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Immunological alterations and associated diseases in mandrills (Mandrillus sphinx) naturally co-infected with SIV and STLV

Author(s) : Souqui?re S, Makuwa M, Sall? B, Lepelletier Y, Mortreux F, Hermine O, Kazanji M,
Journal : Virology

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains.

Author(s) : Jost D, Carrivain P, Cavalli G, Vaillant C,
Journal : Nucleic Acids Res
Genomes of eukaryotes are partitioned into domains of functionally distinct chromatin states. These domains are stably inherited across many cell generations and can be remodeled in response to developmental and external cues, hence contributing to the robustness and plasticity of expression patterns and cell phenotypes. Remarkably, recent studies indicate that these 1D epigenomic domainstend to fold into 3D topologically associated domains forming specialized nuclear chromatin compartments. However, the general mechanisms behind such compartmentalization including the contribution of epigenetic regulation remain unclear. Here, we address the question of the coupling between chromatin foldingand epigenome. Using polymer physics, we analyze the properties of a block copolymer model that accounts for local epigenomic information. Considering copolymers build from the epigenomic landscape of Drosophila, we observe a very good agreement with the folding patterns observed in chromosome conformation capture experiments. Moreover, this model provides a physical basis for the existence of multistability in epigenome folding at sub-chromosomal scale. We show how experiments are fully consistent with multistable conformations where topologically associated domains of the same epigenomic state interact dynamically with each other. Our approach provides a general framework to improve our understanding of chromatin folding during cell cycle and differentiation andits relation to epigenetics.

MyLabStocks: a web-application to manage molecular biology materials.

Author(s) : Chuffart F, Yvert G,
Journal : Yeast
Laboratory stocks are the hardware of research. They must be stored and managed with mimimum loss of material and information. Plasmids, oligonucleotides and strains are regularly exchanged between collaborators within and between laboratories. Managing and sharing information about every item is crucial for retrieval of reagents, for planning experiments and for reproducing past experimental results. We have developed a web-based application to manage stockscommonly used in a molecular biology laboratory. Its functionalities include user-defined privileges, visualization of plasmid maps directly from their sequence and the capacity to search items from fields of annotation or directly from a query sequence using BLAST. It is designed to handle records of plasmids,oligonucleotides, yeast strains, antibodies, pipettes and notebooks. Based on PHP/MySQL, it can easily be extended to handle other types of stocks and it can be installed on any server architecture. MyLabStocks is freely available from: under an open source licence.

Post-transcriptional regulation of gene expression in innate immunity.

Author(s) : Carpenter S, Ricci E, Mercier B, Moore M, Fitzgerald K,
Journal : Nat Rev Immunol
Innate immune responses combat infectious microorganisms by inducing inflammatory responses, antimicrobial pathways and adaptive immunity. Multiple genes within each of these functional categories are coordinately and temporally regulated inresponse to distinct external stimuli. The substantial potential of these responses to drive pathological inflammation and tissue damage highlights the need for rigorous control of these responses. Although transcriptional control of inflammatory gene expression has been studied extensively, the importance of post-transcriptional regulation of these processes is less well defined. In thisReview, we discuss the regulatory mechanisms that occur at the level of mRNA splicing, mRNA polyadenylation, mRNA stability and protein translation, and thathave instrumental roles in controlling both the magnitude and duration of the inflammatory response.

RIPiT-Seq: a high-throughput approach for footprinting RNA:protein complexes.

Author(s) : Singh G, Ricci E, Moore M,
Journal : Methods
Development of high-throughput approaches to map the RNA interaction sites of individual RNA binding proteins (RBPs) transcriptome-wide is rapidly transforming our understanding of post-transcriptional gene regulatory mechanisms. Here we describe a ribonucleoprotein (RNP) footprinting approach we recently developed for identifying occupancy sites of both individual RBPs and multi-subunit RNP complexes. RNA:protein immunoprecipitation in tandem (RIPiT) yields highly specific RNA footprints of cellular RNPs isolated via two sequential purifications; the resulting RNA footprints can then be identified by high-throughput sequencing (Seq). RIPiT-Seq is broadly applicable to all RBPs regardless of their RNA binding mode and thus provides a means to map the RNA binding sites of RBPs with poor inherent ultraviolet (UV) crosslinkability. Further, among current high-throughput approaches, RIPiT has the unique capacityto differentiate binding sites of RNPs with overlapping protein composition. It is therefore particularly suited for studying dynamic RNP assemblages whose composition evolves as gene expression proceeds.

RNA helicases DDX5 and DDX17 dynamically orchestrate transcription, miRNA, and splicing programs in cell differentiation

Author(s) : Dardenne E, Polay Espinoza M, Fattet L, Germann S, Lambert M, Neil H, Zonta E, Mortada H, Gratadou L, Deygas M, Chakrama F, Samaan S, Desmet F, Tranchevent L, Dutertre M, Rimokh R, Bourgeois C, Auboeuf D,
Journal : Cell Rep

RNA processing factors Swd2.2 and Sen1 antagonize RNA Pol III-dependent transcription and the localization of condensin at Pol III genes.

Author(s) : Legros P, Malapert A, Niinuma S, Bernard P, Vanoosthuyse V,
Journal : PLoS Genet
Condensin-mediated chromosome condensation is essential for genome stability upon cell division. Genetic studies have indicated that the association of condensin with chromatin is intimately linked to gene transcription, but what transcription-associated feature(s) direct(s) the accumulation of condensin remains unclear. Here we show in fission yeast that condensin becomes strikinglyenriched at RNA Pol III-transcribed genes when Swd2.2 and Sen1, two factors involved in the transcription process, are simultaneously deleted. Sen1 is an ATP-dependent helicase whose orthologue in Saccharomyces cerevisiae contributes both to terminate transcription of some RNA Pol II transcripts and to antagonizethe formation of DNA:RNA hybrids in the genome. Using two independent mapping techniques, we show that DNA:RNA hybrids form in abundance at Pol III-transcribed genes in fission yeast but we demonstrate that they are unlikely to faciliate the recruitment of condensin. Instead, we show that Sen1 forms a stable and abundantcomplex with RNA Pol III and that Swd2.2 and Sen1 antagonize both the interaction of RNA Pol III with chromatin and RNA Pol III-dependent transcription. When Swd2.2 and Sen1 are lacking, the increased concentration of RNA Pol III and condensin at Pol III-transcribed genes is accompanied by the accumulation of topoisomerase I and II and by local nucleosome depletion, suggesting that Pol III-transcribed genes suffer topological stress. We provide evidence that this topological stress contributes to recruit and/or stabilize condensin at Pol III-transcribed genes in the absence of Swd2.2 and Sen1. Our data challenge the idea that a processive RNA polymerase hinders the binding of condensin and suggest that transcription-associated topological stress could in some circumstances facilitate the association of condensin.

SAS-1 is a C2 domain protein critical for centriole integrity in C. elegans.

Author(s) : von Tobel L, Mikeladze-Dvali T, Delattre M, Balestra F, Blanchoud S, Finger S, Knott G, Muller-Reichert T, Gonczy P,
Journal : PLoS Genet
Centrioles are microtubule-based organelles important for the formation of cilia, flagella and centrosomes. Despite progress in understanding the underlying assembly mechanisms, how centriole integrity is ensured is incompletely understood, including in sperm cells, where such integrity is particularly critical. We identified C. elegans sas-1 in a genetic screen as a locus requiredfor bipolar spindle assembly in the early embryo. Our analysis reveals that sperm-derived sas-1 mutant centrioles lose their integrity shortly after fertilization, and that a related defect occurs when maternal sas-1 function is lacking. We establish that sas-1 encodes a C2 domain containing protein that localizes to centrioles in C. elegans, and which can bind and stabilize microtubules when expressed in human cells. Moreover, we uncover that SAS-1 is related to C2CD3, a protein required for complete centriole formation in human cells and affected in a type of oral-facial-digital (OFD) syndrome.

Staufen1 senses overall transcript secondary structure to regulate translation.

Author(s) : Ricci E, Kucukural A, Cenik C, Mercier B, Singh G, Heyer E, Ashar-Patel A, Peng L, Moore M,
Journal : Nat Struct Mol Biol
Human Staufen1 (Stau1) is a double-stranded RNA (dsRNA)-binding protein implicated in multiple post-transcriptional gene-regulatory processes. Here we combined RNA immunoprecipitation in tandem (RIPiT) with RNase footprinting, formaldehyde cross-linking, sonication-mediated RNA fragmentation and deep sequencing to map Staufen1-binding sites transcriptome wide. We find that Stau1 binds complex secondary structures containing multiple short helices, many of which are formed by inverted Alu elements in annotated 3' untranslated regions (UTRs) or in 'strongly distal' 3' UTRs. Stau1 also interacts with actively translating ribosomes and with mRNA coding sequences (CDSs) and 3' UTRs in proportion to their GC content and propensity to form internal secondary structure. On mRNAs with high CDS GC content, higher Stau1 levels lead to greater ribosome densities, thus suggesting a general role for Stau1 in modulating translation elongation through structured CDS regions. Our results also indicatethat Stau1 regulates translation of transcription-regulatory proteins.

Stochastic fluctuations and distributed control of gene expression impact cellular memory.

Author(s) : Corre G, Stockholm D, Arnaud O, Kaneko G, Vinuelas J, Yamagata Y, Neildez-Nguyen T, Kupiec J, Beslon G, Gandrillon O, Paldi A,
Journal : PLoS One
Despite the stochastic noise that characterizes all cellular processes the cellsare able to maintain and transmit to their daughter cells the stable level of gene expression. In order to better understand this phenomenon, we investigated the temporal dynamics of gene expression variation using a double reporter gene model. We compared cell clones with transgenes coding for highly stable mRNA andfluorescent proteins with clones expressing destabilized mRNA-s and proteins. Both types of clones displayed strong heterogeneity of reporter gene expression levels. However, cells expressing stable gene products produced daughter cells with similar level of reporter proteins, while in cell clones with short mRNA and protein half-lives the epigenetic memory of the gene expression level was completely suppressed. Computer simulations also confirmed the role of mRNA and protein stability in the conservation of constant gene expression levels over several cell generations. These data indicate that the conservation of a stable phenotype in a cellular lineage may largely depend on the slow turnover of mRNA-s and proteins.

The Caenorhabditis elegans HP1 family protein HPL-2 maintains ER homeostasis through the UPR and hormesis.

Author(s) : Kozlowski L, Garvis S, Bedet C, Palladino F,
Journal : Proc Natl Acad Sci U S A
Cellular adaptation to environmental changes and stress relies on a wide range of regulatory mechanisms that are tightly controlled at several levels, including transcription. Chromatin structure and chromatin binding proteins are important factors contributing to the transcriptional response to stress. However, it remains largely unknown to what extent specific chromatin factors influence the response to distinct forms of stress in a developmental context. One of the bestcharacterized stress response pathways is the unfolded protein response (UPR), which is activated by accumulation of misfolded proteins in the endoplasmic reticulum (ER). Here, we show that Caenorhabditis elegans heterochromatin protein like-2 (HPL-2), the homolog of heterochromatin protein 1 (HP1), down-regulates the UPR in the intestine. Inactivation of HPL-2 results in an enhanced resistance to ER stress dependent on the X-box binding protein 1 (XBP-1)/inositol requiringenzyme 1 branch of the UPR and the closely related process of autophagy. Increased resistance to ER stress in animals lacking HPL-2 is associated with increased basal levels of XBP-1 activation and ER chaperone expression under physiological conditions, which may in turn activate an adaptive response known as ER hormesis. HPL-2 expression in intestinal cells is sufficient to rescue stress resistance, whereas expression in neuronal cells negatively influenced the ER stress response through a cell-nonautonomous mechanism. We further show that the retinoblastoma protein homolog LIN-35 and the LIN-13 zinc finger protein actin the same pathway as HPL-2 to limit the ER stress response. Altogether, our results point to multiple functions for HP1 in different cell types to maintain ER homeostasis.

The centrosomal kinase NEK2 is a novel splicing factor kinase involved in cell survival

Author(s) : Naro C, Barbagallo F, Chieffi P, Bourgeois C, Paronetto M, Sette C,
Journal : Nucleic Acids Res

The Ddx5 and Ddx17 RNA helicases are cornerstones in the complex regulatory array of steroid hormone-signaling pathways

Author(s) : Samaan S, Tranchevent L, Dardenne E, Polay Espinoza M, Zonta E, Germann S, Gratadou L, Dutertre M, Auboeuf D,
Journal : Nucleic Acids Res

The ectodysplasin pathway: from diseases to adaptations.

Author(s) : Sadier A, Viriot L, Pantalacci S, Laudet V,
Journal : Trends Genet
The ectodysplasin (EDA) pathway, which is active during the development of ectodermal organs, including teeth, hairs, feathers, and mammary glands, and which is crucial for fine-tuning the developmental network controlling the number, size, and density of these structures, was discovered by studying human patients affected by anhidrotic/hypohidrotic ectodermal dysplasia. It comprises three main gene products: EDA, a ligand that belongs to the tumor necrosis factor (TNF)-alpha family, EDAR, a receptor related to the TNFalpha receptors, and EDARADD, a specific adaptor. This core pathway relies on downstream NF-kappaB pathway activation to regulate target genes. The pathway has recently been foundto be associated with specific adaptations in natural populations: the magnitudeof armor plates in sticklebacks and the hair structure in Asian human populations. Thus, despite its role in human disease, the EDA pathway is a 'hopeful pathway' that could allow adaptive changes in ectodermal appendages which, as specialized interfaces with the environment, are considered hot-spots of morphological evolution.

The effects of genetic variation on gene expression dynamics during development.

Author(s) : Francesconi M, Lehner B,
Journal : Nature
The development of a multicellular organism and physiological responses require massive coordinated changes in gene expression across several cell and tissue types. Polymorphic regions of the genome that influence gene expression levels have been identified by expression quantitative trait locus (eQTL) mapping in many species, including loci that have cell-dependent, tissue-dependent and age-dependent effects. However, there has been no comprehensive characterizationof how polymorphisms influence the complex dynamic patterns of gene expression that occur during development and in physiology. Here we describe an efficient experimental design to infer gene expression dynamics from single expression profiles in different genotypes, and apply it to characterize the effect of local (cis) and distant (trans) genetic variation on gene expression at high temporal resolution throughout a 12-hour period of the development of Caenorhabditis elegans. Taking dynamic variation into account identifies >50% more cis-eQTLs, including more than 900 that alter the dynamics of expression during this period. Local sequence polymorphisms extensively affect the timing, rate, magnitude and shape of expression changes. Indeed, many local sequence variants both increase and decrease gene expression, depending on the time-point profiled. Expression dynamics during this 12-hour period are also influenced extensively in trans by distal loci. In particular, several trans loci influence genes with quite diverse dynamic expression patterns, but they do so primarily during a common time interval. Trans loci can therefore act as modifiers of expression during a particular period of development. This study provides the first characterization, to our knowledge, of the effect of local and distant genetic variation on the dynamics of gene expression throughout an extensive time period. Moreover, the approach developed here should facilitate the genetic dissection of other dynamic processes, including potentially development, physiology and disease progressionin humans.

The p53 control of apoptosis and proliferation: lessons from Drosophila.

Author(s) : Mollereau B, Ma D,
Journal : Apoptosis
The canonical role of p53 in preserving genome integrity and limiting carcinogenesis has been well established. In the presence of acute DNA-damage, oncogene deregulation and other forms of cellular stress, p53 orchestrates a myriad of pleiotropic processes to repair cellular damages and maintain homeostasis. Beside these well-studied functions of p53, recent studies in Drosophila have unraveled intriguing roles of Dmp53 in promoting cell division in apoptosis-induced proliferation, enhancing fitness and proliferation of the winner cell in cell competition and coordinating growth at the organ and organismal level in the presence of stress. In this review, we describe these new functions of Dmp53 and discuss their relevance in the context of carcinogenesis.

The Redox Chemistry of Mono-and Bis (acyl) phosphane Oxides

Author(s) : Zalibera M, Stébé P, Dietliker K, Grützmacher H, Spichty M, Gescheidt G,
Journal : European Journal of Organic Chemistry
Mono- and bis(acyl)phosphane oxides are usually utilized as photoinitiators for radical polymerizations. This manuscript reveals the electrochemically reversible reductions of these molecules, leading to the corresponding radical anions. The radical anions, which have been characterized by EPR and ENDOR spectroscopy, display remarkable delocalization and ion-pairing behavior that can be rationalized by theoretical calculations.

The SET-2/SET1 histone H3K4 methyltransferase maintains pluripotency in the Caenorhabditis elegans germline.

Author(s) : Robert V, Mercier M, Bedet C, Janczarski S, Merlet J, Garvis S, Ciosk R, Palladino F,
Journal : Cell Rep
Histone H3 Lys 4 methylation (H3K4me) is deposited by the conserved SET1/MLL methyltransferases acting in multiprotein complexes, including Ash2 and Wdr5. Although individual subunits contribute to complex activity, how they influence gene expression in specific tissues remains largely unknown. In Caenorhabditis elegans, SET-2/SET1, WDR-5.1, and ASH-2 are differentially required for germlineH3K4 methylation. Using expression profiling on germlines from animals lacking set-2, ash-2, or wdr-5.1, we show that these subunits play unique as well as redundant functions in order to promote expression of germline genes and represssomatic genes. Furthermore, we show that in set-2- and wdr-5.1-deficient germlines, somatic gene misexpression is associated with conversion of germ cells into somatic cells and that nuclear RNAi acts in parallel with SET-2 and WDR-5.1to maintain germline identity. These findings uncover a unique role for SET-2 and WDR-5.1 in preserving germline pluripotency and underline the complexity of the cellular network regulating this process.

The Spartan ortholog maternal haploid is required for paternal chromosome integrity in the Drosophila zygote.

Author(s) : Delabaere L, Orsi G, Sapey-Triomphe L, Horard B, Couble P, Loppin B,
Journal : Curr Biol
The animal sperm nucleus is characterized by an extremely compacted organizationof its DNA after the global replacement of histones with sperm-specific nuclear basic proteins, such as protamines. In the absence of DNA repair activity in themature gamete, the integrity of the paternal genome is potentially challenged bythe unique topological constraints exerted on sperm DNA. In addition, the maintenance of paternal DNA integrity during the rapid remodeling of sperm chromatin at fertilization has long been regarded as a maternal trait. However, little is known about the nature of the egg proteins involved in this essential aspect of zygote formation. We had previously characterized the unique phenotypeof the classical Drosophila maternal effect mutant maternal haploid (mh), which specifically affects the integration of paternal chromosomes in the zygote. Herewe show that MH is the fly ortholog of the recently identified human DVC1/Spartan protein, a conserved regulator of DNA damage tolerance. Like Spartan, MH proteinis involved in the resistance to UV radiation and recruits the p97/TER94 segregase to stalled DNA replication forks in somatic cells. In the zygote, we found that the mh phenotype is consistent with perturbed or incomplete paternal DNA replication. Remarkably, however, the specific accumulation of MH in the male pronucleus before the first S phase suggests that this maternal protein is required to maintain paternal DNA integrity during nuclear decondensation or to set the paternal chromatin landscape in preparation of the first zygotic cycle.

Transgenerational functions of small RNA pathways in controlling gene expression in C. elegans.

Author(s) : Guerin T, Palladino F, Robert V,
Journal : Epigenetics
RNA silencing processes use exogenous or endogenous RNA molecules to specifically and robustly regulate gene expression. In C. elegans, initial mechanistic descriptions of the different silencing processes focused on posttranscriptionalregulation. In this review, we discuss recent work showing that, in this model organism, RNA silencing also controls the transcription of target genes by inducing heterochromatin formation. Specifically, it has been shown that ribonucleoprotein complexes containing small RNAs, either processed from exogenous dsRNA or synthesized from the genome itself, and proteins of the Argonaute family, mediate the deposition of repressive histone marks at the targeted loci. Interestingly, the accumulation of repressive marks is required for the inheritance of the silencing effect and the establishment of an epigenetic memory that discriminates self- from non-self-RNAs.

V-erbA generates ribosomes devoid of RPL11 and regulates translational activity in avian erythroid progenitors.

Author(s) : Nguyen-Lefebvre A, Leprun G, Morin V, Vinuelas J, Coute Y, Madjar J, Gandrillon O, Gonin-Giraud S,
Journal : Oncogene
The v-erbA oncogene transforms chicken erythrocytic progenitors (T2EC) by blocking their differentiation and freezing them in a state of self-renewal. Transcriptomes of T2EC, expressing either v-erbA or a non-transforming form of v-erbA (S61G), were compared using serial analysis of gene expression and some, but not all, mRNA-encoding ribosomal proteins were seen to be affected by v-erbA. These results suggest that this oncogene could modulate the composition of ribosomes. In the present study, we demonstrate, using two-dimensional difference in gel electrophoresis, that v-erbA-expressing cells have a lower amount of RPL11 associated with the ribosomes. The presence of ribosomes devoid of RPL11 in v-erbA-expressing cells was further confirmed by immunoprecipitation. In order to assess the possible impact of these specialized ribosomes on the translational activity, we analyzed proteomes of either v-erbA or S61G-expressing cells using 2D/mass spectrometry, and identified nine proteins present in differing amounts within these cells. Among these proteins, we focused on HSP70 because of its involvement in erythroid differentiation. Our results indicate that, in v-erbA-expressing cells, hsp70 is not only transcribed but also translated more efficiently, as shown by polyribosome fractionation experiments. We demonstrate here, for the first time, the existence of ribosomes with different protein components, notably ribosomes devoid of RPL11, and a regulation of mRNA translation depending on v-erbA oncogene expression.