Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Do we know whether potential G-quadruplexes actually form in long functional RNA molecules?

ABSTRACT: The roles of deoxyribonucleic acid (DNA) G-quadruplex structures in gene expression and telomere maintenance have been well characterized. Recent results suggest that such structures could also play pivotal roles in ribonucleic acid (RNA) biology, such as splicing or translation regulation. However, it has been difficult to show that RNA G-quadruplexes (G4s) exist in specific long RNA sequences, such as precursor messenger RNA, in a functional or cellular context. Most current methods for identifying G4s involve the use of short, purified RNA sequences in vitro, in the absence of competition with secondary structures or protein binding. Therefore, novel methods need to be developed to allow the characterization of G4s in long functional RNAs and in a cellular context. This need has in part been met by our recent development of a method based on a comparison of RNA and 7-deaza-RNA that provides a test for identifying RNA G4s in such conditions.

SUBMITTER: Weldon C

PROVIDER: S-EPMC5135001 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Do we know whether potential G-quadruplexes actually form in long functional RNA molecules?

Weldon Carika C Eperon Ian C IC Dominguez Cyril C

Biochemical Society transactions 20161201 6

The roles of deoxyribonucleic acid (DNA) G-quadruplex structures in gene expression and telomere maintenance have been well characterized. Recent results suggest that such structures could also play pivotal roles in ribonucleic acid (RNA) biology, such as splicing or translation regulation. However, it has been difficult to show that RNA G-quadruplexes (G4s) exist in specific long RNA sequences, such as precursor messenger RNA, in a functional or cellular context. Most current methods for identi ...[more]

PMID: 27913687

Similar Datasets

Identification of G-quadruplexes in long functional RNAs using 7-deazaguanine RNA.

Project description:RNA G-quadruplex (G4) structures are thought to affect biological processes, including translation and pre-mRNA splicing, but it is not possible at present to demonstrate that they form naturally at specific sequences in long functional RNA molecules. We developed a new strategy, footprinting of long 7-deazaguanine-substituted RNAs (FOLDeR), that allows the formation of G4s to be confirmed in long RNAs and under functional conditions.

| S-EPMC5164935 | biostudies-literature

What do medical students actually need to know about artificial intelligence?

Project description:With emerging innovations in artificial intelligence (AI) poised to substantially impact medical practice, interest in training current and future physicians about the technology is growing. Alongside comes the question of what, precisely, should medical students be taught. While competencies for the clinical usage of AI are broadly similar to those for any other novel technology, there are qualitative differences of critical importance to concerns regarding explainability, health equity, and data security. Drawing on experiences at the University of Toronto Faculty of Medicine and MIT Critical Data's "datathons", the authors advocate for a dual-focused approach: combining robust data science-focused additions to baseline health research curricula and extracurricular programs to cultivate leadership in this space.

| S-EPMC7305136 | biostudies-literature

The functional form of specialised predation affects whether Janzen-Connell effects can prevent competitive exclusion.

Project description:Janzen-Connell effects (JCEs), specialised predation of seeds and seedlings near conspecific trees, are hypothesised to maintain species richness. While previous studies show JCEs can maintain high richness relative to neutral communities, recent theoretical work indicates JCEs may weakly inhibit competitive exclusion when species exhibit interspecific fitness variation. However, recent models make somewhat restrictive assumptions about the functional form of specialised predation-that JCEs occur at a fixed rate when offspring are within a fixed distance of a conspecific tree. Using a theoretical model, I show that the functional form of JCEs largely impacts their ability to maintain coexistence. If predation pressure increases additively with adult tree density and decays exponentially with distance, JCEs maintain considerably higher species richness than predicted by recent models. Loosely parameterising the model with data from a Panamanian tree community, I elucidate the conditions under which JCEs are capable of maintaining high species richness.

| S-EPMC9324109 | biostudies-literature

Two Factors in Face Recognition: Whether You Know the Person's Face and Whether You Share the Person's Race.

Project description:One of the best-known phenomena in face recognition is the other-race effect, the observation that own-race faces are better remembered than other-race faces. However, previous studies have not put the magnitude of other-race effect in the context of other influences on face recognition. Here, we compared the effects of (a) a race manipulation (own-race/other-race face) and (b) a familiarity manipulation (familiar/unfamiliar face) in a 2 × 2 factorial design. We found that the familiarity effect was several times larger than the race effect in all performance measures. However, participants expected race to have a larger effect on others than it actually did. Face recognition accuracy depends much more on whether you know the person's face than whether you share the same race.

| S-EPMC8371284 | biostudies-literature

Motif independent identification of potential RNA G-quadruplexes by G4RNA screener.

Project description:G-quadruplex structures in RNA molecules are known to have regulatory impacts in cells but are difficult to locate in the genome. The minimal requirements for G-quadruplex folding in RNA (G?3N1-7?G?3N1-7?G?3N1-7?G?3) is being challenged by observations made on specific examples in recent years. The definition of potential G-quadruplex sequences has major repercussions on the observation of the structure since it introduces a bias. The canonical motif only describes a sub-population of the reported G-quadruplexes. To address these issues, we propose an RNA G-quadruplex prediction strategy that does not rely on a motif definition.We trained an artificial neural network with sequences of experimentally validated G-quadruplexes from the G4RNA database encoded using an abstract definition of their sequence. This artificial neural network, G4NN, evaluates the similarity of a given sequence to known G-quadruplexes and reports it as a score. G4NN has a predictive power comparable to the reported G richness and G/C skewness evaluations that are the current state-of-the-art for the identification of potential RNA G-quadruplexes. We combined these approaches in the G4RNA screener, a program designed to manage and evaluate the sequences to identify potential G-quadruplexes.G4RNA screener is available for download at http://gitlabscottgroup.med.usherbrooke.ca/J-Michel/g4rna_screener.jean-michel.garant@usherbrooke.ca or jean-pierre.perreault@usherbrooke.ca or michelle.scott@usherbrooke.ca.Supplementary data are available at Bioinformatics online.

| S-EPMC5870565 | biostudies-literature

Identification of functional tetramolecular RNA G-quadruplexes derived from transfer RNAs.

Project description:RNA G-quadruplex (RG4) structures are involved in multiple biological processes. Recent genome-wide analyses of human mRNA transcriptome identified thousands of putative intramolecular RG4s that readily assemble in vitro but shown to be unfolded in vivo. Previously, we have shown that mature cytoplasmic tRNAs are cleaved during stress response to produce tRNA fragments that function to repress translation in vivo. Here we report that these bioactive tRNA fragments assemble into intermolecular RG4s. We provide evidence for the formation of uniquely stable tetramolecular RG4 structures consisting of five tetrad layers formed by 5'-terminal oligoguanine motifs of an individual tRNA fragment. RG4 is required for functions of tRNA fragments in the regulation of mRNA translation, a critical component of cellular stress response. RG4 disruption abrogates tRNA fragments ability to trigger the formation of Stress Granules in vivo. Collectively, our data rationalize the existence of naturally occurring RG4-assembling tRNA fragments and emphasize their regulatory roles.

| S-EPMC5655342 | biostudies-literature

What patients want to know, and what we actually tell them: The ABIDE project.

Project description:BackgroundWe studied to what degree and at whose initiative 25 informational topics, formerly identified as important, are discussed in diagnostic consultations.MethodsAudio recordings of clinician-patient consultations of 71 patients and 32 clinicians, collected in eight Dutch memory clinics, were independently content-coded by two coders. The coding scheme encompassed 25 informational topics.ResultsApproximately half (Mdn = 12) of the 25 topics were discussed per patient during the diagnostic process, with a higher frequency among individuals receiving a dementia diagnosis (Mdn = 14) compared to others (Mdn = 11). Individual topics ranged from being discussed with 2/71 (3%) to 70/71 (99%) of patients. Patients and/or care partners rarely initiated topic discussion (10%). When they did, they often enquired about one of the least frequently addressed topics.ConclusionMost patients received information on approximately half of the important informational topics. Providing the topic list to patients and care partners beforehand could allow consultation preparation and stimulate participation.

| S-EPMC7744024 | biostudies-literature

Targeting DNA G-quadruplexes with helical small molecules.

Project description:We previously identified quinoline-based oligoamide helical foldamers and a trimeric macrocycle as selective ligands of DNA quadruplexes. Their helical structures might permit targeting of the backbone loops and grooves of G-quadruplexes instead of the G-tetrads. Given the vast array of morphologies G-quadruplex structures can adopt, this might be a way to achieve sequence selective binding. Here, we describe the design and synthesis of molecules based on macrocyclic and helically folded oligoamides. We tested their ability to interact with the human telomeric G-quadruplex and an array of promoter G-quadruplexes by using FRET melting assay and single-molecule FRET. Our results show that they constitute very potent ligands--comparable to the best so far reported. Their modes of interaction differ from those of traditional tetrad binders, thus opening avenues for the development of molecules specific for certain G-quadruplex conformations.

| S-EPMC4284101 | biostudies-literature

Microbial Phenolic Metabolites: Which Molecules Actually Have an Effect on Human Health?

Project description:The role of gut microbiota in human health has been investigated extensively in recent years. The association of dysbiosis, detrimental changes in the colonic population, with several health conditions has led to the development of pro-, pre- and symbiotic foods. If not absorbed in the small intestine or secreted in bile, polyphenols and other food components can reach the large intestine where they are susceptible to modification by the microbial population, resulting in molecules with potentially beneficial health effects. This review provides an overview of studies that have detected and/or quantified microbial phenolic metabolites using high-performance liquid chromatography as the separation technique, followed by detection through mass spectrometry. Both in vitro experimental studies and human clinical trials are covered. Although many of the microbial phenolic metabolites (MPM) reported in in vitro studies were identified in human samples, further research is needed to associate them with clinical health outcomes.

| S-EPMC6893422 | biostudies-literature

Long Tracts of Guanines Drive Aggregation of RNA G-Quadruplexes in the Presence of Spermine.

Project description:G-Quadruplexes (GQs) are compact, stable structures in DNA and RNA comprised of two or more tiers of quartets whose G-rich motif of tracts of two or more G's occurs commonly within genomes and transcriptomes. While thermodynamically stable in vitro, these structures remain difficult to study in vivo. One approach to understanding GQ in vivo behavior is to test whether conditions and molecules found in cells facilitate their folding. Polyamines are biogenic polycations that interact with RNA. Among common polyamines, spermine contains the highest charge and is found in eukaryotes, making it a good candidate for association with high-charge density nucleic acid structures like GQs. Using a variety of techniques, including ultraviolet-detected thermal denaturation, circular dichroism, size exclusion chromatography, and confocal microscopy, on an array of quadruplex sequence variants, we find that eukaryotic biological concentrations of spermine induce microaggregation of three-tiered G-rich sequences, but not of purely two-tiered structures, although higher spermine concentrations induce aggregation of even these. The formation of microaggregates can also be induced by addition of as little as a single G to a two-tiered structure; moreover, they form at biological temperatures, are sensitive to salt, and can form in the presence of at least some flanking sequence. Notably, GQ aggregation is not observed under prokaryotic-like conditions of no spermine and higher NaCl concentrations. The sequence, polyamine, and salt specificity of microaggregation reported herein have implications for the formation and stability of G-rich nucleic acid aggregates in vivo and for functional roles for understudied GQ sequences with only two quadruplex tiers.

| S-EPMC8755445 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data