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International audience; Si les données constituent l’un des principaux actifs immatériels des entreprises, la légalité du processus de collecte automatisée est un préalable indispensable pour pouvoir valoriser ultérieurement ce patrimoine informationnel.Version complète:https://seraphin.legal/droit-des-donnees-comment-scraper-des-donnees-dans-la-legalite/

Motivation Long-read sequencing technologies are invaluable for determining complex RNA transcript architectures but are error-prone. Numerous ‘hybrid correction’ algorithms have been developed for genomic data that correct long reads by exploiting the accuracy and depth of short reads sequenced from the same sample. These algorithms are not suited for correcting more complex transcriptome sequencing data. Results We have created a novel reference-free algorithm called Transcript-level Aware Long-Read Correction (TALC) which models changes in RNA expression and isoform representation in a weighted De Bruijn graph to correct long reads from transcriptome studies. We show that transcript-level aware correction by TALC improves the accuracy of the whole spectrum of downstream RNA-seq applications and is thus necessary for transcriptome analyses that use long read technology. Availability and implementation TALC is implemented in C++ and available at https://github.com/lbroseus/TALC. Supplementary information Supplementary data are available at Bioinformatics online.

MotivationLong-read sequencing technologies are invaluable for determining complex RNA transcript architectures but are error-prone. Numerous “hybrid correction” algorithms have been developed for genomic data that correct long reads by exploiting the accuracy and depth of short reads sequenced from the same sample. These algorithms are not suited for correcting more complex transcriptome sequencing data.ResultsWe have created a novel reference-free algorithm called TALC (Transcription Aware Long Read Correction) which models changes in RNA expression and isoform representation in a weighted De-Bruijn graph to correct long reads from transcriptome studies. We show that transcription aware correction by TALC improves the accuracy of the whole spectrum of downstream RNA-seq applications and is thus necessary for transcriptome analyses that use long read technology.Availability and ImplementationTALC is implemented in C++ and available athttps://gitlab.igh.cnrs.fr/lbroseus/TALC.Contactwilliam.ritchie@igh.cnrs.fr

Comparative analysis of high throughput sequencing data between multiple conditions often involves mapping of sequencing reads to a reference and downstream bioinformatics analyses. Both of these steps may introduce heavy bias and potential data loss. This is especially true in studies where patient transcriptomes or genomes may vary from their references, such as in cancer. Here we describe a novel approach and associated software that makes use of advances in genetic algorithms and feature selection to comprehensively explore massive volumes of sequencing data to classify and discover new sequences of interest without a mapping step and without intensive use of specialized bioinformatics pipelines. We demonstrate that our approach called GECKO for GEnetic Classification using k-mer Optimization is effective at classifying and extracting meaningful sequences from multiple types of sequencing approaches including mRNA, microRNA, and DNA methylome data., Aubin Thomas, Sylvain Barriere et al. present a computational method for classifying and extracting meaningful sequences from high-throughput sequencing data. The method, called GECKO, uses k-mer counts that are able to classify the input data with high accuracy.

En juin 2014, la DILA ( Direction de l'information légale et administrative des services du Premier ministre) ouvrait des données juridiques. Cette démarche a suscité l'émergence d'une communauté Open Law autour des données juridiques ouvertes afin de favoriser l'innovation collaborative entre les acteurs de l'Open Data et les professionnels publics et privés de l'information juridique.

Le cadre juridique des données numériques est essentiellement constitué d'obligationss: obligations déclaratives liées au traitement des données personnelles, obligations d'acheminement des données, obligations de conservation et de communication des données pour le compte des autorités judiciaires et même, parfois, obligations de mise à disposition des données publiques. Au niveau des droits, la capacité juridique à réutiliser, à agréger et à valoriser les gisements de données détenues ou produites fait débat. L'universalité des données détenues et produites par une personne physique ou morale constitue un patrimoine numérique, composante de son patrimoine immatériel. Il s'agit d'un ensemble de droits et de devoirs, d'actifs et de passifs, en mutation permanente en fonction des événements juridiques de la vie numérique d'une donnée. Pour recenser son actif numérique à un instant donné et déterminer sa capacité à valoriser les données, il faut pouvoir connaître précisément le passif, principalement constitué des droits concurrents des tiers. Pour les données collectées sur le réseau, c'est la problématique des droits concurrents de l'ensemble des acteurs de la chaîne numérique qui se pose. La problématique des données personnelles se situe au carrefour des possibles. Les possibilités d'agrégation et la granularité admise pour les croiser avec l'ensemble des autres ressources disponibles en interne ou en externe soulèvent des questions juridiques pour lesquelles le droit ne propose pas aa priori de réponses immédiatement applicables. Pour définir le champ des possibles, il faut déterminer le régime juridique des données à partir du droit existant, en dégageant un ensemble de critères de qualification. Pour chaque donnée, le régime juridique applicable peut être synthétisé autour des droits d'usage, des droits d'exploitation et des obligations de conservation sur ce patrimoine informationnel numérique. À partir de cette catégorisation juridique des données, il faut recenser des variables qui déterminent les règles de changement de régime et de reconnaissance de droits des tiers.

Polycomb group proteins form two main complexes, PRC2 and PRC1, which generally coregulate their target genes. Here we show that PRC1 components act as neoplastic tumor suppressors independently of PRC2 function. By mapping the distribution of PRC1 components and trimethylation of histone H3 at Lys27 (H3K27me3) across the genome, we identify a large set of genes that acquire PRC1 in the absence of H3K27me3 in Drosophila larval tissues. These genes massively outnumber canonical targets and are mainly involved in the regulation of cell proliferation, signaling and polarity. Alterations in PRC1 components specifically deregulate this set of genes, whereas canonical targets are derepressed in both PRC1 and PRC2 mutants. In human embryonic stem cells, PRC1 components colocalize with H3K27me3 as in Drosophila embryos, whereas in differentiated cell types they are selectively recruited to a large set of proliferation and signaling-associated genes that lack H3K27me3, suggesting that the redeployment of PRC1 components during development is evolutionarily conserved.

International audience; Les décisions de justice, ou juridictionnelles, s’entendent comme l’ensemble des jugements, ordonnances et arrêts rendus par les juridictions judiciaires et administratives.En France, suite à une saisine du ministère de la Justice, le régime juridique de la décision de Justice a été précisé par un avis n° 20103040-AL de la CADA du 28 juillet 2010.La commission considère que les décisions juridictionnelles prononcées publiquement sont constituées d’informations publiques au sens de l’article 10 de la loi du 17 juillet1978La commission considère que les décisions juridictionnelles qui ne sont pas prononcées publiquement ne sont pas constituées d’informations publiques, sauf dans 2 hypothèses :• Les décisions anonymisées qui ont fait l’objet d’une diffusion publique (notammentsur Légifrance.fr)• Les décisions comprenant des données personnelles à l’expiration d’un délai de 75 ansà compter de leur élaboration ou de 25 ans à compter du décès de l’intéressé Le caractère public ou non de la décision et la nature du contentieux sont donc des premiers critères à prendre pour déterminer le statut juridique de la décision. A priori, les décisions de Justice prononcées publiquement sont donc constituées de donnéesqui répondent à plusieurs qualifications juridiques : - Des données personnelles ( nom et adresse des parties et des témoins par exemple)- Des données individuelles : il s’agit de données propres au comportement d’unepersonne susceptible de permettre son identification par recoupement, y compris aprèsanonymisation de la décision (nom de l’employeur, éléments de vie privée comprisdans les faits…)- Des informations publiques

Summary: Metazoan genomes are partitioned into modular chromosomal domains containing active or repressive chromatin. In flies, Polycomb group (PcG) response elements (PREs) recruit PHO and other DNA-binding factors and act as nucleation sites for the formation of Polycomb repressive domains. The sequence specificity of PREs is not well understood. Here, we use comparative epigenomics and transgenic assays to show that Drosophila domain organization and PRE specification are evolutionarily conserved despite significant cis-element divergence within Polycomb domains, whereas cis-element evolution is strongly correlated with transcription factor binding divergence outside of Polycomb domains. Cooperative interactions of PcG complexes and their recruiting factor PHO stabilize PHO recruitment to low-specificity sequences. Consistently, PHO recruitment to sites within Polycomb domains is stabilized by PRC1. These data suggest that cooperative rather than hierarchical interactions among low-affinity sequences, DNA-binding factors, and the Polycomb machinery are giving rise to specific and strongly conserved 3D structures in Drosophila. : Schuettengruber et al. present an extensive comparative epigenomics data set, providing new insights into cis-driven versus buffered evolution of Polycomb recruitment and Polycomb domain specificity. Using chromatin immunoprecipitation sequencing and transgenic assays, they demonstrate an extremely high conservation of Polycomb repressive domains in five Drosophila species. Using Hi-C and knockout experiments, they challenge the standard hierarchical Polycomb recruitment model and demonstrate that cooperative rather than hierarchical interactions among DNA motifs, transcription factors, and Polycomb group complexes define Polycomb domains.

Polycomb group (PcG) proteins dynamically define cellular identities through epigenetic repression of key developmental genes. PcG target gene repression can be stabilized through the interaction in the nucleus at PcG foci. Here, we report the results of a high-resolution microscopy genome-wide RNAi screen that identifies 129 genes that regulate the nuclear organization of Pc foci. Candidate genes include PcG components and chromatin factors, as well as many protein-modifying enzymes, including components of the SUMOylation pathway. In the absence of SUMO, Pc foci coagulate into larger aggregates. Conversely, loss of function of the SUMO peptidase Velo disperses Pc foci. Moreover, SUMO and Velo colocalize with PcG proteins at PREs, and Pc SUMOylation affects its chromatin targeting, suggesting that the dynamic regulation of Pc SUMOylation regulates PcG-mediated silencing by modulating the kinetics of Pc binding to chromatin as well as its ability to form Polycomb foci.

Topoisomerase I (Top1) is a key enzyme in functioning at the interface between DNA replication, transcription and mRNA maturation. Here, we show that Top1 suppresses genomic instability in mammalian cells by preventing a conflict between transcription and DNA replication. Using DNA combing and ChIP (chromatin immunoprecipitation)-on-chip, we found that Top1-deficient cells accumulate stalled replication forks and chromosome breaks in S phase, and that breaks occur preferentially at gene-rich regions of the genome. Notably, these phenotypes were suppressed by preventing the formation of RNA-DNA hybrids (R-loops) during transcription. Moreover, these defects could be mimicked by depletion of the splicing factor ASF/SF2 (alternative splicing factor/splicing factor 2), which interacts functionally with Top1. Taken together, these data indicate that Top1 prevents replication fork collapse by suppressing the formation of R-loops in an ASF/SF2-dependent manner. We propose that interference between replication and transcription represents a major source of spontaneous replication stress, which could drive genomic instability during the early stages of tumorigenesis.

Maintenance of genome integrity relies on surveillance mechanisms that detect and signal arrested replication forks. Although evidence from budding yeast indicates that the DNA replication checkpoint (DRC) is primarily activated by single-stranded DNA (ssDNA), studies in higher eukaryotes have implicated primer ends in this process. To identify factors that signal primed ssDNA in Saccharomyces cerevisiae, we have screened a collection of checkpoint mutants for their ability to activate the DRC, using the repression of late origins as readout for checkpoint activity. This quantitative analysis reveals that neither RFC(Rad24) and the 9-1-1 clamp nor the alternative clamp loader RFC(Elg1) is required to signal paused forks. In contrast, we found that RFC(Ctf18) is essential for the Mrc1-dependent activation of Rad53 and for the maintenance of paused forks. These data identify RFC(Ctf18) as a key DRC mediator, potentially bridging Mrc1 and primed ssDNA to signal paused forks.

International audience