A common core RNP structure shared between the small nuclear box C/D RNPs and the spliceosomal U 4 snRNP.

AbstractThe box C/D snoRNAs function in directing 2′-O-methylation and/or as chaperones in the processing of ribosomal RNA. We show here that Snu13p (15.5kD in human), a component of the U4/U6.U5 tri-snRNP, is also associated with the box C/D snoRNAs. Indeed, genetic depletion of Snu13p in yeast leads to a major defect in RNA metabolism. The box C/D motif can be folded into a stem-internal loop-stem structure, almost identical to the 15.5kD binding site in the U4 snRNA. Consistent with this, the box C/D motif binds Snu13p/15.5kD in vitro. The similarities in structure and function observed between the U4 snRNP (chaperone for U6) and the box C/D snoRNPs raises the interesting possibility that these particles may have evolved from a common ancestral RNP

Pseudouridine synthase 1: a site-specific synthase without strict sequence recognition requirements

Pseudouridine synthase 1 (Pus1p) is an unusual site-specific modification enzyme in that it can modify a number of positions in tRNAs and can recognize several other types of RNA. No consensus recognition sequence or structure has been identified for Pus1p. Human Pus1p was used to determine which structural or sequence elements of human tRNASer are necessary for pseudouridine (Ψ) formation at position 28 in the anticodon stem-loop (ASL). Some point mutations in the ASL stem of tRNASer had significant effects on the levels of modification and compensatory mutation, to reform the base pair, restored a wild-type level of Ψ formation. Deletion analysis showed that the tRNASer TΨC stem-loop was a determinant for modification in the ASL. A mini-substrate composed of the ASL and TΨC stem-loop exhibited significant Ψ formation at position 28 and a number of mutants were tested. Substantial base pairing in the ASL stem (3 out of 5 bp) is required, but the sequence of the TΨC loop is not required for modification. When all nucleotides in the ASL stem other than U28 were changed in a single mutant, but base pairing was retained, a near wild-type level of modification was observed

Functionally important structural elements of U12 snRNA

U12 snRNA is analogous to U2 snRNA of the U2-dependent spliceosome and is essential for the splicing of U12-dependent introns in metazoan cells. The essential region of U12 snRNA, which base pairs to the branch site of minor class introns is well characterized. However, other regions which are outside of the branch site base pairing region are not yet characterized and the requirement of these structures in U12-dependent splicing is not clear. U12 snRNA is predicted to form an intricate secondary structure containing several stem–loops and single-stranded regions. Using a previously characterized branch site genetic suppression assay, we generated second-site mutations in the suppressor U12 snRNA to investigate the in vivo requirement of structural elements in U12-dependent splicing. Our results show that stem–loop IIa is essential and required for in vivo splicing. Interestingly, an evolutionarily conserved stem–loop IIb is dispensable for splicing. We also show that stem–loop III, which binds to a p65 RNA binding protein of the U11-U12 di.snRNP complex, is essential for in vivo splicing. The data validate the existence of proposed stem–loops of U12 snRNA and provide experimental support for individual secondary structures

A second base pair interaction between U3 small nucleolar RNA and the 5′-ETS region is required for early cleavage of the yeast pre-ribosomal RNA

In eukaryotes, U3 snoRNA is essential for pre-rRNA maturation. Its 5′-domain was found to form base pair interactions with the 18S and 5′-ETS parts of the pre-rRNA. In Xenopus laevis, two segments of U3 snoRNA form base-pair interactions with the 5′-ETS region and only one of them is essential to the maturation process. In Saccharomyces cerevisiae, two similar U3 snoRNA–5′ ETS interactions are possible; but, the functional importance of only one of them had been tested. Surprisingly, this interaction, which corresponds to the non-essential one in X. laevis, is essential for cell growth and pre-rRNA maturation in yeast. In parallel with [Dutca et al. (2011) The initial U3 snoRNA:pre-rRNA base pairing interaction required for pre-18S rRNA folding revealed by in vivo chemical probing. Nucleic Acids Research, 39, 5164–5180], here we show, that the second possible 11-bp long interaction between the 5′ domain of S. cerevisiae U3 snoRNA and the pre-rRNA 5′-ETS region (helix VI) is also essential for pre-rRNA processing and cell growth. Compensatory mutations in one-half of helix VI fully restored cell growth. Only a partial restoration of growth was obtained upon extension of compensatory mutations to the entire helix VI, suggesting sequence requirement for binding of specific proteins. Accordingly, we got strong evidences for a role of segment VI in the association of proteins Mpp10, Imp4 and Imp3

Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in ribosomal RNAs

How far do H/ACA sRNPs contribute to rRNA pseudouridylation in Archaea was still an open question. Hence here, by computational search in three Pyrococcus genomes, we identified seven H/ACA sRNAs and predicted their target sites in rRNAs. In parallel, we experimentally identified 17 Ψ residues in P. abyssi rRNAs. By in vitro reconstitution of H/ACA sRNPs, we assigned 15 out of the 17 Ψ residues to the 7 identified H/ACA sRNAs: one H/ACA motif can guide up to three distinct pseudouridylations. Interestingly, by using a 23S rRNA fragment as the substrate, one of the two remaining Ψ residues could be formed in vitro by the aCBF5/aNOP10/aGAR1 complex without guide sRNA. Our results shed light on structural constraints in archaeal H/ACA sRNPs: the length of helix H2 is of 5 or 6 bps, the distance between the ANA motif and the targeted U residue is of 14 or 15 nts, and the stability of the interaction formed by the substrate rRNA and the 3′-guide sequence is more important than that formed with the 5′-guide sequence. Surprisingly, we showed that a sRNA–rRNA interaction with the targeted uridine in a single-stranded 5′-UNN-3′ trinucleotide instead of the canonical 5′-UN-3′ dinucleotide is functional

Wikipedia as a trusted method of information assessment during the COVID-19 crisis

International audienceThis chapter describes the coverage of the COVID-19 pandemic on Wikipedia and attempts to examine it in light of the broader media crisis. The analysis of the content, references and discussion pages of the articles appears to indicate that a strict observance of the encyclopaedia’s rules regarding information quality allowed a precise and robust description of the events. The chapter also investigates the media and community discourse around this coverage. It illustrates how this crisis reinforced the framing of Wikipedia as a trusted method to deal with information and a method which presents a strong potential for the development of information literacies

Historic Graphs : Cartographie dynamique des liens sur Wikipédia

International audienceThis paper investigates the evolution of the hypertext links that connect articles on Wikipedia’s online encyclopedia. We aim to use the data stored in the articles’ revision history to build dynamic maps, displaying the changes in link structures over time. We present Historic Graphs, a dedicated tool and describe it use through a few case studies. We then discuss the interpretation of such maps, and how it integrates in a reseach process.Cet article propose d’étudier l‘évolution des liens hypertextes qui interconnectent les articles de l’encyclopédie en ligne Wikipédia. Il s’agit d’exploiter les données stockées dans les historiques des versions des articles pour dresser des cartes dynamiques de la structure des liens au cours du temps. Nous présentons Historic Graphs, un outil dédié, puis décrivons son usage à travers quelques cas d’étude. Nous discutons ensuite l’interprétation de ces cartes dynamiques et leur intégration dans une démarche de recherche complète

Crisis communication in a post-nuclear accident phase : knowledge organisation and sharing on the Web

Les accidents nucléaires majeurs constituent des crises à grande échelle, susceptibles de contaminer de large territoires pour des décennies. Les habitants de ces territoires doivent alors acquérir de nouvelles connaissances et adapter leur mode de vie pour limiter l'impact sanitaire et sociétal des radiations. Si la France a développé un plan de gestion d'une telle situation, les stratégies de communication proposées laissent peu de place au dialogue entre les autorités et les citoyens ainsi qu'aux usages du Web social. Cette thèse s'inscrit dans le cadre du projet de recherche SCOPANUM (Stratégies de COmmunication de crise en gestion Post-Accident NUcléaire via les Médias Sociaux) soutenu par le CSFRS (Conseil Supérieur Pour la Formation et la Recherche Stratégique). Elle vise à examiner le potentiel des technologies de l'information et de la communication pour la mise en œuvre d'une communication de crise plus adaptée aux situations post-accidentelles nucléaires. Après l'accident nucléaire de Fukushima Daiichi, les mesures de la radioactivité ont fait l'objet de pratiques collaboratives de collecte et d’agrégation s’appuyant sur les médias sociaux. L'étude des usages de Twitter a révélé que les modalités de diffusion de ces mesures ne sont pas adaptées aux spécificités de la situation post-accidentelle nucléaire. Sur la base de ces résultats, nous avons proposé des recommandations et un prototype d'outil logiciel pour favoriser la réutilisabilité de mesures de la radioactivité ainsi partagées. Nos travaux portent également sur les connaissances pratiques susceptibles d'aider les personnes à adapter leur quotidien à la vie dans les territoires contaminés par un accident nucléaire. Plusieurs méthodes sont présentées pour faciliter l'identification de ces connaissances et leur représentation formelle à l'aide des technologies du Web Sémantique. À partir de ces modèles, nous décrivons la conception et l'évaluation d'une application web, Ginkgo, visant à faciliter l'appropriation et le partage des connaissances en matière de radioprotection.Major nuclear accidents generate large scale crisis that may contaminate wide areas for decades. The inhabitants of these areas must then gain new knowledge and adapt their lifestyle to limit the health and social consequences of radioactivity. France developed a procedures to manage such a situation, but the communication stragies presented do not fully support neither dialogue between authorities and citizen nor the use of social Web tools. This thesis was part of the SCOPANUM (Stratégies de COmmunication de crise en gestion Post-Accident NUcléaire via les Médias Sociaux) research project, backed by a grant from CSFRS (Conseil Supérieur Pour la Formation et la Recherche Stratégique). It aims to assess the benefits of information-communication technologies to develop more suitable crisis communication strategies for post-nuclear-accident situations. After the Fukushima Daiichi nuclear disaster, collaborative practices have emerged to collect and aggregate radiation measurements thanks to social media. The analysis of Twitter uses revealed that the diffusion of these measurements is not well adapted to the post-nuclear-accident situation. We developed a set of guidelines and a software prototype to support the re-usability of the radiation measurements that are shared on social media. Our work also focused on the practical knowledge that may help people to adapt their life in the contaminated areas. We presented several methods to support the identification and the formal representation of this knowledge using Semantic Web technologies. From these models, we built and tested Ginkgo, a mobile web application designed to support knowledge sharing and appropriation

Radiation Measurements Sharing Online

International audienc