Targeted Detection of G‐Quadruplexes in Cellular RNAs

Kwok, C. Y.; Balasubramanian, Shankar

doi:10.1002/ange.201500891

Cited by 11 publications

(2 citation statements)

References 42 publications

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“…Interestingly, the Reverse Transcriptase stop (RT stop) assay indicated that the reverse transcriptions of all lncRNA G4s into full-length cDNAs were modulated by K + and Li + , albeit in somewhat erratic manner (Figure S4A-G; Table S3). [67][68][69][70][71] Collectively, these findings suggest a modest concentration-dependent modulation of G4s formed by these lncRNAs, which warrants a separate investigation.…”

Section: G4s In Vitromentioning

confidence: 82%

G-quadruplex formation in long non-coding RNAs dysregulated in colorectal cancer

Sharma,

Shukla,

Mitteaux

et al. 2024

Preprint

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Non-coding RNAs (ncRNAs) in human cells do not lead to protein synthesis and constitute a substantial portion of the transcriptome. Human long non-coding RNAs (lncRNAs) orchestrate critical cellular functions influencing development, differentiation, and metabolism. Dysregulation of lncRNAs has been correlated with several pathological conditions such as neurodegenerative and autoimmune disorders, diabetes, and cancer. Recent reports have suggested the involvement of G4s in lncRNAs to regulate colorectal cancer (CRC) carcinogenesis. In this study, we investigate the occurrence and distribution of G4s in theLINC01589,MELTF-AS1,andUXT-AS1lncRNAs, which have been reported to be dysregulated in CRC. Using a combination ofin silicotools andin vitrobiophysical techniques, we show that these lncRNAs form stable, parallel, and intramolecular G4s. Furthermore, we establish the formation of G4s within these lncRNAs in CRC using cell-based assays, including RNA G4-Immuno-FISH and G4RP-RT-qPCR. This is the first systematic study of G4s in lncRNAs dysregulated in CRC, and our findings highlight the diagnostic and therapeutic potential of G4s in CRC.

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Section: G4s In Vitromentioning

confidence: 82%

G-quadruplex formation in long non-coding RNAs dysregulated in colorectal cancer

Sharma,

Shukla,

Mitteaux

et al. 2024

Preprint

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“…The reverse transcriptase stalling (RTS) assays were performed using in vitro synthesized RNA transcripts as described previously with the modifications described below 35 . Each experiment was performed in the presence of 4.4 pmol of RNA and 5 pmol of Cy5-labeled primer in RTS buffer (50 mM Tris, 5 mM MgCl 2, and 75 mM of either LiCl or KCl) in a final volume of 7.5 μL.…”

Section: Rts-stop Assaymentioning

confidence: 99%

G-quadruplexe as a structural modulator of Intron Retention upon viral infection

Lejault

Terrier

Vannutelli

et al. 2023

Preprint

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Amongst the wide array of alternative splicing events (ASE), the intrinsic mechanisms of intron retention have remained elusive. This particular type of ASE has long been characterized as an artifact, but recent studies have shown its implication in numerous diseases. It has also been revealed that numerous viruses choose to disrupt alternative splicing to escape cellular immune response and further their proliferation. The main focus of this study was to investigate the G-quadruplex role in Alternative Splicing Events (ASEs) that occur following Flavivirus infections. After having demonstrated that G-quadruplexes structures are mainly formed in Intron Retained Transcripts by RNA-seq, our attention turned toward the ULK3 gene, coding for a serine/threonine kinase regulating autophagy, an essential mechanism in the cellular response to stress and even pathogen infections. In this study, we revealed the presence of a G-quadruplex in the first intron of the ULK3 gene near the 3' splice site. Furthermore, we assayed the formation and stability of this G-quadruplex in vitro and showed that its formation affects IR, as demonstrated by comparisons between wild-type and mutant transfected mini-genes. Finally, we identified the specific RNA-binding protein signature for this G-quadruplex, thereby uncovering the novel role of G-quadruplexes in Alternative Splicing.

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Structural Analysis using SHALiPE to Reveal RNA G‐Quadruplex Formation in Human Precursor MicroRNA

2016

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RNA G-quadruplex (rG4) structures are of fundamental importance to biology. A novel approach is introduced to detect and structurally map rG4s at single-nucleotide resolution in RNAs. The approach, denoted SHALiPE, couples selective 2'-hydroxyl acylation with lithium ion-based primer extension, and identifies characteristic structural fingerprints for rG4 mapping. We apply SHALiPE to interrogate the human precursor microRNA 149, and reveal the formation of an rG4 structure in this non-coding RNA. Additional analyses support the SHALiPE results and uncover that this rG4 has a parallel topology, is thermally stable, and is conserved in mammals. An in vitro Dicer assay shows that this rG4 inhibits Dicer processing, supporting the potential role of rG4 structures in microRNA maturation and post-transcriptional regulation of mRNAs.

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Targeted Detection of G‐Quadruplexes in Cellular RNAs

Cited by 11 publications

References 42 publications

G-quadruplex formation in long non-coding RNAs dysregulated in colorectal cancer

G-quadruplex formation in long non-coding RNAs dysregulated in colorectal cancer

G-quadruplexe as a structural modulator of Intron Retention upon viral infection

Structural Analysis using SHALiPE to Reveal RNA G‐Quadruplex Formation in Human Precursor MicroRNA

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