by RNA G-quadruplex structures. In addition, several proteins were identified that have not previously been described to interact with RNA. Gene ontology analysis of the set of candidate proteins revealed that many interaction partners are known to be tumor related. The majority of the identified RNA G-quadruplex interacting proteins are thought to be involved in post-transcriptional processes, particularly in splicing. These findings indicate that protein-G-quadruplex interactions may be relevant to the regulation of mRNA maturation and may play an important role in tumor biology.
2017-11-14 | PXD005761 | Pride
Project description:Dimeric G-quadruplex motifs-induced NFRs determine strong replication origins in vertebrates
| PRJNA966151 | ENA
Project description:Landscape of G-quadruplex DNA structural regions in breast cancer
| PRJNA638648 | ENA
Project description:RG/RGG boxes are common binding motifs in RNA-G-quadruplex-interacting proteins
| PRJNA417119 | ENA
Project description:The effect of bisquinolinium compounds PhenDC3 and 360A genome wide gene expression changes modulated via promoter based G-quadruplex (G4) motifs. The total RNA was extracted after treating HeLa S3 cells with 10 µM of no molecule (DMSO), 8979A (control molecule), PhenDC3 (G4 specific molecule) or 360A (G4 specific molecule) for 48 hrs in triplicate.
2012-05-29 | E-GEOD-32170 | biostudies-arrayexpress
Project description:Enhancer elements interact with target genes at a distance to modulate their expression, but the molecular details of enhancer-promoter interaction are incompletely understood. G-quadruplex DNA secondary structures (G4s) have recently been shown to co-occur with 3D chromatin interactions, however, the functional importance of G4s within enhancers remains unclear. Results: In this study we identify novel G4 structures within two locus control regions at the human - and - globin loci. We find that mutating G4 motifs by genome editing prevents their folding into G4 structures in cells and disrupts 3D enhancer-promoter interactions and target gene expression in a manner comparable to whole enhancer deletion. Furthermore, restoration of G4 structure formation using a dissimilar G4-forming primary sequence recovers specific enhancer-gene interactions and gene expression. Through proteomic, biophysical, and genomic profiling, we find that enhancer G4s are tightly linked to the maintenance of an active chromatin state and RNA polymerase II recruitment to regulate target gene expression.
2025-06-05 | PXD063882 | Pride
Project description:Considerable progress has been made towards associating transcription factor binding sites (TFBS) with cell-type-specific gene expression, however, the full repertoire of DNA sequence motifs that regulate transcription remains unknown. Improving our understanding of transcriptional regulation is especially important in T cells, given the enormous potential of genetically engineered T cells as an emerging class of therapeutics. Here, we report results from a comprehensive and unbiased survey investigating whether there are novel motifs enriched in regulatory regions of genes with the highest constitutive and selective expression across diverse T-cell subsets. Using computational and experimental methods, we identified 2,036 novel motifs and 629 previously curated TFBS that are enriched, both individually and in specific combinations, in the regulatory regions of genes exhibiting T-cell-specific gene expression. We then used the self-transcribing active regulatory region sequencing (STARR-seq) assay to evaluate all possible three-way combinations of a subset of 18 candidate motifs to test their ability to modulate transcription in immortalized lymphoblastic cell lines of T-cell origin (Jurkat E6) versus myeloid origin (K562). Our results revealed novel motifs that modulate gene transcription in T cells, with some exhibiting stronger regulatory effects than TFBS for TFs with established roles in T cells. The regulatory activity of these novel motifs was influenced by the motif’s orientation, position, and copy number. Overall, these results highlight our incomplete understanding of the relationship between sequence composition and T-cell gene regulation, and indicate that previously annotated TFBS represent only a subset of motifs capable of modulating gene transcription in T cells.
2025-07-12 | GSE301996 | GEO