The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions.

Control of gene transcription relies on concomitant regulation by multiple transcriptional regulators (TRs). However, how recruitment of a myriad of TRs is orchestrated at cis-regulatory modules (CRMs) to account for coregulation of specific biological pathways is only partially understood. Here, we have used mouse liver CRMs involved in regulatory activities of the hepatic TR, NR1H4 (FXR; farnesoid X receptor), as our model system to tackle this question. Using integrative cistromic, epigenomic, transcriptomic, and interactomic analyses, we reveal a logical organization where trans-regulatory modules (TRMs), which consist of subsets of preferentially and coordinately corecruited TRs, assemble into hierarchical combinations at hepatic CRMs. Different combinations of TRMs add to a core TRM, broadly found across the whole landscape of CRMs, to discriminate promoters from enhancers. These combinations also specify distinct sets of CRM differentially organized along the genome and involved in regulation of either housekeeping/cellular maintenance genes or liver-specific functions. In addition to these TRMs which we define as obligatory, we show that facultative TRMs, such as one comprising core circadian TRs, are further recruited to selective subsets of CRMs to modulate their activities. TRMs transcend TR classification into ubiquitous versus liver-identity factors, as well as TR grouping into functional families. Hence, hierarchical superimpositions of obligatory and facultative TRMs bring about independent transcriptional regulatory inputs defining different sets of CRMs with logical connection to regulation of specific gene sets and biological pathways. Altogether, our study reveals novel principles of concerted transcriptional regulation by multiple TRs at CRMs

Immune Response and Mitochondrial Metabolism Are Commonly Deregulated in DMD and Aging Skeletal Muscle

Duchenne Muscular Dystrophy (DMD) is a complex process involving multiple pathways downstream of the primary genetic insult leading to fatal muscle degeneration. Aging muscle is a multifactorial neuromuscular process characterized by impaired muscle regeneration leading to progressive atrophy. We hypothesized that these chronic atrophying situations may share specific myogenic adaptative responses at transcriptional level according to tissue remodeling. Muscle biopsies from four young DMD and four AGED subjects were referred to a group of seven muscle biopsies from young subjects without any neuromuscular disorder and explored through a dedicated expression microarray. We identified 528 differentially expressed genes (out of 2,745 analyzed), of which 328 could be validated by an exhaustive meta-analysis of public microarray datasets referring to DMD and Aging in skeletal muscle. Among the 328 validated co-expressed genes, 50% had the same expression profile in both groups and corresponded to immune/fibrosis responses and mitochondrial metabolism. Generalizing these observed meta-signatures with large compendia of public datasets reinforced our results as they could be also identified in other pathological processes and in diverse physiological conditions. Focusing on the common gene signatures in these two atrophying conditions, we observed enrichment in motifs for candidate transcription factors that may coordinate either the immune/fibrosis responses (ETS1, IRF1, NF1) or the mitochondrial metabolism (ESRRA). Deregulation in their expression could be responsible, at least in part, for the same transcriptome changes initiating the chronic muscle atrophy. This study suggests that distinct pathophysiological processes may share common gene responses and pathways related to specific transcription factors

Anthropisation et introduction d’espèces exogènes : mise en place de l’analyse génétique d’une population invasive de bigorneaux perceurs <I>Ocinebrellus inornatus</I> (Récluz, 1851) dans le bassin de Marennes Oléron

Colloques Union des Océanographes de France "Zones littorales et anthropisation : gestion et nuisances". Miramand P., Guyot T. & Aligner N. (eds.), La Rochelle 4-6 juillet 2000.National audienceBien qu'elles aient existé depuis plusieurs siècles, les invasions biologiques en milieu marin se sontconsidérablement accélérées durant les dernières décennies, suite à l'accroissement du trafic maritime à travers les océans et aux transferts intercontinentaux d'espèces à des fins d'aquaculture. Ainsi, la découverte dans le bassin de Marennes-Oléron d'une nouvelle espèce de bigorneau perceur Ocinebrellus inornatus (Récluz, 1851), originaire du Pacifique asiatique, laisse présager un accroissement des risques de mortalité pour les cheptels cultivés (huître, moule) et pour les ressources de la pêche littorale. Notre premier objectif est avant d'en étudier la dynamique de population d'en définir les caractéristiques génétiques en comparaison de celles de l'espèce indigène Ocenebra erinacea (Linné, 1758). Nous avons d'ores et déjà, mis en évidence des marqueurs nucléaires, spécifiques des populations atlantiques des deux espèces afin d'identifier avec certitude les juvéniles et d'analyser sans ambiguïté le profil démographique des cohortes envahissantes

Enterocytic Differentiation of cultured human colon cancer cells by replacement of glucose by galactose in the medium

International audienc

Recent invasion of the Japanese oyster drill along the French Atlantic coast: identification of specific molecular markers that differentiate Japanese, <I>Ocinebrellus inornatus</I>, and European, <I>Ocenebra erinacea</I>, oyster drills

International audienceThe direct amplification of length polymorphism technique (DALP) has been used to distinguish species-specific banding patterns in two marine gastropod oyster drills Ocenebra erinacea (Linnaeus, 1758) and Ocinebrellus inornatus (Récluz, 1851). Ocenebra erinacea is the European oyster drill, common along all European coasts. Ocinebrellus inornatus, the Japanese oyster drill, was recorded in oyster growing areas of the Marennes-Oléron Bay (SW France) for the first time in 1995. This new biological invasion could lead to an increase, which must be evaluated, in the predation risk for cultivated species i.e. oysters and blue mussels, and for littoral fishing resources along the French Atlantic coasts. As a result, since specific identification of early life stages of both species (egg capsules and juveniles) was previously found to be both difficult and unsure using only morphological criteria, four Ocenebra erinacea and two Ocinebrellus inornatus specific molecular markers were identified and sequenced. These markers will facilitate the assessment of respective ecological impacts (reproductive patterns, abundance and spatial distribution of juveniles), resulting from the exotic species versus the native species and will allow us to analyse with certainty demographic profiles of the two oyster drill populations

An extended transcription factor regulatory network controls hepatocyte identity

Cell identity is specified by a core transcriptional regulatory circuitry (CoRC), typically limited to a small set of interconnected cell-specific transcription factors (TFs). By mining global hepatic TF regulons, we reveal a more complex organization of the transcriptional regulatory network controlling hepatocyte identity. We show that tight functional interconnections controlling hepatocyte identity extend to non-cell-specific TFs beyond the CoRC, which we call hepatocyte identity (Hep-ID) CONNECT TFs. Besides controlling identity effector genes, Hep-ID CONNECT TFs also engage in reciprocal transcriptional regulation with TFs of the CoRC. In homeostatic basal conditions, this translates into Hep-ID CONNECT TFs being involved in fine tuning CoRC TF expression including their rhythmic expression patterns. Moreover, a role for Hep-ID CONNECT TFs in the control of hepatocyte identity is revealed in dedifferentiated hepatocytes where Hep-ID CONNECT TFs are able to reset CoRC TF expression. This is observed upon activation of NR1H3 or THRB in hepatocarcinoma or in hepatocytes subjected to inflammationinduced loss of identity. Our study establishes that hepatocyte identity is controlled by an extended array of TFs beyond the CoRC

Functional assessment of creatine transporter in control and X-linked SLC6A8-deficient fibroblasts

International audienceCreatine transporter is currently the focus of renewed interest with emerging roles in brain neurotransmission and physiology, and the bioenergetics of cancer metastases. We here report on amendments of a standard creatine uptake assay which might help clinical chemistry laboratories to extend their current range of measurements of creatine and metabolites in body fluids to functional enzyme explorations. In this respect, short incubation times and the use of a stable-isotope-labeled substrate (D-3-creatine) preceded by a creatine wash-out step from cultured fibroblast cells by removal of fetal bovine serum (rich in creatine) from the incubation medium are recommended. Together, these measures decreased, by a first order of magnitude, creatine concentrations in the incubation medium at the start of creatine-uptake studies and allowed to functionally discriminate between 4 hemizygous male and 4 heterozygous female patients with X-linked SLC6A8 deficiency, and between this cohort of eight patients and controls. The functional assay corroborated genetic diagnosis of SLC6A8 deficiency. Gene anomalies in our small cohort included splicing site (c.912G \textgreater A [p.Ile260_Gln304del], c.778-2A \textgreater G and c.1495 + 2 T \textgreater G), substitution (c.407C \textgreater T) [p.Ala136Val] and deletion (c.635\₆36delAG [p.Glu212Valfs*84] and c.1324delC [p.Gln442Lysfs*21]) variants with reduced creatine transporter function validating their pathogenicity, including that of a previously unreported c.1324delC variant. The present assay adaptations provide an easy, reliable and discriminative manner for exploring creatine transporter activity and disease variations. It might apply to drug testing or other evaluations in the genetic and metabolic horizons covered by the emerging functions of creatine and its transporter, in a way, however, requiring and completed by additional studies on female patients and blood-brain barrier permeability properties of selected compounds. As a whole, the proposed assay of creatine transporter positively adds to currently existing measurements of this transporter activity, and determining on a large scale the extent of its exact suitability to detect female patients should condition in the future its transfer in clinical practice