RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualizations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualization, accessible at https://r2dt.bio.
- MeSH
- jednonukleotidový polymorfismus MeSH
- konformace nukleové kyseliny * MeSH
- počítačová grafika MeSH
- RNA * chemie MeSH
- sbalování RNA MeSH
- software * MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- RNA * MeSH
RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualizations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualization, accessible at https://r2dt.bio.
- MeSH
- jednonukleotidový polymorfismus MeSH
- konformace nukleové kyseliny * MeSH
- počítačová grafika MeSH
- RNA * chemie MeSH
- sbalování RNA MeSH
- software * MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- RNA * MeSH
Single-cell RNA-seq methods can be used to delineate cell types and states at unprecedented resolution but do little to explain why certain genes are expressed. Single-cell ATAC-seq and multiome (ATAC + RNA) have emerged to give a complementary view of the cell state. It is however unclear what additional information can be extracted from ATAC-seq data besides transcription factor binding sites. Here, we show that ATAC-seq telomere-like reads counter-inituively cannot be used to infer telomere length, as they mostly originate from the subtelomere, but can be used as a biomarker for chromatin condensation. Using long-read sequencing, we further show that modern hyperactive Tn5 does not duplicate 9 bp of its target sequence, contrary to common belief. We provide a new tool, Telomemore, which can quantify nonaligning subtelomeric reads. By analyzing several public datasets and generating new multiome fibroblast and B-cell atlases, we show how this new readout can aid single-cell data interpretation. We show how drivers of condensation processes can be inferred, and how it complements common RNA-seq-based cell cycle inference, which fails for monocytes. Telomemore-based analysis of the condensation state is thus a valuable complement to the single-cell analysis toolbox.
- MeSH
- analýza jednotlivých buněk * metody MeSH
- B-lymfocyty metabolismus cytologie MeSH
- buněčný cyklus * genetika MeSH
- ChiP sekvenování metody MeSH
- chromatin * metabolismus chemie genetika MeSH
- fibroblasty metabolismus cytologie MeSH
- lidé MeSH
- sekvenování transkriptomu metody MeSH
- telomery * genetika MeSH
- vazebná místa MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- chromatin * MeSH
The RNA chaperone Hfq plays crucial roles in bacterial gene expression and is a major facilitator of small regulatory RNA (sRNA) action. The toroidal architecture of the Hfq hexamer presents three well-characterized surfaces that allow it to bind sRNAs to stabilize them and engage target transcripts. Hfq-interacting sRNAs are categorized into two classes based on the surfaces they use to bind Hfq. By characterizing a systematic alanine mutant library of Hfq to identify amino acid residues that impact survival of Escherichia coli experiencing nitrogen (N) starvation, we corroborated the important role of the three RNA-binding surfaces for Hfq function. We uncovered two, previously uncharacterized, conserved residues, V22 and G34, in the hydrophobic core of Hfq, to have a profound impact on Hfq's RNA-binding activity in vivo. Transcriptome-scale analysis revealed that V22A and G34A Hfq mutants cause widespread destabilization of both sRNA classes, to the same extent as seen in bacteria devoid of Hfq. However, the alanine substitutions at these residues resulted in only modest alteration in stability and structure of Hfq. We propose that V22 and G34 have impact on Hfq function, especially critical under cellular conditions when there is an increased demand for Hfq, such as N starvation.
- MeSH
- bakteriální RNA * metabolismus genetika chemie MeSH
- dusík metabolismus MeSH
- Escherichia coli * genetika metabolismus MeSH
- hydrofobní a hydrofilní interakce * MeSH
- konzervovaná sekvence MeSH
- malá nekódující RNA * metabolismus genetika chemie MeSH
- mutace MeSH
- protein hostitelského faktoru 1 * metabolismus genetika chemie MeSH
- proteiny z Escherichia coli * metabolismus genetika chemie MeSH
- regulace genové exprese u bakterií MeSH
- stabilita RNA * genetika MeSH
- stanovení celkové genové exprese MeSH
- transkriptom genetika MeSH
- vazba proteinů MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- bakteriální RNA * MeSH
- dusík MeSH
- Hfq protein, E coli MeSH Prohlížeč
- malá nekódující RNA * MeSH
- protein hostitelského faktoru 1 * MeSH
- proteiny z Escherichia coli * MeSH
Protein synthesis (translation) consumes a substantial proportion of cellular resources, prompting specialized mechanisms to reduce translation under adverse conditions. Ribosome inactivation often involves ribosome-interacting proteins. In both bacteria and eukaryotes, various ribosome-interacting proteins facilitate ribosome dimerization or hibernation, and/or prevent ribosomal subunits from associating, enabling the organisms to adapt to stress. Despite extensive studies on bacteria and eukaryotes, understanding factor-mediated ribosome dimerization or anti-association in archaea remains elusive. Here, we present cryo-electron microscopy structures of an archaeal 30S dimer complexed with an archaeal ribosome dimerization factor (designated aRDF), from Pyrococcus furiosus, resolved at a resolution of 3.2 Å. The complex features two 30S subunits stabilized by aRDF homodimers in a unique head-to-body architecture, which differs from the disome architecture observed during hibernation in bacteria and eukaryotes. aRDF interacts directly with eS32 ribosomal protein, which is essential for subunit association. The binding mode of aRDF elucidates its anti-association properties, which prevent the assembly of archaeal 70S ribosomes.
- MeSH
- archeální proteiny * chemie metabolismus ultrastruktura MeSH
- dimerizace MeSH
- elektronová kryomikroskopie * MeSH
- malé podjednotky ribozomu archebakteriální chemie metabolismus MeSH
- molekulární modely MeSH
- multimerizace proteinu MeSH
- Pyrococcus furiosus * metabolismus MeSH
- ribozomální proteiny * chemie metabolismus MeSH
- ribozomy metabolismus ultrastruktura chemie MeSH
- vazba proteinů MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- archeální proteiny * MeSH
- ribozomální proteiny * MeSH
In RNA interference (RNAi), long double-stranded RNA is cleaved by the Dicer endonuclease into small interfering RNAs (siRNAs), which guide degradation of complementary RNAs. While RNAi mediates antiviral innate immunity in plants and many invertebrates, vertebrates have adopted a sequence-independent response and their Dicer produces siRNAs inefficiently because it is adapted to process small hairpin microRNA precursors in the gene-regulating microRNA pathway. Mammalian endogenous RNAi is thus a rudimentary pathway of unclear significance. To investigate its antiviral potential, we modified the mouse Dicer locus to express a truncated variant (DicerΔHEL1) known to stimulate RNAi and we analyzed how DicerΔHEL1/wt mice respond to four RNA viruses: coxsackievirus B3 and encephalomyocarditis virus from Picornaviridae; tick-borne encephalitis virus from Flaviviridae; and lymphocytic choriomeningitis virus (LCMV) from Arenaviridae. Increased Dicer activity in DicerΔHEL1/wt mice did not elicit any antiviral effect, supporting an insignificant antiviral function of endogenous mammalian RNAi in vivo. However, we also observed that sufficiently high expression of DicerΔHEL1 suppressed LCMV in embryonic stem cells and in a transgenic mouse model. Altogether, mice with increased Dicer activity offer a new benchmark for identifying and studying viruses susceptible to mammalian RNAi in vivo.
In RNA interference (RNAi), the enzyme Dicer cuts long double-stranded RNA into small interfering RNAs that degrade matching RNAs. RNAi is a key antiviral defense in plants and invertebrates but vertebrates evolved a principally different antiviral defense. The authors genetically modified Dicer in mice to activate RNAi in mammals. These modified mice were tested against four RNA viruses but showed no significant antiviral response. However, further increased expression of modified Dicer did suppress one virus (lymphocytic choriomeningitis virus) in embryonic stem cells and in a transgenic mouse model, suggesting that some viruses might be sensitive to increased RNAi activity in mammals.
- MeSH
- DEAD-box RNA-helikasy genetika metabolismus MeSH
- malá interferující RNA genetika MeSH
- myši inbrední C57BL MeSH
- myši MeSH
- přirozená imunita * genetika MeSH
- ribonukleasa III * genetika metabolismus MeSH
- RNA interference * MeSH
- virus encefalomyokarditidy genetika imunologie MeSH
- virus lymfocytární choriomeningitidy imunologie genetika MeSH
- viry klíšťové encefalitidy genetika imunologie MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- DEAD-box RNA-helikasy MeSH
- Dicer1 protein, mouse MeSH Prohlížeč
- malá interferující RNA MeSH
- ribonukleasa III * MeSH
Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.
The European Chemical Biology Database (ECBD, https://ecbd.eu) serves as the central repository for data generated by the EU-OPENSCREEN research infrastructure consortium. It is developed according to FAIR principles, which emphasize findability, accessibility, interoperability and reusability of data. This data is made available to the scientific community following open access principles. The ECBD stores both positive and negative results from the entire chemical biology project pipeline, including data from primary or counter-screening assays. The assays utilize a defined and diverse library of over 107 000 compounds, the annotations of which are continuously enriched by external user supported screening projects and by internal EU-OPENSCREEN bioprofiling efforts. These compounds were screened in 89 currently deposited datasets (assays), with 48 already being publicly accessible, while the remaining will be published after a publication embargo period of up to 3 years. Together these datasets encompass ∼4.3 million experimental data points. All public data within ECBD can be accessed through its user interface, API or by database dump under the CC-BY 4.0 license.
The RNA editing enzyme adenosine deaminase acting on RNA 1 (ADAR1) is essential for correct functioning of innate immune responses. The ADAR1p110 isoform is mainly nuclear and ADAR1p150, which is interferon (IFN) inducible, is predominately cytoplasmic. Using three different methods - co-immunoprecipitation (co-IP) of endogenous ADAR1, Strep-tag co-IP and BioID with individual ADAR1 isoforms - a comprehensive interactome was generated during both homeostasis and the IFN response. Both known and novel interactors as well as editing regulators were identified. Nuclear proteins were detected as stable interactors with both ADAR1 isoforms. In contrast, BioID identified distinct protein networks for each ADAR1 isoform, with nuclear components observed with ADAR1p110 and components of cytoplasmic cellular condensates with ADAR1p150. RNase A digestion distinguished between distal and proximal interactors, as did a double-stranded RNA (dsRNA)-binding mutant of ADAR1 which demonstrated the importance of dsRNA binding for ADAR1 interactions. IFN treatment did not affect the core ADAR1 interactomes but resulted in novel interactions, the majority of which are proximal interactions retained after RNase A treatment. Short treatment with high molecular weight poly(I:C) during the IFN response resulted in dsRNA-binding-dependent changes in the proximal protein network of ADAR1p110 and association of the ADAR1p150 proximal protein network with some components of antiviral stress granules.
- MeSH
- adenosindeaminasa * metabolismus genetika MeSH
- buněčné jádro * metabolismus MeSH
- cytoplazma * metabolismus MeSH
- dvouvláknová RNA metabolismus genetika MeSH
- editace RNA MeSH
- HEK293 buňky MeSH
- HeLa buňky MeSH
- interferony metabolismus genetika MeSH
- lidé MeSH
- mapy interakcí proteinů MeSH
- poly I-C farmakologie MeSH
- protein - isoformy * metabolismus genetika MeSH
- proteiny vázající RNA * metabolismus genetika MeSH
- vazba proteinů MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- ADAR protein, human MeSH Prohlížeč
- adenosindeaminasa * MeSH
- dvouvláknová RNA MeSH
- interferony MeSH
- poly I-C MeSH
- protein - isoformy * MeSH
- proteiny vázající RNA * MeSH
DNA double-strand breaks (DSBs) represent a lethal form of DNA damage that can trigger cell death or initiate oncogenesis. The activity of RNA polymerase II (RNAPII) at the break site is required for efficient DSB repair. However, the regulatory mechanisms governing the transcription cycle at DSBs are not well understood. Here, we show that Integrator complex subunit 6 (INTS6) associates with the heterotrimeric sensor of ssDNA (SOSS1) complex (comprising INTS3, INIP and hSSB1) to form the tetrameric SOSS1 complex. INTS6 binds to DNA:RNA hybrids and promotes Protein Phosphatase 2A (PP2A) recruitment to DSBs, facilitating the dephosphorylation of RNAPII. Furthermore, INTS6 prevents the accumulation of damage-associated RNA transcripts (DARTs) and the stabilization of DNA:RNA hybrids at DSB sites. INTS6 interacts with and promotes the recruitment of senataxin (SETX) to DSBs, facilitating the resolution of DNA:RNA hybrids/R-loops. Our results underscore the significance of the tetrameric SOSS1 complex in the autoregulation of DNA:RNA hybrids and efficient DNA repair.
- MeSH
- DNA vazebné proteiny metabolismus MeSH
- DNA-helikasy metabolismus genetika MeSH
- DNA * metabolismus chemie MeSH
- dvouřetězcové zlomy DNA * MeSH
- fosforylace MeSH
- homeostáza genetika MeSH
- lidé MeSH
- oprava DNA * MeSH
- proteinfosfatasa 2 metabolismus genetika MeSH
- R-smyčka MeSH
- RNA-helikasy metabolismus genetika MeSH
- RNA-polymerasa II * metabolismus MeSH
- RNA * metabolismus genetika chemie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- DNA vazebné proteiny MeSH
- DNA-helikasy MeSH
- DNA * MeSH
- proteinfosfatasa 2 MeSH
- RNA-helikasy MeSH
- RNA-polymerasa II * MeSH
- RNA * MeSH
