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315 results for “RNA structure”
Deep sequencing datasets from: Witnessing the structural evolution of an RNA enzyme
<p>An RNA polymerase ribozyme that has been the subject of extensive directed evolution efforts has attained the ability to synthesize complex functional RNAs, including a full-length copy of its own evolutionary ancestor. During the course of evolution, the catalytic core of the ribozyme has undergone a major structural rearrangement, resulting in a novel tertiary structural element that lies in close proximity to the active site. Through a combination of site-directed mutagenesis, structural probing, and deep sequencing analysis, the trajectory of evolution was seen to involve the progressive stabilization of the new structure, which provides the basis for improved catalytic activity of the ribozyme. Multiple paths to the new structure were explored by the evolving population, converging upon a common solution. Tertiary structural remodeling of RNA is known to occur in nature, as evidenced by the phylogenetic analysis of extant organisms, but this type of structural innovation had not previously been observed in an experimental setting. Despite prior speculation that the catalytic core of the ribozyme had become trapped in a narrow local fitness optimum, the evolving population has broken through to a new fitness locale, raising the possibility that further improvement of polymerase activity may be achievable.</p> <p> </p>
Data for: A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA
<p><span>Productive transcriptional elongation of many cellular and viral mRNAs requires transcriptional factors to extract pTEFb from the 7SK snRNP by modulating the association between the HEXIM protein and the 7SK snRNA. Here we report the structure of the HEXIM arginine-rich motif in complex with the apical stemloop-1 of 7SK (7SK-SL1<sup>apical</sup>) and detail how the HIV transcriptional regulator Tat from various subtypes overcome the structural constraints required to displace HEXIM. While most interactions between 7SK and HEXIM and Tat are similar, critical differences exist that guide function. First, the conformational plasticity of 7SK enables the formation of three different base pair configurations at a critical remodeling site, which allows for the modulation required for HEXIM binding and its subsequent displacement by Tat. Furthermore, the specific sequence variations observed in various Tat subtypes all converge on remodeling 7SK at this region. Second, we show that HEXIM primes its own displacement by causing specific local destabilization upon binding </span>— <span>a feature that is then exploited by Tat to bind 7SK more efficiently. Overall, our study details the molecular environment presented by HEXIM and uncovers a destabilization-driven displacement strategy that increases the conformational sampling of 7SK-snRNP, which may allow diverse transcriptional factors to competitively regulate pTEFb.</span></p>
Datasets for benchmarking RNA 2D structure prediction algorithms.
<p>Datasets for benchmarking ML approaches in RNA 2D structure prediction task.</p>
RNA 3D structure modeling by fragment assembly with Small Angle X-ray Scattering restraints
<p>Structure determination is a key step in the functional characterization of many non-coding RNA molecules. High-resolution RNA 3D structure determination efforts, however, are not keeping up with the pace of discovery of new non-coding RNA sequences. This increases the importance of computational approaches and low-resolution experimental data, such as from the Small Angle X-ray Scattering experiments. We present RNA Masonry, a computer program and a web service for a fully automated modeling of RNA 3D structures. It assemblies RNA fragments into geometrically plausible models that meet user-provided secondary structure constraints, restraints on tertiary contacts and Small Angle X-ray Scattering data. We illustrate the method description with detailed benchmarks and its application to structural studies of viral RNAs with SAXS restraints.</p>
Data for: A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA
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Deep sequencing datasets from: Witnessing the structural evolution of an RNA enzyme
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The datasets used in "RNA secondary structure prediction using deep learning with thermodynamic integration"
<p>The datasets used in "RNA secondary structure prediction using deep learning with thermodynamic integration"</p>
Structural insights into distinct mechanisms of RNA polymerase II and III recruitment to snRNA promoters - segmented EM density used in integrative modeling
<p>segmented cryoEM map and derived gaussian mixture model used in the integrative modeling of the human SNAPc complex </p>
Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding
<p>This dataset contains files of the molecular dynamics simulations performed in "Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding" study. Further information in presented in README.md file and the abstract of the study is presented below:</p> <p>"The nucleocapsid (N) protein of the SARS-CoV-2 virus, the causal agent of COVID-19, is a multifunction phosphoprotein that plays critical roles in the virus life cycle, including transcription and packaging of the viral RNA. To play such diverse roles, the N protein has two globular RNA-binding modules, the N- (NTD) and C-terminal (CTD) domains, which are connected by an intrinsically disordered region. Despite the wealth of structural data available for the isolated NTD and CTD, how these domains are arranged in the full-length protein and how the oligomerization of N influences its RNA-binding activity remains largely unclear. Herein, using experimental data from electron microscopy and biochemical/biophysical techniques combined with molecular modeling and molecular dynamics simulations, we showed that, in the absence of RNA, the N protein formed structurally dynamic dimers, with the NTD and CTD arranged in extended conformations. However, in the presence of RNA, the N protein assumed a more compact conformation where the NTD and CTD are packed together. We also provided an octameric model for the full-length N bound to RNA that was consistent with electron microscopy images of the N protein in the presence of RNA. Together, our results shed new light on the dynamics and higher-order oligomeric structure of this versatile protein."</p>
EMRNA: Accurate RNA structure determination from cryo-EM maps by deep learning and integrated modeling
<p>EMRNA: Accurate RNA structure determination from cryo-EM maps by deep learning and integrated modeling.</p><p>Here stores the input files and output structures of EMRNA and the reproduction result of auto-DRRAFTER.</p>
RNA 3D structural models used to train, test and validate lociPARSE
<p>This repository contains all the training, validation and test decoy sets to train and evalaute lociPARSE. It also contains training and benchmarks set-2 decoys from ARES.</p>
SQUID: Transcriptomic Structural Variation Detection from RNA-seq -- simulation data part 3
<p>Simulation data part 3 for SQUID software.</p>
SQUID: Transcriptomic Structural Variation Detection from RNA-seq -- simulation data part 2
<p>Simulation data part 2 for SQUID software.</p>
SQUID: Transcriptomic Structural Variation Detection from RNA-seq -- simulation data part 1
<p>Simulation data part 1 for SQUID software.</p>
Datasets of RNA structures for benchmarking entanglement detection and removal protocol using RNAspider and SPQR.
<p>Datasets of RNA structures for benchmarking entanglement detection and removal protocol using RNAspider and SPQR.</p>
Investigating the interplay between RNA structural dynamics and RNA chemical probing experiments
<p>Normalized SHAPE reactivity for pre-miR20b and CDE2GG as reported in 'Investigating the interplay between RNA structural dynamics and RNA chemical probing experiments'.</p>
Structural 3D domain reconstruction of the RNA genome from viruses from a secondary structure model
<p>Fragments and final models of reconstructed STMV genome from in virio and in vitro secondary structures reported in Larman et al. (2017).</p> <p>Simulation scripts for simulations of genome and fragments.</p> <p>Full code of SPQR package for performing simulations.</p>
Engineering 'smart' viral RNA structures for stable and targeted siRNA delivery
<p>Innovative delivery strategies are needed in order to realize the potential of small interfering RNA (siRNA) in medicine. SiRNAs are short, double-stranded RNA molecules that silence genes by co-opting an endogenous RNA interference (RNAi) pathway. Because they act on messenger RNA (mRNA) sequences via RNAi, siRNAs hold promise as potentially curative therapies for genetic defects, autoimmune disorders, cancers, and other diseases that cannot be treated with traditional, protein-binding small molecule drugs and biologics. However, key physiological barriers largely have precluded the translation of siRNA drugs into clinical practice. <em>In vivo</em>, naked siRNAs are degraded rapidly by nucleases and cleared by the kidneys, resulting in a half-life of less than five minutes. Moreover, by comparison to small molecule drugs, siRNA drugs are relatively large, hydrophilic molecules that do not distribute widely to tissues or passively cross the cell membrane. Therefore, without an effective strategy for delivery, the accumulation of siRNA drugs at target sites is minimal. Today, there are few prominent siRNA delivery approaches, and each has significant limitations. For example, chemical modifications can improve nuclease resistance, but with the increase in stability also come tradeoffs in potency and safety. Lipid nanoparticles (LNPs) physically shield siRNAs from degradation and can be modified to promote biodistribution and uptake; but as LNPs are optimized for efficacy, they become increasingly complex, posing quality assurance, cost, and evaluation problems. Finally, conjugation to the <em>N</em>-Acetylgalactosamine (GalNAc) ligand is a promising delivery strategy for the liver, but targeted delivery to other tissues is a problem that still remains to be solved. Advances in nucleic acid nanotechnology have shown that RNA is an emerging platform for drug delivery. In particular, a three-way junction (3WJ) derived from bacteriophage prohead RNA (pRNA) has gained prominence as a vector for small molecule, microRNA (miRNA), anti-miRNA, and siRNA delivery. As a delivery solution for siRNA, RNA-based platforms like the pRNA 3WJ have many notable advantages. For example, size and shape can be controlled to minimize clearance, and functionalization with aptamers can drive cell uptake. Also, RNA is a fundamentally biocompatible molecule that is simple, straightforward to produce, and multifunctional. However, its metabolic instability is limiting. Exciting new research has uncovered 'smart' RNA structures that are produced by flaviviruses (<em>e.g.</em>, Zika, Dengue, West Nile) to thwart nuclease degradation. Compared to other RNA structures used for drug delivery, these nuclease-resistant structures (NRSs) may be uniquely positioned for <em>in vivo</em> applications. The aim of this project is to harness the inherent stability of flaviviral NRSs in the creation of a supramolecular platform for siRNA delivery. This project has the potential to address a critical need in the field of oligonucleotide therapeutics, which has few promising solutions for harnessing the power of RNAi in the clinic. Additionally, this project will validate new stable structures as building blocks for use in RNA nanotechnology and therefore will help researchers design supramolecular structures for a variety of applications well beyond those described in this proposal.</p>
Engineering ‘smart’ viral RNA structures for stable and targeted siRNA delivery
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Data from: Compensatory evolution in RNA secondary structures increases substitution rate variation among sites
There is growing evidence that interactions between biological molecules (e.g., RNA-RNA, protein-protein, RNA-protein) place limits on the rate and trajectory of molecular evolution. Here, by extending Kimura's model of compensatory evolution at interacting sites, we show that the ratio of transition to transversion substitutions (κ) at interacting sites should be equal to the square of the ratio at independent sites. Because transition mutations generally occur at a higher rate than transversions, the model predicts that κ should be higher at interacting sites than at independent sites. We tested this prediction in 10 RNA secondary structures by comparing phylogenetically derived estimates of κ in paired sites within stems (κ(p)) and unpaired sites within loops (κ(u)). Eight of the 10 structures showed an excellent match to the quantitative predictions of the model, and 9 of the 10 structures matched the qualitative prediction κ(p) > κ(u). Only the Rev response element from the human immunovirus (HIV) genome showed the reverse pattern, with κ(p) < κ(u). Although a variety of evolutionary forces could produce quantitative deviations from the model predictions, the reversal in magnitude of κ(p) and κ(u) could be achieved only by violating the model assumption that the underlying transition (or transversion) mutation rates were identical in paired and unpaired regions of the molecule. We explore the ability of the APOBEC3 enzymes, host defense mechanisms against retroviruses, which induce transition mutations preferentially in single-stranded regions of the HIV genome, to explain this exception to the rule. Taken as a whole, our findings suggest that kappa may have utility as a simple diagnostic to evaluate proposed secondary structures.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.