MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses

International audienceThe development of high-throughput technologies revealed the existence of noncanonical short open reading frames (sORFs) on most eukaryotic ribonucleic acids. They are ubiquitous genetic elements conserved across species and suspected to be involved in numerous cellular processes. MetamORF (https://metamorf.hb.univ-amu.fr/) aims to provide a repository of unique sORFs identified in the human and mouse genomes with both experimental and computational approaches. By gathering publicly available sORF data, normalizing them and summarizing redundant information, we were able to identify a total of 1 162 675 unique sORFs. Despite the usual characterization of ORFs as short, upstream or downstream, there is currently no clear consensus regarding the definition of these categories. Thus, the data have been reprocessed using a normalized nomenclature. MetamORF enables new analyses at locus, gene, transcript and ORF levels, which should offer the possibility to address new questions regarding sORF functions in the future. The repository is available through an user-friendly web interface, allowing easy browsing, visualization, filtering over multiple criteria and export possibilities. sORFs can be searched starting from a gene, a transcript and an ORF ID, looking in a genome area or browsing the whole repository for a species. The database content has also been made available through track hubs at UCSC Genome Browser. Finally, we demonstrate

In Depth Exploration of the Alternative Proteome of Drosophila melanogaster.

Recent studies have shown that hundreds of small proteins were occulted when protein-coding genes were annotated. These proteins, called alternative proteins, have failed to be annotated notably due to the short length of their open reading frame (less than 100 codons) or the enforced rule establishing that messenger RNAs (mRNAs) are monocistronic. Several alternative proteins were shown to be biologically active molecules and seem to be involved in a wide range of biological functions. However, genome-wide exploration of the alternative proteome is still limited to a few species. In the present article, we describe a deep peptidomics workflow which enabled the identification of 401 alternative proteins in Drosophila melanogaster. Subcellular localization, protein domains, and short linear motifs were predicted for 235 of the alternative proteins identified and point toward specific functions of these small proteins. Several alternative proteins had approximated abundances higher than their canonical counterparts, suggesting that these alternative proteins are actually the main products of their corresponding genes. Finally, we observed 14 alternative proteins with developmentally regulated expression patterns and 10 induced upon the heat-shock treatment of embryos, demonstrating stage or stress-specific production of alternative proteins

Toulouse, une métropole méridionale

De la fondation de la cité romaine au XXIe siècle, de Tolosa à Toulouse, la ville de la Garonne a préservé son rôle de métropole régionale. Le Congrès de la Fédération historique de Midi-Pyrénées, tenu en 2008 à l’université de Toulouse-Le Mirail, a réuni plus de 80 intervenants, dont les communications rassemblées apportent dans cet ouvrage l’essentiel des recherches les plus récentes. La première partie porte sur ce qui a fait la force de la ville : la formation de son territoire et son urbanisation, les caractères de sa société, les divers pouvoirs qui y siègent, ses activités économiques, commerciales comme industrielles. Un bilan qui remet en cause bien des idées reçues en montrant la vitalité dont ont fait preuve ses habitants au fil des siècles ! La deuxième partie offre des communications qui se sont attachées à l’activité culturelle dont Toulouse a été un foyer particulièrement actif dans sa longue histoire. Celle-ci a revêtu des formes multiples, parfois inattendues. La religion l’a marquée de son empreinte, longtemps sous l’ascendant de l’Église catholique, avant que la ville ne fasse place à d’autres croyances. Elle s’est affirmée aussi comme un pôle d’élaboration et de transmission du savoir, dans lequel l’université a pris naturellement sa place. Elle a entretenu un goût, et même une passion, pour la littérature, la musique, les arts plastiques, autant d’expressions qui ont contribué à modeler la personnalité de la « ville rose »