Differentiation of the human PAX7-positive myogenic precursors/satellite cell lineage in vitro.

Satellite cells (SC) are muscle stem cells that can regenerate adult muscles upon injury. Most SC originate from PAX7+ myogenic precursors set aside during development. Although myogenesis has been studied in mouse and chicken embryos, little is known about human muscle development. Here, we report the generation of human induced pluripotent stem cell (iPSC) reporter lines in which fluorescent proteins have been introduced into the PAX7 and MYOG loci. We use single cell RNA sequencing to analyze the developmental trajectory of the iPSC-derived PAX7+ myogenic precursors. We show that the PAX7+ cells generated in culture can produce myofibers and self-renew in vitro and in vivo Together, we demonstrate that cells exhibiting characteristics of human fetal satellite cells can be produced in vitro from iPSC, opening interesting avenues for muscular dystrophy cell therapy. This work provides significant insights into the development of the human myogenic lineage.

TAF8 regions important for TFIID lobe B assembly or for TAF2 interactions are required for embryonic stem cell survival.

The human general transcription factor TFIID is composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). In eukaryotic cells, TFIID is thought to nucleate RNA polymerase II (Pol II) preinitiation complex formation on all protein coding gene promoters and thus, be crucial for Pol II transcription. TFIID is composed of three lobes, named A, B, and C. A 5TAF core complex can be assembled in vitro constituting a building block for the further assembly of either lobe A or B in TFIID. Structural studies showed that TAF8 forms a histone fold pair with TAF10 in lobe B and participates in connecting lobe B to lobe C. To better understand the role of TAF8 in TFIID, we have investigated the requirement of the different regions of TAF8 for the in vitro assembly of lobe B and C and the importance of certain TAF8 regions for mouse embryonic stem cell (ESC) viability. We have identified a region of TAF8 distinct from the histone fold domain important for assembling with the 5TAF core complex in lobe B. We also delineated four more regions of TAF8 each individually required for interacting with TAF2 in lobe C. Moreover, CRISPR/Cas9-mediated gene editing indicated that the 5TAF core-interacting TAF8 domain and the proline-rich domain of TAF8 that interacts with TAF2 are both required for mouse embryonic stem cell survival. Thus, our study defines distinct TAF8 regions involved in connecting TFIID lobe B to lobe C that appear crucial for TFIID function and consequent ESC survival.

Recapitulating early development of mouse musculoskeletal precursors of the paraxial mesoderm in vitro.

Body skeletal muscles derive from the paraxial mesoderm, which forms in the posterior region of the embryo. Using microarrays, we characterize novel mouse presomitic mesoderm (PSM) markers and show that, unlike the abrupt transcriptome reorganization of the PSM, neural tube differentiation is accompanied by progressive transcriptome changes. The early paraxial mesoderm differentiation stages can be efficiently recapitulated in vitro using mouse and human pluripotent stem cells. While Wnt activation alone can induce posterior PSM markers, acquisition of a committed PSM fate and efficient differentiation into anterior PSM Pax3+ identity further requires BMP inhibition to prevent progenitors from drifting to a lateral plate mesoderm fate. When transplanted into injured adult muscle, these precursors generated large numbers of immature muscle fibers. Furthermore, exposing these mouse PSM-like cells to a brief FGF inhibition step followed by culture in horse serum-containing medium allows efficient recapitulation of the myogenic program to generate myotubes and associated Pax7+ cells. This protocol results in improved in vitro differentiation and maturation of mouse muscle fibers over serum-free protocols and enables the study of myogenic cell fusion and satellite cell differentiation.

Homozygous TAF8 mutation in a patient with intellectual disability results in undetectable TAF8 protein, but preserved RNA polymerase II transcription.

The human general transcription factor TFIID is composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). In eukaryotic cells, TFIID is thought to nucleate RNA polymerase II (Pol II) preinitiation complex formation on all protein coding gene promoters and thus, be crucial for Pol II transcription. In a child with intellectual disability, mild microcephaly, corpus callosum agenesis and poor growth, we identified a homozygous splice-site mutation in TAF8 (NM_138572.2: c.781-1G > A). Our data indicate that the patient's mutation generates a frame shift and an unstable TAF8 mutant protein with an unrelated C-terminus. The mutant TAF8 protein could not be detected in extracts from the patient's fibroblasts, indicating a loss of TAF8 function and that the mutation is most likely causative. Moreover, our immunoprecipitation and proteomic analyses show that in patient cells only partial TAF complexes exist and that the formation of the canonical TFIID is impaired. In contrast, loss of TAF8 in mouse embryonic stem cells and blastocysts leads to cell death and to a global decrease in Pol II transcription. Astonishingly however, in human TAF8 patient cells, we could not detect any cellular phenotype, significant changes in genome-wide Pol II occupancy and pre-mRNA transcription. Thus, the disorganization of the essential holo-TFIID complex did not affect global Pol II transcription in the patient's fibroblasts. Our observations further suggest that partial TAF complexes, and/or an altered TFIID containing a mutated TAF8, could support human development and thus, the absence of holo-TFIID is less deleterious for transcription than originally predicted.

Convergent Signaling Pathways Controlled by LRP1 (Receptor-related Protein 1) Cytoplasmic and Extracellular Domains Limit Cellular Cholesterol Accumulation.

The low density lipoprotein receptor-related protein 1 (LRP1) is a ubiquitously expressed cell surface receptor that protects from intracellular cholesterol accumulation. However, the underlying mechanisms are unknown. Here we show that the extracellular (α) chain of LRP1 mediates TGFß-induced enhancement of Wnt5a, which limits intracellular cholesterol accumulation by inhibiting cholesterol biosynthesis and by promoting cholesterol export. Moreover, we demonstrate that the cytoplasmic (ß) chain of LRP1 suffices to limit cholesterol accumulation in LRP1(-/-) cells. Through binding of Erk2 to the second of its carboxyl-terminal NPXY motifs, LRP1 ß-chain positively regulates the expression of ATP binding cassette transporter A1 (ABCA1) and of neutral cholesterol ester hydrolase (NCEH1). These results highlight the unexpected functions of LRP1 and the canonical Wnt5a pathway and new therapeutic potential in cholesterol-associated disorders including cardiovascular diseases.

A no-stop mutation in MAGEB4 is a possible cause of rare X-linked azoospermia and oligozoospermia in a consanguineous Turkish family.

PURPOSE: The purpose of this study was to identify mutations that cause non-syndromic male infertility using whole exome sequencing of family cases. METHODS: We recruited a consanguineous Turkish family comprising nine siblings with male triplets; two of the triplets were infertile as well as one younger infertile brother. Whole exome sequencing (WES) performed on two azoospermic brothers identified a mutation in the melanoma antigen family B4 (MAGEB4) gene which was confirmed via Sanger sequencing and then screened for on control groups and unrelated infertile subjects. The effect of the mutation on messenger RNA (mRNA) and protein levels was tested after in vitro cell transfection. Structural features of MAGEB4 were predicted throughout the conserved MAGE domain. RESULTS: The novel single-base substitution (c.1041A>T) in the X-linked MAGEB4 gene was identified as a no-stop mutation. The mutation is predicted to add 24 amino acids to the C-terminus of MAGEB4. Our functional studies were unable to detect any effect either on mRNA stability, intracellular localization of the protein, or the ability to homodimerize/heterodimerize with other MAGE proteins. We thus hypothesize that these additional amino acids may affect the proper protein interactions with MAGEB4 partners. CONCLUSION: The whole exome analysis of a consanguineous Turkish family revealed MAGEB4 as a possible new X-linked cause of inherited male infertility. This study provides the first clue to the physiological function of a MAGE protein.

Mutations in amphiphysin 2 (BIN1) disrupt interaction with dynamin 2 and cause autosomal recessive centronuclear myopathy.

Centronuclear myopathies are characterized by muscle weakness and abnormal centralization of nuclei in muscle fibers not secondary to regeneration. The severe neonatal X-linked form (myotubular myopathy) is due to mutations in the phosphoinositide phosphatase myotubularin (MTM1), whereas mutations in dynamin 2 (DNM2) have been found in some autosomal dominant cases. By direct sequencing of functional candidate genes, we identified homozygous mutations in amphiphysin 2 (BIN1) in three families with autosomal recessive inheritance. Two missense mutations affecting the BAR (Bin1/amphiphysin/RVS167) domain disrupt its membrane tubulation properties in transfected cells, and a partial truncation of the C-terminal SH3 domain abrogates the interaction with DNM2 and its recruitment to the membrane tubules. Our results suggest that mutations in BIN1 cause centronuclear myopathy by interfering with remodeling of T tubules and/or endocytic membranes, and that the functional interaction between BIN1 and DNM2 is necessary for normal muscle function and positioning of nuclei.

Temporally controlled targeted somatic mutagenesis in mouse eye pigment epithelium.

To generate temporally controlled site-specific somatic mutations in the mouse eye pigment epithelium, we generated a TRP1-Cre-ER(T2) transgenic mouse line that expresses the tamoxifen-dependent Cre-ER(T2) recombinase under the control of the tyrosinase-related protein 1 (TRP1) promoter. Cre-ER(T2) transcripts were readily detected in the retinal pigment epithelium (RPE), and tamoxifen treatment of adult TRP1-Cre-ER(T2) transgenic mice induced efficient excision of floxed DNA in patches of RPE cells, in numerous epithelial cells of the iris and ciliary body, and in very few cells of the neural retina. Importantly, no excision was detected in any cells in the absence of tamoxifen treatment. Thus, the TRP1-Cre-ER(T2) mouse line provides a powerful tool to study in vivo gene functions in the mouse eye pigment epithelium.

RSK2 signaling in brain habenula contributes to place aversion learning.

RSK2 is a Ser/Thr kinase acting in the Ras/MAPK pathway. Rsk2 gene deficiency leads to the Coffin-Lowry Syndrome, notably characterized by cognitive deficits. We found that mrsk2 knockout mice are unable to associate an aversive stimulus with context in a lithium-induced conditioned place aversion task requiring both high-order cognition and emotional processing. Virally mediated shRNA-RSK2 knockdown in the habenula, whose involvement in cognition is receiving increasing attention, also ablated contextual conditioning. RSK2 signaling in the habenula, therefore, is essential for this task. Our study reveals a novel role for RSK2 in cognitive processes and uncovers the critical implication of an intriguing brain structure in place aversion learning.

The V0-ATPase mediates apical secretion of exosomes containing Hedgehog-related proteins in Caenorhabditis elegans.

Polarized intracellular trafficking in epithelia is critical in development, immunity, and physiology to deliver morphogens, defensins, or ion pumps to the appropriate membrane domain. The mechanisms that control apical trafficking remain poorly defined. Using Caenorhabditis elegans, we characterize a novel apical secretion pathway involving multivesicularbodies and the release of exosomes at the apical plasma membrane. By means of two different genetic approaches, we show that the membrane-bound V0 sector of the vacuolar H+-ATPase (V-ATPase) acts in this pathway, independent of its contribution to the V-ATPase proton pump activity. Specifically, we identified mutations in the V0 "a" subunit VHA-5 that affect either the V0-specific function or the V0+V1 function of the V-ATPase. These mutations allowed us to establish that the V0 sector mediates secretion of Hedgehog-related proteins. Our data raise the possibility that the V0 sector mediates exosome and morphogen release in mammals.

Vectors for recombinational cloning and gene expression in mammalian cells using modified vaccinia virus Ankara.

Modified vaccinia virus Ankara (MVA) is a safe vector for high-level expression of proteins in mammalian cells. To simplify the molecular cloning procedures for shuttling genes into the MVA genome, we constructed generic destination plasmids that allow in vitro recombinational cloning (Gateway) and quick isolation of expression plasmids for any gene to be incorporated into the virus. Downstream purification steps were simplified by including N-terminal peptide tags (His, Strep, and Flag) in the generic plasmids. We demonstrate the ability to produce 10mg of beta-glucuronidase from 10(8) hamster cells and to purify tagged proteins with affinity gels.

Structural adaptability in the ligand-binding pocket of the ecdysone hormone receptor.

The ecdysteroid hormones coordinate the major stages of insect development, notably moulting and metamorphosis, by binding to the ecdysone receptor (EcR); a ligand-inducible nuclear transcription factor. To bind either ligand or DNA, EcR must form a heterodimer with ultraspiracle (USP), the homologue of retinoid-X receptor. Here we report the crystal structures of the ligand-binding domains of the moth Heliothis virescens EcR-USP heterodimer in complex with the ecdysteroid ponasterone A and with a non-steroidal, lepidopteran-specific agonist BYI06830 used in agrochemical pest control. The two structures of EcR-USP emphasize the universality of heterodimerization as a general mechanism common to both vertebrates and invertebrates. Comparison of the EcR structures in complex with steroidal and non-steroidal ligands reveals radically different and only partially overlapping ligand-binding pockets that could not be predicted by molecular modelling and docking studies. These findings offer new perspectives for the design of insect-specific, environmentally safe insecticides. The concept of a ligand-dependent binding pocket in EcR provides an insight into the moulding of nuclear receptors to their ligand, and has potential applications for human nuclear receptors.

A set of baculovirus transfer vectors for screening of affinity tags and parallel expression strategies.

We report a set of baculovirus transfer vectors for parallel expression of proteins in fusion with a panel of affinity tags including GST, protein A, thioredoxin, CBP, and FLAG. This suite includes vectors to generate recombinant baculovirus by homologous recombination in insect cells or using the Bac-to-Bac technology. An application of the vector suite approach to the vitamin D receptor (VDR), a protein mainly expressed as inclusion bodies in Escherichia coli, is presented. We found that expression in fusion with GST and protein A provided an efficient compromise of excellent purification with acceptable yields and costs.

Modelling geochemical and kinetic processes involved in lead (Pb) remobilization during resuspension events of contaminated sediments.

The objective of this paper is to present a model simulating and predicting the exchange kinetics of lead (Pb) between contaminated sediments and water during resuspension events potentially occurring in reservoirs. We developed an innovative model that combines thermodynamic speciation of particulate surfaces (oxides and Particulate Organic Carbon (POC)), thermodynamic Pb speciation in water, and kinetic modelling of exchanges between free Pb and particulate sites (i.e., dissolution of a carbonate carrier phase, adsorption/coprecipitation and desorption/dissolution to/from oxides, and adsorption and desorption/degradation to/from particulate organic particles). We used results from laboratory resuspension experiments performed on sediments from three contaminated dam reservoirs to calibrate a new chemical speciation model. Uptake and release processes to/from sediments were found to be controlled by at least two successive reactions that are associated with two particulate pools (here oxides and POC). Kinetic adsorption and desorption rates were calibrated for seven experimental conditions. Variability in kinetic rates allowed evaluation of the effect of the solid-to-liquid ratio and sediment origin on exchange kinetics at the water-particle interface. The kinetic release of dissolved Pb by desorption or dissolution from the oxides was reproduced almost identically between the experiments, regardless of the solid-to-liquid ratio or sediment origin. Long-term readsorption on POC sites is more variable, even if ranges of variation in the adsorption and desorption kinetic rates related to POC remain limited, considering that tested sediments vary significantly. CAPSULE: A kinetic model simulating the dynamics of lead (Pb) during sediment resuspension was developed and calibrated to laboratory experiments performed on three contaminated sediments.

How to assess trace elements bioavailability for benthic organisms in lowly to moderately contaminated coastal sediments?

The bioavailability of trace elements (As, Cd, Co, Cr, Cu, Hg, Ni, Pb, Zn) in lowly to moderately contaminated coastal sediments from the Berre lagoon, France, was assessed by comparing their potentially bioavailable concentrations and bioaccumulated concentrations in the polychaete Alitta succinea. No linear correlations were observed contrarily to what is generally observed in similar works in areas with highly contaminated sediment. Correlations between trace and major elements (Fe, Ca, S, Mg, P, Al) in Alitta succinea tissues and their distribution in organism tissues show that, in such lowly to moderately contaminated sediments, biological variabilities should be considered. Normalization procedures allow to take into account these variabilities and to identify that sediment contamination is partly involved in the benthic ecosystem degradation of the Berre lagoon. Alitta succinea cannot be used as relevant bioindicator for Zn and Co bioavailability in sediment, since these elements are regulated by this organism.

Co-translational assembly of mammalian nuclear multisubunit complexes.

Cells dedicate significant energy to build proteins often organized in multiprotein assemblies with tightly regulated stoichiometries. As genes encoding subunits assembling in a multisubunit complex are dispersed in the genome of eukaryotes, it is unclear how these protein complexes assemble. Here, we show that mammalian nuclear transcription complexes (TFIID, TREX-2 and SAGA) composed of a large number of subunits, but lacking precise architectural details are built co-translationally. We demonstrate that dimerization domains and their positions in the interacting subunits determine the co-translational assembly pathway (simultaneous or sequential). The lack of co-translational interaction can lead to degradation of the partner protein. Thus, protein synthesis and complex assembly are linked in building mammalian multisubunit complexes, suggesting that co-translational assembly is a general principle in mammalian cells to avoid non-specific interactions and protein aggregation. These findings will also advance structural biology by defining endogenous co-translational building blocks in the architecture of multisubunit complexes.

The WHHERE coactivator complex is required for retinoic acid-dependent regulation of embryonic symmetry.

Bilateral symmetry is a striking feature of the vertebrate body plan organization. Vertebral precursors, called somites, provide one of the best illustrations of embryonic symmetry. Maintenance of somitogenesis symmetry requires retinoic acid (RA) and its coactivator Rere/Atrophin2. Here, using a proteomic approach we identify a protein complex, containing Wdr5, Hdac1, Hdac2 and Rere (named WHHERE), which regulates RA signaling and controls embryonic symmetry. We demonstrate that Wdr5, Hdac1, and Hdac2 are required for RA signaling in vitro and in vivo. Mouse mutants for Wdr5 and Hdac1 exhibit asymmetrical somite formation characteristic of RA-deficiency. We also identify the Rere-binding histone methyltransferase Ehmt2/G9a, as a RA coactivator controlling somite symmetry. Upon RA treatment, WHHERE and Ehmt2 become enriched at RA target genes to promote RNA polymerase II recruitment. Our work identifies a protein complex linking key epigenetic regulators acting in the molecular control of embryonic bilateral symmetry.Retinoic acid (RA) regulates the maintenance of somitogenesis symmetry. Here, the authors use a proteomic approach to identify a protein complex of Wdr5, Hdac1, Hdac2 that act together with RA and coactivator Rere/Atrophin2 and a histone methyltransferase Ehmt2 to regulate embryonic symmetry.

ADA3-containing complexes associate with estrogen receptor alpha.

Transcriptional repression and activation by nuclear receptors (NRs) are brought about by coregulator complexes. These complexes modify the chromatin environment of target genes and affect the activity of the basal transcription machinery. We have previously implicated the yeast ADA3 protein in transcriptional activation by estrogen and retinoid X receptors in yeast and mammalian cells. Here we report the cloning of the mouse homolog of ADA3 and its characterization with respect to the estrogen receptor alpha (ERalpha) function. Mouse mADA3 is 23% identical and 47% similar to yeast yADA3, and mADA3 in contrast to yADA3 does not interact with NRs directly even though it contains two LxxLL NR boxes. However, the ADA3-containing TBP-free-TAF-containing complex (TFTC) can interact with ERalpha in a ligand-independent manner, indicating that other subunits of the complex are sufficient to mediate interaction with NRs.

Comparative kinetic desorption of 60Co, 85Sr and 134Cs from a contaminated natural silica sand column: influence of varying physicochemical conditions and dissolved organic matter.

In order to determine the mechanisms of the retention of 60Co, 85Sr and 134Cs in natural silica sand columns, desorption experiments were performed by changes of pH and ionic strength and by injection of natural organic matter (NOM). Injection of KCl (0.1 M) resulted in a high release of 60Co (60-100%) and 85Sr (72-100%) but a smaller release of 134Cs (31-66%). Only limited release of 60Co (66%) and 85Sr (71%) and no release of 134Cs were observed by injection of NOM. The different percentages of desorption were related to the chemical characteristics of the organic colloids previously retained in columns before the desorption step. The results evidenced different sorption processes on energetically heterogeneous surface sites. According to the initial conditions, the binding of the radionuclides to the solid phase resulted from weak and easily reversible sorption processes to strong association probably by inner sphere complexes. The rather weak release of 134Cs by KCl was attributed to the strong retention of 134Cs by clay coatings on the natural silica sand surfaces.

Implications of short and long term (30 days) sorption on the desorption kinetic of trace metals (Cd, Zn, Co, Mn, Fe, Ag, Cs) associated with river suspended matter.

The desorption kinetic of trace elements (Cd, Zn, Co, Mn, Fe, Ag, and Cs) associated with Loire river natural suspended particulate matter (SPM; 0.4-63 microm) was followed up on times varying from 0.5 h to 30 days, from SPM previously contaminated during 1 h, 24 h and 30 days. Long term sorption kinetics indicated that the difference between sorption occurring during the period 0-30 days (time investigated in this study) and the period 0-48 h (time often used for sorption experiments) ranges from few to 25% according to the element. Desorption kinetics show that, whatever the age of the complex formed during the sorption step, the release tends to equilibrium between complexed and dissolved elements equivalent to the equilibrium obtained for sorption after a given time. However, the time to get this equilibrium depends on the aging of the complex and on the element. All the above features indicate different types of complexes formation and strength of the binding according to the age of the complex and according to the element. Using a multi-compartmental model, simulating the transfer of metals between water and different types of particulate sites, the relationships between the parameters describing slow and rapid processes helped in explaining the "aging" effect observed.