Transcriptome-wide mapping reveals an RNA-dependent mechanism of platinum cancer drugs [RIP-seq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE310413 | GEO | 2026/02/23
REPOSITORIES: GEO
Similar Datasets
Project description:Clinically used small molecules has been predicted to off-target to RNAs. However, the extend of this interaction is small molecule cancer therapeutics has not been characterized. Here, we screened for anticancer smalll molecules for their RNA interactions and uncovered widespread RNA off-targeting. Cisplatin was found to be one among the RNA binders. We used it as a model agent to identify the specific transcripts it interact with. We developed Plat-RNAseq, a click-chemistry-mediated transcriptome-wide assay to map transcriptome-wide interaction of cisplatin. Our results revealed that cisplatin binding was enriched at guanine-rich regions capable of forming RNA G-quadruplexes (rG4s). We use an rG4 ligand, carboxy-Pyridostatin (cPDS), to block access of platin-drug to rG4. This experiment test whether cPDS blocked platinum drug accumulation on cellular RNAs.
2026-02-23 | GSE310419 | GEO
Project description:Clinically used small molecules has been predicted to off-target to RNAs. However, the extend of this interaction is small molecule cancer therapeutics has not been characterized. Here, we screened for anticancer smalll molecules for their RNA interactions and uncovered widespread RNA off-targeting. Cisplatin was found to be one among the RNA binders. We used it as a model agent to identify the specific transcripts it interact with. To accomplish this, we developed Plat-RNAseq, a click-chemistry-mediated transcriptome-wide assay. Our results revealed that cisplatin binding was enriched at guanine-rich regions capable of forming RNA G-quadruplexes (rG4s) .We found that the recruitment of cisplatin to rG4s partially contributed to its cytotoxicity, revealing a noncanonical mechanism of action for this widely used chemotherapeutic agent.
2026-02-23 | GSE310416 | GEO
Project description:Clinically used small molecules has been predicted to off-target to RNAs. However, the extend of this interaction is small molecule cancer therapeutics has not been characterized. Here, we screened for anticancer smalll molecules for their RNA interactions and uncovered widespread RNA off-targeting. Cisplatin was found to be one among the RNA binders. We used it as a model agent to identify the specific transcripts it interact with. To accomplish this, we developed Plat-RNAseq, a click-chemistry-mediated transcriptome-wide assay. Our results revealed that cisplatin binding was enriched at guanine-rich regions capable of forming RNA G-quadruplexes (rG4s) .We found that the recruitment of cisplatin to rG4s partially contributed to its cytotoxicity, revealing a noncanonical mechanism of action for this widely used chemotherapeutic agent. RNA seq was performed to catalogue all non-ribosomal RNAs present in A2780 cells.
2026-02-23 | GSE310424 | GEO
Project description:Clinically used small molecules has been predicted to off-target to RNAs. However, the extend of this interaction is small molecule cancer therapeutics has not been characterized. Here, we screened for anticancer smalll molecules for their RNA interactions and uncovered widespread RNA off-targeting. Cisplatin was found to be one among the RNA binders. We used it as a model agent to identify the specific transcripts it interact with. We developed Plat-RNAseq, a click-chemistry-mediated transcriptome-wide assay to map transcriptome-wide interaction of cisplatin. Our results revealed that cisplatin binding was enriched at guanine-rich regions capable of forming RNA G-quadruplexes (rG4s). To test the relationship with RNA-DNA hybrid R-loop structures and cisplatin-RNA interaction, we used CUT&Tag experiment using S9.6 R-loop specfic antibody. This result revealed an increased cisplatin interacitn on R-loop engaged RNAs.
2026-02-23 | GSE310421 | GEO
Project description:Small molecules developed to target proteins and DNA may also bind RNA, but the extent and biological significance of these interactions remain poorly defined. Here, we systematically profiled RNA interactions of clinically approved chemotherapeutics and uncovered widespread RNA off-targeting. Cisplatin, a frontline chemotherapeutic for solid tumors, emerged as a prominent RNA-binding drug. To map these interactions in vivo, we developed Plat-RNAseq, a click-chemistry-mediated transcriptome-wide assay. Cisplatin binding was enriched at guanine-rich regions capable of forming RNA G-quadruplexes (rG4s) and preferentially accumulated at the 5′ ends of nascent transcripts that exhibited rG4 enrichment and R-loop formation. Cisplatin stabilized pre-formed rG4s while interfering with their de novo assembly, thereby altering RNA structure and function. The recruitment of cisplatin to rG4s contributed to its cytotoxicity, revealing a noncanonical mechanism of action for this widely used chemotherapeutic agent. Consistent with this mechanism, the expression level of rG4 cisplatin-RNA targets predicted the platinum sensitivity in ovarian cancer patients. Collectively, these findings broaden platinum pharmacology by revealing RNA interactions as a functionally relevant, non-canonical component of cisplatin’s mechanism of action. Our study highlights the importance of incorporating RNA interactions into drug design and establishes a framework for considering RNA as a functionally relevant target in small-molecule therapeutics.
2026-02-23 | GSE309934 | GEO
Project description:Small molecules developed to target proteins and DNA may also bind RNA, but the extent and biological significance of these interactions remain poorly defined. Here, we systematically profiled RNA interactions of clinically approved chemotherapeutics and uncovered widespread RNA off-targeting. Cisplatin, a frontline chemotherapeutic for solid tumors, emerged as a prominent RNA-binding drug. To map these interactions in vivo, we developed Plat-RNAseq, a click-chemistry-mediated transcriptome-wide assay. Cisplatin binding was enriched at guanine-rich regions capable of forming RNA G-quadruplexes (rG4s) and preferentially accumulated at the 5′ ends of nascent transcripts that exhibited rG4 enrichment and R-loop formation. Cisplatin stabilized pre-formed rG4s while interfering with their de novo assembly, thereby altering RNA structure and function. The recruitment of cisplatin to rG4s contributed to its cytotoxicity, revealing a noncanonical mechanism of action for this widely used chemotherapeutic agent. Consistent with this mechanism, the expression level of rG4 cisplatin-RNA targets predicted the platinum sensitivity in ovarian cancer patients. Collectively, these findings broaden platinum pharmacology by revealing RNA interactions as a functionally relevant, non-canonical component of cisplatin’s mechanism of action. Our study highlights the importance of incorporating RNA interactions into drug design and establishes a framework for considering RNA as a functionally relevant target in small-molecule therapeutics.
2026-02-23 | GSE309812 | GEO
Project description:RNA structures are of crucial importance for biological function and gene regulation. Guanine (G)-rich sequences in RNA can assemble to form RNA G-quadruplex (rG4) structures; specific rG4s have been shown to regulate gene expression, and are associated with human diseases. However, no transcriptome-wide method has been reported to map rG4s, limiting our understanding of the rG4 structure and its relationship with function and regulation. Here we introduce a transcriptome-wide rG4 profiling method, rG4-Seq, in which the rG4-mediated reverse transcriptase stalling is read out by next-generation sequencing at nucleotide resolution. We apply this method to human RNA and report the first global map of rG4 structures for any organism. Our analysis identifies over 3,000 rG4s, and increases to over 11,000 upon addition of a rG4 stabilizing ligand Pyridostatin (PDS). Notably, we discover that besides canonical rG4s, many rG4s are non-canonical with novel structural features such as long-loops, bulges, and 2-quartet. We also find that rG4 formation is associated with its stability, Cytosine (C)-content, and the stability of alternative RNA structures. Our data reveals that rG4s can be found in messenger RNAs (mRNAs) and long intergenic noncoding RNAs (lincRNAs). In mRNAs, rG4s are enriched in untranslated regions, and are significantly correlated with microRNA target sites and polyadenylation signals. Remarkably, we found that majority of our in vitro identified rG4s can change the in silico predicted RNA structure to uncover alternative RNA conformation.. Futhermore, the rG4s that have analogues in many ortholog genes across different species show a preferential association with RNA processing and stability. rG4-seq is a broadly applicable method that enables the RNA G4 structurome and its biological roles to be interrogated and can be readily applied in other organisms on a transcriptome-wide scale. 12 samples, 150 bp single-ended RNA-Seq libraries from cell extracts after performing RTS reaction in different buffers (Li, K and K+PDS rich buffer). Each of the 3 conditions has 4 libraries from independent biological replicates.
2016-08-10 | E-GEOD-77282 | biostudies-arrayexpress
Project description:RNA structures are of crucial importance for biological function and gene regulation. Guanine (G)-rich sequences in RNA can assemble to form RNA G-quadruplex (rG4) structures; specific rG4s have been shown to regulate gene expression, and are associated with human diseases. However, no transcriptome-wide method has been reported to map rG4s, limiting our understanding of the rG4 structure and its relationship with function and regulation. Here we introduce a transcriptome-wide rG4 profiling method, rG4-Seq, in which the rG4-mediated reverse transcriptase stalling is read out by next-generation sequencing at nucleotide resolution. We apply this method to human RNA and report the first global map of rG4 structures for any organism. Our analysis identifies over 3,000 rG4s, and increases to over 11,000 upon addition of a rG4 stabilizing ligand Pyridostatin (PDS). Notably, we discover that besides canonical rG4s, many rG4s are non-canonical with novel structural features such as long-loops, bulges, and 2-quartet. We also find that rG4 formation is associated with its stability, Cytosine (C)-content, and the stability of alternative RNA structures. Our data reveals that rG4s can be found in messenger RNAs (mRNAs) and long intergenic noncoding RNAs (lincRNAs). In mRNAs, rG4s are enriched in untranslated regions, and are significantly correlated with microRNA target sites and polyadenylation signals. Remarkably, we found that majority of our in vitro identified rG4s can change the in silico predicted RNA structure to uncover alternative RNA conformation.. Futhermore, the rG4s that have analogues in many ortholog genes across different species show a preferential association with RNA processing and stability. rG4-seq is a broadly applicable method that enables the RNA G4 structurome and its biological roles to be interrogated and can be readily applied in other organisms on a transcriptome-wide scale.
2016-08-10 | GSE77282 | GEO
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
Project description:Whether RNA G-quadruplexes (rG4) form extensively in vivo and what roles they play remain actively debated. Among their proposed functions is recognition of Polycomb repressive complex 2 (PRC2), but how the interaction results in epigenetic regulation is not understood. Here we demonstrate that rG4s form dynamically during ES cell differentiation and require ATRX’s helicase function to unwind competing secondary structures. Mutating ATRX causes rG4 depletion on a transcriptome-wide basis and dramatically increases gene expression. We identify and mutate rG4s within Xist RNA and mechanistically separate PRC2’s recruitment versus catalysis. Surprisingly, although rG4s recruit PRC2, unfolding the rG4 structure causes PRC2 hyperactivation, entrapment of PRC2 in the S1 chromosomal compartment, and loss of gene silencing. Thus, we link dynamic rG4 folding and unfolding to PRC2 recruitment, trans-compartmental Xist migration, regulated activation of PRC2, and whole-chromosome gene silencing.
2024-05-17 | GSE219079 | GEO