Workflow-BS an integrative workflow for RRBS and WGBS data. From the BS-seq to the DMR

Workflow-BS an integrative workflow for RRBS and WGBS data. From the BS-seq to the DMR. NGS'16 Genome Annotatio

Séquençage De Novo du transcriptome de la fourmi Tetramorium bicarinatum

International audienceBackground: Arthropod venoms are invaluable sources of bioactive substances with biotechnological application. The limited availability of some venoms, such as those from ants, has restricted the knowledge about the composition and the potential that these biomolecules could represent. In order to provide a global insight on the transcripts expressed in the venom gland of the Brazilian ant species Tetramorium bicarinatum and to unveil the potential of its products, high-throughput approach using Illumina technology has been applied to analyze the genes expressed in active venom glands of this ant species

An expanded protein-protein interaction network in Bacillus subtilis reveals a group of hubs: Exploration by an integrative approach

We have generated a protein-protein interaction network in Bacillus subtilis focused on several essential cellular processes such as cell division, cell responses to various stresses, the bacterial cytoskeleton, DNA replication and chromosome maintenance by careful application of the yeast two-hybrid approach. This network, composed of 793 interactions linking 287 proteins with an average connectivity of five interactions per protein, represents a valuable resource for future functional analyses. A striking feature of the network is a group of highly connected hubs (GoH) linking many different cellular processes. Most of the proteins of the GoH have unknown functions and are associated to the membrane. By the integration of available knowledge, in particular of transcriptome data sets, the GoH was decomposed into subgroups of party hubs corresponding to protein complexes or regulatory pathways expressed under different conditions. At a global level, the GoH might function as a very robust group of date hubs having partially redundant functions to integrate information from the different cellular pathways. Our analyses also provide a rational way to study the highly redundant functions of the GoH by a genetic approach

RNAbrowse: RNA-Seq de novo assembly results browser.

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse

Complete Genome Sequence and Annotation of the Staphylococcus aureus Strain HG001

Staphylococcus aureus is an opportunistic Gram-positive pathogen responsible for a wide range of infections from minor skin abscesses to life-threatening diseases. Here, we report the draft genome assembly and current annotation of the HG001 strain, a derivative of the RN1 (NCT8325) strain with restored rbsU (a positive activator of SigB)

Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula.

ancienne clé UT : WOS 000387312400012International audienceThe legume-Rhizobium symbiosis leads to the formation of a new organ, the root nodule, involving coordinated and massive induction of specific genes. Several genes controlling DNA methylation are spatially regulated within the Medicago truncatula nodule, notably the demethylase gene, DEMETER (DME), which is mostly expressed in the differentiation zone. Here, we show that MtDME is essential for nodule development and regulates the expression of 1,425 genes, some of which are critical for plant and bacterial cell differentiation. Bisulphite sequencing coupled to genomic capture enabled the identification of 474 regions that are differentially methylated during nodule development, including nodule-specific cysteine-rich peptide genes. Decreasing DME expression by RNA interference led to hypermethylation and concomitant downregulation of 400 genes, most of them associated with nodule differentiation. Massive reprogramming of gene expression through DNA demethylation is a new epigenetic mechanism controlling a key stage of indeterminate nodule organogenesis during symbiotic interactions

Whole blood transcriptome analysis reveals potential competition in metabolic pathways between negative energy balance and response to inflammatory challenge

Negative Energy Balance (NEB) is considered to increase susceptibility to mastitis. The objective of this study was to improve our understanding of the underlying mechanisms by comparing transcriptomic profiles following NEB and a concomitant mammary inflammation. Accordingly, we performed RNAseq analysis of blood cells in energy-restricted ewes and control-diet ewes at four different time points before and after intra mammary challenge with phlogogenic ligands. Blood leucocytes responded to NEB by shutting down lipid-generating processes, including cholesterol and fatty acid synthesis, probably under transcriptional control of SREBF 1. Furthermore, fatty acid oxidation was activated and glucose oxidation and transport inhibited in response to energy restriction. Among the differentially expressed genes (DEGs) in response to energy restriction, 64 genes were also differential in response to the inflammatory challenge. Opposite response included the activation of cholesterol and fatty acid synthesis during the inflammatory challenge. Moreover, activation of glucose oxidation and transport coupled with the increase of plasma glucose concentration in response to the inflammatory stimuli suggested a preferential utilization of glucose as the energy source during this stress. Leucocyte metabolism therefore undergoes strong metabolic changes during an inflammatory challenge, which could be in competition with those induced by energy restriction

A comparative transcriptomic approach to understanding the formation of cork

International audienceCork oak, Quercus suber, differs from other Mediterranean oaks such as holm oak (Quercus ilex) by the thickness and organization of the external bark. While holm oak outer bark contains sequential periderms interspersed with dead secondary phloem (rhytidome), the cork oak outer bark only contains thick layers of phellem (cork rings) that accumulate until reaching a thickness that allows industrial uses. Here we compare the cork oak outer bark transcriptome with that of holm oak. Both transcriptomes present similitudes in their complexity, but whereas cork oak external bark is enriched with upregulated genes related to suberin, which is the main polymer responsible for the protective function of periderm, the upregulated categories of holm oak are enriched in abiotic stress and chromatin assembly. Concomitantly with the upregulation of suberin-related genes, there is also induction of regulatory and meristematic genes, whose predicted activities agree with the increased number of phellem layers found in the cork oak sample. Further transcript profiling among different cork oak tissues and conditions suggests that cork and wood share many regulatory mechanisms, probably reflecting similar ontogeny. Moreover, the analysis of transcripts accumulation during the cork growth season showed that most regulatory genes are upregulated early in the season when the cork cambium becomes active. Altogether our work provides the first transcriptome comparison between cork oak and holm oak outer bark, which unveils new regulatory candidate genes of phellem development

Bacillus subtilis serine/threonine protein kinase YabT is involved in spore development via phosphorylation of a bacterial recombinase.

We characterized YabT, a serine/threonine kinase of the Hanks family, from Bacillus subtilis. YabT is a putative transmembrane kinase that lacks the canonical extracellular signal receptor domain. We demonstrate that YabT possesses a DNA-binding motif essential for its activation. In vivo YabT is expressed during sporulation and localizes to the asymmetric septum. Cells devoid of YabT sporulate more slowly and exhibit reduced resistance to DNA damage during sporulation. We established that YabT phosphorylates DNA-recombinase RecA at the residue serine 2. A non-phosphorylatable mutant of RecA exhibits the same phenotype as the ΔyabT mutant, and a phosphomimetic mutant of RecA complements ΔyabT, suggesting that YabT acts via RecA phosphorylation in vivo. During spore development, phosphorylation facilitates the formation of transient and mobile RecA foci that exhibit a scanning-like movement associated to the nucleoid in the mother cell. In some cells these foci persist at the end of spore development. We show that persistent RecA foci, which presumably coincide with irreparable lesions, are mutually exclusive with the completion of spore morphogenesis. Our results highlight similarities between the bacterial serine/threonine kinase YabT and eukaryal kinases C-Abl and Mec1, which are also activated by DNA, and phosphorylate proteins involved in DNA damage repair

Analyse du méthylome chez l'embryon de poulet par séquençage haut-débit

Investigating the molecular causes of phenotypic variations observed in farmed species usually involves thestudy of the variability in the DNA sequence. Recently, many studies have described the important role of theenvironment in the regulation of gene expression, particularly through epigenetic mechanisms. In order tocharacterize one of these epigenetic marks in chicken, DNA methylation, we have used 8 embryos (4 males and4 females) from the reciprocal cross of two lines. We developed a bioinformatic analysis pipeline to analyzemethylation marks from high-throughput sequencing. We have observed a lower methylation rate in thepromoter regions than within the genes and intergenic regions. Thanks to the transcriptomic data also availableon these embryos, we have shown that the gene expression level was higher when the promoter regions werepoorly methylated, and vice versa. The possible interaction of the genetic background or sex with themethylation level and the link with expression level in these 8 embryos is being analyzed. These analyses will beextended as part of the ANR ChickStress project, which studies the methylome response to changes intemperature and the use of a low-energy diet in chicken.L'étude des causes moléculaires des variations phénotypiques observées chez les espèces d’élevage passegénéralement par l'analyse de la variabilité de la séquence d’ADN. Récemment, de nombreuses études décriventle rôle important de l’environnement dans la régulation de l’expression des gènes, notamment via desphénomènes épigénétiques. Afin de caractériser une des marques épigénétiques chez le poulet, la méthylation del'ADN, un dispositif de 8 embryons (4 mâles et 4 femelles) issus du croisement réciproque de deux lignées a étéutilisé. À partir d'une technique d'analyse par séquençage à haut-débit des marques de méthylation, un pipelined’analyse bioinformatique a été développé. Un taux de méthylation plus faible dans les régions promotrices quedans les régions géniques et intergéniques a été observé. Grâce aux données transcriptomiques égalementdisponibles sur ces embryons, nous avons confirmé que le niveau d’expression des gènes est plus fort quand lesrégions promotrices sont peu méthylées, et inversement. La possible interaction du fond génétique ou du sexeavec le niveau de méthylation, et son lien avec les niveaux d’expression chez les 8 embryons est en coursd’analyse. Ces analyses vont être étendues dans le cadre du projet ANR ChickStress qui étudie la réponse duméthylome à des variations de température et à l’utilisation d’un aliment de faible valeur énergétique chez lapoule