Microarray-Based Sketches of the HERV Transcriptome Landscape

Human endogenous retroviruses (HERVs) are spread throughout the genome and their long terminal repeats (LTRs) constitute a wide collection of putative regulatory sequences. Phylogenetic similarities and the profusion of integration sites, two inherent characteristics of transposable elements, make it difficult to study individual locus expression in a large-scale approach, and historically apart from some placental and testis-regulated elements, it was generally accepted that HERVs are silent due to epigenetic control. Herein, we have introduced a generic method aiming to optimally characterize individual loci associated with 25-mer probes by minimizing cross-hybridization risks. We therefore set up a microarray dedicated to a collection of 5,573 HERVs that can reasonably be assigned to a unique genomic position. We obtained a first view of the HERV transcriptome by using a composite panel of 40 normal and 39 tumor samples. The experiment showed that almost one third of the HERV repertoire is indeed transcribed. The HERV transcriptome follows tropism rules, is sensitive to the state of differentiation and, unexpectedly, seems not to correlate with the age of the HERV families. The probeset definition within the U3 and U5 regions was used to assign a function to some LTRs (i.e. promoter or polyA) and revealed that (i) autonomous active LTRs are broadly subjected to operational determinism (ii) the cellular gene density is substantially higher in the surrounding environment of active LTRs compared to silent LTRs and (iii) the configuration of neighboring cellular genes differs between active and silent LTRs, showing an approximately 8 kb zone upstream of promoter LTRs characterized by a drastic reduction in sense cellular genes. These gathered observations are discussed in terms of virus/host adaptive strategies, and together with the methods and tools developed for this purpose, this work paves the way for further HERV transcriptome projects

High Resolution Genome-Wide Analysis of Chromosomal Alterations in Burkitt's Lymphoma

Additional chromosomal abnormalities are currently detected in Burkitt's lymphoma. They play major roles in the progression of BL and in prognosis. The genes involved remain elusive. A whole-genome oligonucleotide array CGH analysis correlated with karyotype and FISH was performed in a set of 27 Burkitt's lymphoma-derived cell lines and primary tumors. More than half of the 145 CNAs<2 Mb were mapped to Mendelian CNVs, including GSTT1, glutathione s-transferase and BIRC6, an anti-apoptotic protein, possibly predisposing to some cancers. Somatic cell line-specific CNVs localized to the IG locus were consistently observed with the 244 K aCGH platform. Among 136 CNAs >2 Mb, gains were found in 1q (12/27), 13q (7/27), 7q (6/27), 8q(4/27), 2p (3/27), 11q (2/27) and 15q (2/27). Losses were found in 3p (5/27), 4p (4/27), 4q (4/27), 9p (4/27), 13q (4/27), 6p (3/27), 17p (3/27), 6q (2/27),11pterp13 (2/27) and 14q12q21.3 (2/27). Twenty one minimal critical regions (MCR), (range 0.04–71.36 Mb), were delineated in tumors and cell lines. Three MCRs were localized to 1q. The proximal one was mapped to 1q21.1q25.2 with a 6.3 Mb amplicon (1q21.1q21.3) harboring BCA2 and PIAS3. In the other 2 MCRs, 1q32.1 and 1q44, MDM4 and AKT3 appeared as possible drivers of these gains respectively. The 13q31.3q32.1 <89.58–96.81> MCR contained an amplicon and ABCC4 might be the driver of this amplicon. The 40 Kb 2p16.1 <60.96–61> MCR was the smallest gained MCR and specifically encompassed the REL oncogene which is already implicated in B cell lymphomas. The most frequently deleted MCR was 3p14.1 <60.43–60.53> that removed the fifth exon of FHIT. Further investigations which combined gene expression and functional studies are essential to understand the lymphomagenesis mechanism and for the development of more effective, targeted therapeutic strategies

Astrovirus Diagnostics

Various methods exist to detect an astrovirus infection. Current methods include electron microscopy (EM), cell culture, immunoassays, polymerase chain reaction (PCR) and various other molecular approaches that can be applied in the context of diagnostic or in surveillance studies. With the advent of metagenomics, novel human astrovirus (HAstV) strains have been found in immunocompromised individuals in association with central nervous system (CNS) infections. This work reviews the past and current methods for astrovirus detection and their uses in both research laboratories and for medical diagnostic purposes

Astrovirus Diagnostics

Various methods exist to detect an astrovirus infection. Current methods include electron microscopy (EM), cell culture, immunoassays, polymerase chain reaction (PCR) and various other molecular approaches that can be applied in the context of diagnostic or in surveillance studies. With the advent of metagenomics, novel human astrovirus (HAstV) strains have been found in immunocompromised individuals in association with central nervous system (CNS) infections. This work reviews the past and current methods for astrovirus detection and their uses in both research laboratories and for medical diagnostic purposes

From Viruses to Genes: Syncytins

International audienceThe content of 5–90 million years old retroviruses and even older retrotransposons of animal genomes and the wide variety of modern retroviruses infecting the same range of species suggest that these elements can be assimilated to shuttle across evolution. A snapshot taken a few decades ago showed us the capture of cellular proto-oncogenes by infectious elements, representing the dark side of the communication between the worlds of viruses and animals. Another snapshot we took more recently shows multiple captures by animal genomes of envelope genes originating from infectious retroviruses, illustrating a phenomenon of convergent evolution. This could be seen as the bright side of these relations as those envelopes were shown to be involved in the earlier steps of human development, i.e. fusion of placental syncytiotrophoblastic layer, therefore they were dubbed Syncytins. Sequencing of more and more animal genomes allowed comparative genomic analyses that revealed how these envelopes have been domesticated in human, mouse, goat, rabbit, etc. More generally, we illustrate in this chapter how close are the viral and animal genome worlds and, focusing mainly on the hominoid ERVWE1 locus encoding Synctin-1, how the different proviruses encoding Syncytins have been domesticated to achieve placental functions. Influence of the chromosomal integration context, the epigenetic control and the splicing strategy upon transcription, and protein maturation processes as well will be discussed in order to illustrate what makes these nowadays genes different from their ancestral infectious counterpart. The price to pay for this beneficial invasion will be illustrated by the possible implications of Syncytin-1 in a wide range of diseases. Last, the apparent stringency of placental regulation will await to be challenged as regard to the evidence of expression in other physiological fusogenic contexts such as myoblasts and osteoclasts

Vulnérabilité des chênaies de la région Centre Val De Loire au changement de climat -C 4 Rapport de fin de projet

La probabilité est forte pour que les chênaies de la région Centre Val de Loire soient dans les prochaines décades le sujet, à la fois, de dépérissements marqués et d’un manque de régénération permettant le renouvellement des peuplements. Sur le dispositif OPTMix (Oak Pine Tree Mixture, https://optmix.inrae.fr/), environ un tiers des chênes (Q. petraea) sont dépérissants, à des degrés divers en 2021. La première variable affectée par ces dépérissements est la croissance, notamment en épaisseur. La deuxième variable est la surface foliaire, réduite d’environ un tiers. Ces réductions résultent notamment des fortes contraintes hydrique et thermique subies durant les années 2018 à 2020. La durée de la contrainte hydrique (nombre de jours sur la période de croissance), plus que son intensité, est un facteur déterminant des dépérissements observés. Par ailleurs, la proportion de chênes dépérissants est plus élevée dans les peuplements les moins denses. Cet effet résulte sans doute des plus fortes contraintes hydrique et thermique subies par la couronne des arbres dans ces peuplements ouverts, le microclimat y étant moins tamponné. Les arbres dépérissants en 2021 ont tous eu une croissance réduite dans le passé, et ce quelle que soit l’année considérée (depuis 2014). Cette propriété pourrait être exploitée pour réaliser des éclaircies sans sacrifice sur la base de la croissance passée des chênes. En absence de régulation de la pression d’herbivorie et de la gestion de la végétation interférente, la régénération naturelle de chêne sessile sur les placettes OPTMix ne permettra pas de constituer un stock suffisant pour renouveler ces peuplements dépérissants. Cela réduit considérablement les capacités d’adaptation génétique de ces peuplements aux contraintes du climat

RVDB-prot, a reference viral protein database and its HMM profiles [version 2; peer review: 2 approved]

International audienceWe present RVDB-prot, a database corresponding to the protein equivalent of the nucleic acid reference virus database RVDB. Protein databases can be helpful to perform more sensitive protein sequence comparisons. Similarly to its homologous public repository, RVDB-prot aims to provide reliable and accurately annotated unique entries, while including also an Hidden Markov Model (HMM) protein profiles database for distant protein searching

Impact inattendu de la disponibilité en azote sur les interactions entre Quercus et Deschampsia cespitosa

International audienceEcological theories on species occurrence and interactions between them deeply rely on resources availability. Grasses are known for their ability to preempt belowground resources, especially nitrogen to the detriment of tree seedlings. Objective of the study was to determine how combination in contrasted soil inorganic nitrogen x light availability influence plants in terms of growth and resource acquisition in mixed stand of oak seedling (Quercus petraea) and Deschampsia cespitosa during early phase of mixture growth. We designed a greenhouse experiment testing the Deschampsia effect on oak, grown in pots, alone or as a mixture under two levels of crossed resources, nitrogen (fertilized, N+, or unfertilized pots, N-), and light (shaded, L-, or well-lit pots, L+). Our results showed oak endured competition from grass in all resource combinations except in N-/L-. Light environment increased intensity and importance of competition on oak. Unexpectedly Deschampsia was facilitated by oak in N+ pot. A higher root biomass, length, SRL, and lower root diameter confer to Deschampsia better prospection and capitation capacities, allowing it to take 96.6% of a source of 15N labeled inorganic nitrogen up. No root plasticity concordant with the foraging theory was observed. Why was Deschampsia facilitated by oak when nitrogen was not limiting is an intriguing question. One answer, still needing research, is that a better oak growth, and so production of more exudates, fosters Deschampsia growth. As a result, Deschampsia ability to harvest resources is reinforced. Oak seedling responds through driving the few resources it can collect to storage organs, following a conservative strategy