Patterning and growth control by membrane-tethered Wingless

Cyrille Alexandre,     Alberto Baena-Lopez     & Jean-Paul Vincent

                                                          

Abstract:

Wnts are evolutionarily conserved secreted signalling proteins that, in various developmental contexts, spread from their site of synthesis to form a gradient and activate target-gene expression at a distance. However, the requirement for Wnts to spread has never been directly tested. Here we used genome engineering to replace the endogenous wingless gene, which encodes the main Drosophila Wnt, with one that expresses a membrane-tethered form of the protein. Surprisingly, the resulting flies were viable and produced normally patterned appendages of nearly the right size, albeit with a delay. We show that, in the prospective wing, prolonged wingless transcription followed by memory of earlier signalling allows persistent expression of relevant target genes. We suggest therefore that the spread of Wingless is dispensable for patterning and growth even though it probably contributes to increasing cell proliferation.

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Keywords:patterning,membrane,wingless,drosophila

Elephant shark genome provides unique insights into gnathostome evolution

Byrappa Venkatesh,     Alison P. Lee,     Vydianathan Ravi,     Ashish K. Maurya,     Michelle M. Lian, Jeremy B. Swann,     Yuko Ohta,     Martin F. Flajnik,     Yoichi Sutoh,     Masanori Kasahara,     Shawn Hoon,     Vamshidhar Gangu,     Scott W. Roy,     Manuel Irimia,     Vladimir Korzh,     Igor Kondrychyn, Zhi Wei Lim,     Boon-Hui Tay,     Sumanty Tohari,     Kiat Whye Kong,     Shufen Ho,     Belen Lorente-Galdos,     Javier Quilez,     Tomas Marques-Bonet,     Brian J. Raney     et al.

                                                                    

Abstract:

The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged into two groups, the cartilaginous fishes and the bony vertebrates. Here we report the whole-genome analysis of a cartilaginous fish, the elephant shark (Callorhinchus milii). We find that the C. milii genome is the slowest evolving of all known vertebrates, including the ‘living fossil’ coelacanth, and features extensive synteny conservation with tetrapod genomes, making it a good model for comparative analyses of gnathostome genomes. Our functional studies suggest that the lack of genes encoding secreted calcium-binding phosphoproteins in cartilaginous fishes explains the absence of bone in their endoskeleton. Furthermore, the adaptive immune system of cartilaginous fishes is unusual: it lacks the canonical CD4 co-receptor and most transcription factors, cytokines and cytokine receptors related to the CD4 lineage, despite the presence of polymorphic major histocompatibility complex class II molecules. It thus presents a new model for understanding the origin of adaptive immunity.

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keywords:genome,gnathostome,evolution,living fossil

Diversity of ageing across the tree of life

Owen R. Jones,     Alexander Scheuerlein,     Roberto Salguero-Gómez,     Carlo Giovanni Camarda,     Ralf Schaible,     Brenda B. Casper,     Johan P. Dahlgren,     Johan Ehrlén,     María B. García,     Eric S. Menges,     Pedro F. Quintana-Ascencio,     Hal Caswell,     Annette Baudisch     & James W. Vaupel

                                                                          

Abstract:

Evolution drives, and is driven by, demography. A genotype moulds its phenotype’s age patterns of mortality and fertility in an environment; these two patterns in turn determine the genotype’s fitness in that environment. Hence, to understand the evolution of ageing, age patterns of mortality and reproduction need to be compared for species across the tree of life. However, few studies have done so and only for a limited range of taxa. Here we contrast standardized patterns over age for 11 mammals, 12 other vertebrates, 10 invertebrates, 12 vascular plants and a green alga. Although it has been predicted that evolution should inevitably lead to increasing mortality and declining fertility with age after maturity, there is great variation among these species, including increasing, constant, decreasing, humped and bowed trajectories for both long- and short-lived species. This diversity challenges theoreticians to develop broader perspectives on the evolution of ageing and empiricists to study the demography of more species.

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Keywords:ageing,vertebrates,taxa

UvrD facilitates DNA repair by pulling RNA polymerase backwards

Vitaly Epshtein,     Venu Kamarthapu,     Katelyn McGary,     Vladimir Svetlov,     Beatrix Ueberheide, Sergey Proshkin,     Alexander Mironov     & Evgeny Nudle

                                                                          

Abstract:

UvrD helicase is required for nucleotide excision repair, although its role in this process is not well defined. Here we show that Escherichia coli UvrD binds RNA polymerase during transcription elongation and, using its helicase/translocase activity, forces RNA polymerase to slide backward along DNA. By inducing backtracking, UvrD exposes DNA lesions shielded by blocked RNA polymerase, allowing nucleotide excision repair enzymes to gain access to sites of damage. Our results establish UvrD as a bona fide transcription elongation factor that contributes to genomic integrity by resolving conflicts between transcription and DNA repair complexes. Furthermore, we show that the elongation factor NusA cooperates with UvrD in coupling transcription to DNA repair by promoting backtracking and recruiting nucleotide excision repair enzymes to exposed lesions. Because backtracking is a shared feature of all cellular RNA polymerases, we propose that this mechanism enables RNA polymerases to function as global DNA damage scanners in bacteria and eukaryotes.

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Keywords:UvrD,dna repair,RNA polymerase,helicase

Biochemical reconstitution of topological DNA binding by the cohesin ring

Yasuto Murayama     & Frank Uhlmann

                                                               

Abstract;

Cohesion between sister chromatids, mediated by the chromosomal cohesin complex, is a prerequisite for faithful chromosome segregation in mitosis. Cohesin also has vital roles in DNA repair and transcriptional regulation. The ring-shaped cohesin complex is thought to encircle sister DNA strands, but its molecular mechanism of action is poorly understood and the biochemical reconstitution of cohesin activity in vitro has remained an unattained goal. Here we reconstitute cohesin loading onto DNA using purified fission yeast cohesin and its loader complex, Mis4Scc2–Ssl3Scc4 (Schizosaccharomyces pombe gene names appear throughout with their more commonly known Saccharomyces cerevisiae counterparts added in superscript). Incubation of cohesin with DNA leads to spontaneous topological loading, but this remains inefficient. The loader contacts cohesin at multiple sites around the ring circumference, including the hitherto enigmatic Psc3Scc3 subunit, and stimulates cohesin’s ATPase, resulting in efficient topological loading. The in vitro reconstitution of cohesin loading onto DNA provides mechanistic insight into the initial steps of the establishment of sister chromatid cohesion and other chromosomal processes mediated by cohesin.

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Keywords:DNA binding,cohesin ring,saccharomyces cervisiae

CNVs conferring risk of autism or schizophrenia affect cognition in controls

Hreinn Stefansson,     Andreas Meyer-Lindenberg,     Stacy Steinberg,     Brynja Magnusdottir, Katrin Morgen,     Sunna Arnarsdottir,     Gyda Bjornsdottir,     G. Bragi Walters,     Gudrun A. Jonsdottir,     Orla M. Doyle,     Heike Tost,     Oliver Grimm,     Solveig Kristjansdottir,     Heimir Snorrason,     Solveig R. Davidsdottir,     Larus J. Gudmundsson,     Gudbjorn F. Jonsson, Berglind Stefansdottir,     Isafold Helgadottir,     Magnus Haraldsson,     Birna Jonsdottir,     Johan H. Thygesen,     Adam J. Schwarz,     Michael Didriksen,     Tine B. Stensbøl     et al.

                                                                              

Abstract:

In a small fraction of patients with schizophrenia or autism, alleles of copy-number variants (CNVs) in their genomes are probably the strongest factors contributing to the pathogenesis of the disease. These CNVs may provide an entry point for investigations into the mechanisms of brain function and dysfunction alike. They are not fully penetrant and offer an opportunity to study their effects separate from that of manifest disease. Here we show in an Icelandic sample that a few of the CNVs clearly alter fecundity (measured as the number of children by age 45). Furthermore, we use various tests of cognitive function to demonstrate that control subjects carrying the CNVs perform at a level that is between that of schizophrenia patients and population controls. The CNVs do not all affect the same cognitive domains, hence the cognitive deficits that drive or accompany the pathogenesis vary from one CNV to another. Controls carrying the chromosome 15q11.2 deletion between breakpoints 1 and 2 (15q11.2(BP1-BP2) deletion) have a history of dyslexia and dyscalculia, even after adjusting for IQ in the analysis, and the CNV only confers modest effects on other cognitive traits. The 15q11.2(BP1-BP2) deletion affects brain structure in a pattern consistent with both that observed during first-episode psychosis in schizophrenia and that of structural correlates in dyslexia.

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Keywords:autism,schizophrenia,cognition,brain function

Architecture of the large subunit of the mammalian mitochondrial ribosome

Basil J. Greber,     Daniel Boehringer,     Alexander Leitner,     Philipp Bieri,     Felix Voigts-Hoffmann,     Jan P. Erzberger,     Marc Leibundgut,     Ruedi Aebersold     & Nenad Ban

                                                                 

Abstact:

Mitochondrial ribosomes synthesize a number of highly hydrophobic proteins encoded on the genome of mitochondria, the organelles in eukaryotic cells that are responsible for energy conversion by oxidative phosphorylation. The ribosomes in mammalian mitochondria have undergone massive structural changes throughout their evolution, including ribosomal RNA shortening and acquisition of mitochondria-specific ribosomal proteins. Here we present the three-dimensional structure of the 39S large subunit of the porcine mitochondrial ribosome determined by cryo-electron microscopy at 4.9 Å resolution. The structure, combined with data from chemical crosslinking and mass spectrometry experiments, reveals the unique features of the 39S subunit at near-atomic resolution and provides detailed insight into the architecture of the polypeptide exit site. This region of the mitochondrial ribosome has been considerably remodelled compared to its bacterial counterpart, providing a specialized platform for the synthesis and membrane insertion of the highly hydrophobic protein components of the respiratory chain

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Keywords:mammalian,mitochondrial,ribosome,phosphorylation,remodelled

Cell death by pyroptosis drives CD4 T-cell depletion in HIV-1 infection

Gilad Doitsh,     Nicole L. K. Galloway,     Xin Geng,     Zhiyuan Yang,     Kathryn M. Monroe,     Orlando Zepeda,     Peter W. Hunt,     Hiroyu Hatano,     Stefanie Sowinski,     Isa Muñoz-Arias     & Warner C. Greene

                                                                        

Abstract:

The pathway causing CD4 T-cell death in HIV-infected hosts remains poorly understood although apoptosis has been proposed as a key mechanism. We now show that caspase-3-mediated apoptosis accounts for the death of only a small fraction of CD4 T cells corresponding to those that are both activated and productively infected. The remaining over 95% of quiescent lymphoid CD4 T cells die by caspase-1-mediated pyroptosis triggered by abortive viral infection. Pyroptosis corresponds to an intensely inflammatory form of programmed cell death in which cytoplasmic contents and pro-inflammatory cytokines, including IL-1β, are released. This death pathway thus links the two signature events in HIV infection—CD4 T-cell depletion and chronic inflammation—and creates a pathogenic vicious cycle in which dying CD4 T cells release inflammatory signals that attract more cells to die. This cycle can be broken by caspase 1 inhibitors shown to be safe in humans, raising the possibility of a new class of ‘anti-AIDS’ therapeutics targeting the host rather than the virus.

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Keywords:pyroptosis,CD4,T-cells,HIV-1 \,caspase-1

Immunological and virological mechanisms of vaccine-mediated protection against SIV and HIV

Mario Roederer,     Brandon F. Keele,     Stephen D. Schmidt,     Rosemarie D. Mason,     Hugh C. Welles,     Will Fischer,     Celia Labranche,     Kathryn E. Foulds,     Mark K. Louder,     Zhi-Yong Yang, John-Paul M. Todd,     Adam P. Buzby,     Linh V. Mach,     Ling Shen,     Kelly E. Seaton,     Brandy M. Ward,     Robert T. Bailer,     Raphael Gottardo,     Wenjuan Gu,     Guido Ferrari,     S. Munir Alam, Thomas N. Denny,     David C. Montefiori,     Georgia D. Tomaras,     Bette T. Korber     et al.

                                                                           

Abstact:

A major challenge for the development of a highly effective AIDS vaccine is the identification of mechanisms of protective immunity. To address this question, we used a nonhuman primate challenge model with simian immunodeficiency virus (SIV). We show that antibodies to the SIV envelope are necessary and sufficient to prevent infection. Moreover, sequencing of viruses from breakthrough infections revealed selective pressure against neutralization-sensitive viruses; we identified a two-amino-acid signature that alters antigenicity and confers neutralization resistance. A similar signature confers resistance of human immunodeficiency virus (HIV)-1 to neutralization by monoclonal antibodies against variable regions 1 and 2 (V1V2), suggesting that SIV and HIV share a fundamental mechanism of immune escape from vaccine-elicited or naturally elicited antibodies. These analyses provide insight into the limited efficacy seen in HIV vaccine trials.

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Keywords:virological,immunological,siv,vaccine,hiv,antigenicity

Discovery and saturation analysis of cancer genes across 21 tumour types

Michael S. Lawrence,     Petar Stojanov,     Craig H. Mermel,     James T. Robinson,     Levi A. Garraway,     Todd R. Golub,     Matthew Meyerson,     Stacey B. Gabriel,     Eric S. Lander     & Gad Getz

                                                                      

Abstract:

Although a few cancer genes are mutated in a high proportion of tumours of a given type (>20%), most are mutated at intermediate frequencies (2–20%). To explore the feasibility of creating a comprehensive catalogue of cancer genes, we analysed somatic point mutations in exome sequences from 4,742 human cancers and their matched normal-tissue samples across 21 cancer types. We found that large-scale genomic analysis can identify nearly all known cancer genes in these tumour types. Our analysis also identified 33 genes that were not previously known to be significantly mutated in cancer, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis. Down-sampling analysis indicates that larger sample sizes will reveal many more genes mutated at clinically important frequencies. We estimate that near-saturation may be achieved with 600–5,000 samples per tumour type, depending on background mutation frequency. The results may help to guide the next stage of cancer genomics.

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Keywords:cancer genes,tumours,exome sequence,homeostatis

ANP32E is a histone chaperone that removes H2A.Z from chromatin

Arnaud Obri,     Khalid Ouararhni,     Christophe Papin,     Marie-Laure Diebold,     Kiran Padmanabhan,     Martin Marek,     Isabelle Stoll,     Ludovic Roy,     Patrick T. Reilly,     Tak W. Mak, Stefan Dimitrov,     Christophe Romier     & Ali Hamiche

                                                                                

Abstract:

H2A.Z is an essential histone variant implicated in the regulation of key nuclear events. However, the metazoan chaperones responsible for H2A.Z deposition and its removal from chromatin remain unknown. Here we report the identification and characterization of the human protein ANP32E as a specific H2A.Z chaperone. We show that ANP32E is a member of the presumed H2A.Z histone-exchange complex p400/TIP60. ANP32E interacts with a short region of the docking domain of H2A.Z through a new motif termed H2A.Z interacting domain (ZID). The 1.48 Å resolution crystal structure of the complex formed between the ANP32E-ZID and the H2A.Z/H2B dimer and biochemical data support an underlying molecular mechanism for H2A.Z/H2B eviction from the nucleosome and its stabilization by ANP32E through a specific extension of the H2A.Z carboxy-terminal α-helix. Finally, analysis of H2A.Z localization in ANP32E−/− cells by chromatin immunoprecipitation followed by sequencing shows genome-wide enrichment, redistribution and accumulation of H2A.Z at specific chromatin control regions, in particular at enhancers and insulators.

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Keywords:ANP32E,histone,chaperone,chromatin

Stimulus-triggered fate conversion of somatic cells into pluripotency

Haruko Obokata,     Teruhiko Wakayama,     Yoshiki Sasai,     Koji Kojima,     Martin P. Vacanti,     Hitoshi Niwa,     Masayuki Yamato     & Charles A. Vacanti

                                                                              

Abstract:

Here we report a unique cellular reprogramming phenomenon, called stimulus-triggered acquisition of pluripotency (STAP), which requires neither nuclear transfer nor the introduction of transcription factors. In STAP, strong external stimuli such as a transient low-pH stressor reprogrammed mammalian somatic cells, resulting in the generation of pluripotent cells. Through real-time imaging of STAP cells derived from purified lymphocytes, as well as gene rearrangement analysis, we found that committed somatic cells give rise to STAP cells by reprogramming rather than selection. STAP cells showed a substantial decrease in DNA methylation in the regulatory regions of pluripotency marker genes. Blastocyst injection showed that STAP cells efficiently contribute to chimaeric embryos and to offspring via germline transmission. We also demonstrate the derivation of robustly expandable pluripotent cell lines from STAP cells. Thus, our findings indicate that epigenetic fate determination of mammalian cells can be markedly converted in a context-dependent manner by strong environmental cues.

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Keywords:somatic cells,pluripotency,methylation,blastocyst

The evolution of lncRNA repertoires and expression patterns in tetrapods

Anamaria Necsulea,     Magali Soumillon,     Maria Warnefors,     Angélica Liechti,     Tasman Daish, Ulrich Zeller,     Julie C. Baker,     Frank Grützner     & Henrik Kaessmann

                                                                         

Abstract:

Only a very small fraction of long noncoding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but the absence of lncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of lncRNA repertoires and expression patterns, in 11 tetrapod species. We identify approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have originated more than 300 million years ago. We find that lncRNAs, in particular ancient ones, are in general actively regulated and may function predominantly in embryonic development. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network suggests potential functions for lncRNAs in fundamental processes such as spermatogenesis and synaptic transmission, but also in more specific mechanisms such as placenta development through microRNA production.

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Keywords:IncRNA,tetrapods,microRNA

An environmental bacterial taxon with a large and distinct metabolic repertoire

Micheal C. Wilson,     Tetsushi Mori,     Christian Rückert,     Agustinus R. Uria,     Maximilian J. Helf, Kentaro Takada,     Christine Gernert,     Ursula A. E. Steffens,     Nina Heycke,     Susanne Schmitt, Christian Rinke,     Eric J. N. Helfrich,     Alexander O. Brachmann,     Cristian Gurgui,     Toshiyuki Wakimoto,     Matthias Kracht,     Max Crüsemann,     Ute Hentschel,     Ikuro Abe,     Shigeki Matsunaga,     Jörn Kalinowski,     Haruko Takeyama     & Jörn Piel

                                                  

Abstract:

Cultivated bacteria such as actinomycetes are a highly useful source of biomedically important natural products. However, such ‘talented’ producers represent only a minute fraction of the entire, mostly uncultivated, prokaryotic diversity. The uncultured majority is generally perceived as a large, untapped resource of new drug candidates, but so far it is unknown whether taxa containing talented bacteria indeed exist. Here we report the single-cell- and metagenomics-based discovery of such producers. Two phylotypes of the candidate genus ‘Entotheonella’ with genomes of greater than 9 megabases and multiple, distinct biosynthetic gene clusters co-inhabit the chemically and microbially rich marine sponge Theonella swinhoei. Almost all bioactive polyketides and peptides known from this animal were attributed to a single phylotype. ‘Entotheonella’ spp. are widely distributed in sponges and belong to an environmental taxon proposed here as candidate phylum ‘Tectomicrobia’. The pronounced bioactivities and chemical uniqueness of ‘Entotheonella’ compounds provide significant opportunities for ecological studies and drug discovery.

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Keywords:taxon,acitomycetes,phylotypes,entotheonella

In vivo discovery of immunotherapy targets in the tumour microenvironment

Penghui Zhou,     Donald R. Shaffer,     Diana A. Alvarez Arias,     Yukoh Nakazaki,     Wouter Pos, Alexis J. Torres,     Viviana Cremasco,     Stephanie K. Dougan,     Glenn S. Cowley,     Kutlu Elpek, Jennifer Brogdon,     John Lamb,     Shannon J. Turley,     Hidde L. Ploegh,     David E. Root,     J. Christopher Love,     Glenn Dranoff,     Nir Hacohen,     Harvey Cantor     & Kai W. Wucherpfennig

                                                     

Abstract:

Recent clinical trials showed that targeting of inhibitory receptors on T cells induces durable responses in a subset of cancer patients, despite advanced disease. However, the regulatory switches controlling T-cell function in immunosuppressive tumours are not well understood. Here we show that such inhibitory mechanisms can be systematically discovered in the tumour microenvironment. We devised an in vivo pooled short hairpin RNA (shRNA) screen in which shRNAs targeting negative regulators became highly enriched in murine tumours by releasing a block on T-cell proliferation upon tumour antigen recognition. Such shRNAs were identified by deep sequencing of the shRNA cassette from T cells infiltrating tumour or control tissues. One of the target genes was Ppp2r2d, a regulatory subunit of the PP2A phosphatase family. In tumours, Ppp2r2d knockdown inhibited T-cell apoptosis and enhanced T-cell proliferation as well as cytokine production. Key regulators of immune function can therefore be discovered in relevant tissue microenvironments

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Keywords:immunotherapy,tumour,RNA[shRNA],phosphate

Fifty thousand years of Arctic vegetation and megafaunal diet

Eske Willerslev,     John Davison,     Mari Moora,     Martin Zobel,     Eric Coissac,     Mary E. Edwards, Eline D. Lorenzen,     Mette Vestergård,     Galina Gussarova,     James Haile,     Joseph Craine, Ludovic Gielly,     Sanne Boessenkool,     Laura S. Epp,     Peter B. Pearman,     Rachid Cheddadi, David Murray,     Kari Anne Bråthen,     Nigel Yoccoz,     Heather Binney,     Corinne Cruaud,     Patrick Wincker,     Tomasz Goslar,     Inger Greve Alsos,     Eva Bellemain     et al.

                                                                                        

Abstract:

Although it is generally agreed that the Arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of Arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we also explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr BP (before present). For much of the period investigated, Arctic vegetation consisted of dry steppe-tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25–15 kyr BP), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr BP, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such, our findings question the predominance of a Late Quaternary graminoid-dominated Arctic mammoth steppe.

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Keywords:megafaunal diet,meta barcoding,graminoids

Molecular control of δ-opioid receptor signalling

Gustavo Fenalti,     Patrick M. Giguere,     Vsevolod Katritch,     Xi-Ping Huang,     Aaron A. Thompson,     Vadim Cherezov,     Bryan L. Roth     & Raymond C. Stevens

                                                                                  

Abstract:

Opioids represent widely prescribed and abused medications, although their signal transduction mechanisms are not well understood. Here we present the 1.8 Å high-resolution crystal structure of the human δ-opioid receptor (δ-OR), revealing the presence and fundamental role of a sodium ion in mediating allosteric control of receptor functional selectivity and constitutive activity. The distinctive δ-OR sodium ion site architecture is centrally located in a polar interaction network in the seven-transmembrane bundle core, with the sodium ion stabilizing a reduced agonist affinity state, and thereby modulating signal transduction. Site-directed mutagenesis and functional studies reveal that changing the allosteric sodium site residue Asn 131 to an alanine or a valine augments constitutive β-arrestin-mediated signalling. Asp95Ala, Asn310Ala and Asn314Ala mutations transform classical δ-opioid antagonists such as naltrindole into potent β-arrestin-biased agonists. The data establish the molecular basis for allosteric sodium ion control in opioid signalling, revealing that sodium-coordinating residues act as ‘efficacy switches’ at a prototypic G-protein-coupled receptor.

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Keywords:opioids,allosteric control,beta arrestin mediated signalling,Asn 131

A polygenic burden of rare disruptive mutations in schizophrenia

Shaun M. Purcell,     Jennifer L. Moran,     Menachem Fromer,     Douglas Ruderfer,     Nadia Solovieff,     Panos Roussos,     Colm O’Dushlaine,     Kimberly Chambert,     Sarah E. Bergen,     Anna Kähler,     Laramie Duncan,     Eli Stahl,     Giulio Genovese,     Esperanza Fernández,     Mark O. Collins,     Noboru H. Komiyama,     Jyoti S. Choudhary,     Patrik K. E. Magnusson,     Eric Banks, Khalid Shakir,     Kiran Garimella,     Tim Fennell,     Mark DePristo,     Seth G. N. Grant,     Stephen J. Haggarty     et al.

                                                                           

Abstract:

Schizophrenia is a common disease with a complex aetiology, probably involving multiple and heterogeneous genetic factors. Here, by analysing the exome sequences of 2,536 schizophrenia cases and 2,543 controls, we demonstrate a polygenic burden primarily arising from rare (less than 1 in 10,000), disruptive mutations distributed across many genes. Particularly enriched gene sets include the voltage-gated calcium ion channel and the signalling complex formed by the activity-regulated cytoskeleton-associated scaffold protein (ARC) of the postsynaptic density, sets previously implicated by genome-wide association and copy-number variation studies. Similar to reports in autism, targets of the fragile X mental retardation protein (FMRP, product of FMR1) are enriched for case mutations. No individual gene-based test achieves significance after correction for multiple testing and we do not detect any alleles of moderately low frequency (approximately 0.5 to 1 per cent) and moderately large effect. Taken together, these data suggest that population-based exome sequencing can discover risk alleles and complements established gene-mapping paradigms in neuropsychiatric disease.

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Keywords:aetiology,schizophrenia,scaffold protein

De novo mutations in schizophrenia implicate synaptic networks

Menachem Fromer,     Andrew J. Pocklington,     David H. Kavanagh,     Hywel J. Williams,     Sarah Dwyer,     Padhraig Gormley,     Lyudmila Georgieva,     Elliott Rees,     Priit Palta,     Douglas M. Ruderfer,     Noa Carrera,     Isla Humphreys,     Jessica S. Johnson,     Panos Roussos,     Douglas D. Barker,     Eric Banks,     Vihra Milanova,     Seth G. Grant,     Eilis Hannon,     Samuel A. Rose,     Kimberly Chambert,     Milind Mahajan,     Edward M. Scolnick,     Jennifer L. Moran,     George Kirov     et al.

                                                                                  

Abstract:

Inherited alleles account for most of the genetic risk for schizophrenia. However, new (de novo) mutations, in the form of large chromosomal copy number changes, occur in a small fraction of cases and disproportionally disrupt genes encoding postsynaptic proteins. Here we show that small de novo mutations, affecting one or a few nucleotides, are overrepresented among glutamatergic postsynaptic proteins comprising activity-regulated cytoskeleton-associated protein (ARC) and N-methyl-D-aspartate receptor (NMDAR) complexes. Mutations are additionally enriched in proteins that interact with these complexes to modulate synaptic strength, namely proteins regulating actin filament dynamics and those whose messenger RNAs are targets of fragile X mental retardation protein (FMRP). Genes affected by mutations in schizophrenia overlap those mutated in autism and intellectual disability, as do mutation-enriched synaptic pathways. Aligning our findings with a parallel case–control study, we demonstrate reproducible insights into aetiological mechanisms for schizophrenia and reveal pathophysiology shared with other neurodevelopmental disorders.

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Keywords:schizophrenia,synaptic networks,glutamatergic

Protein-guided RNA dynamics during early ribosome assembly

Hajin Kim,     Sanjaya C. Abeysirigunawarden,     Ke Chen,     Megan Mayerle,     Kaushik Ragunathan,     Zaida Luthey-Schulten,     Taekjip Ha     & Sarah A. Woodson

                                                                               

Abstract:

The assembly of 30S ribosomes requires the precise addition of 20 proteins to the 16S ribosomal RNA. How early binding proteins change the ribosomal RNA structure so that later proteins may join the complex is poorly understood. Here we use single-molecule fluorescence resonance energy transfer (FRET) to observe real-time encounters between Escherichia coli ribosomal protein S4 and the 16S 5′ domain RNA at an early stage of 30S assembly. Dynamic initial S4–RNA complexes pass through a stable non-native intermediate before converting to the native complex, showing that non-native structures can offer a low free-energy path to protein–RNA recognition. Three-colour FRET and molecular dynamics simulations reveal how S4 changes the frequency and direction of RNA helix motions, guiding a conformational switch that enforces the hierarchy of protein addition. These protein-guided dynamics offer an alternative explanation for induced fit in RNA–protein complexes.

Source:

Keywords:ribosome,RNA helix motion,RNA-protein complexes

Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia

Liran I. Shlush,     Sasan Zandi,     Amanda Mitchell,     Weihsu Claire Chen,     Joseph M. Brandwein, Vikas Gupta,     James A. Kennedy,     Aaron D. Schimmer,     Andre C. Schuh,     Karen W. Yee, Jessica L. McLeod,     Monica Doedens,     Jessie J. F. Medeiros,     Rene Marke,     Hyeoung Joon Kim,     Kwon Lee,     John D. McPherson,     Thomas J. Hudson,     The HALT Pan-Leukemia Gene Panel Consortium,     Andrew M. K. Brown,     Quang M. Trinh,     Lincoln D. Stein,     Mark D. Minden, Jean C. Y. Wang     & John E. Dick

                                                                                              

Abstract:

In acute myeloid leukaemia (AML), the cell of origin, nature and biological consequences of initiating lesions, and order of subsequent mutations remain poorly understood, as AML is typically diagnosed without observation of a pre-leukaemic phase. Here, highly purified haematopoietic stem cells (HSCs), progenitor and mature cell fractions from the blood of AML patients were found to contain recurrent DNMT3A mutations (DNMT3Amut) at high allele frequency, but without coincident NPM1 mutations (NPM1c) present in AML blasts. DNMT3Amut-bearing HSCs showed a multilineage repopulation advantage over non-mutated HSCs in xenografts, establishing their identity as pre-leukaemic HSCs. Pre-leukaemic HSCs were found in remission samples, indicating that they survive chemotherapy. Therefore DNMT3Amut arises early in AML evolution, probably in HSCs, leading to a clonally expanded pool of pre-leukaemic HSCs from which AML evolves. Our findings provide a paradigm for the detection and treatment of pre-leukaemic clones before the acquisition of additional genetic lesions engenders greater therapeutic resistance.

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Keywords:pre-leukaemic,haematopoietic,stem cells

In situ identification of bipotent stem cells in the mammary gland

Anne C. Rios,     Nai Yang Fu,     Geoffrey J. Lindeman     & Jane E. Visvader

                                                                      

Abstract:

The mammary epithelium undergoes profound morphogenetic changes during development. Architecturally, it comprises two primary lineages, the inner luminal and outer myoepithelial cell layers. Two opposing concepts on the nature of mammary stem cells (MaSCs) in the postnatal gland have emerged. One model, based on classical transplantation assays, postulates that bipotent MaSCs have a key role in coordinating ductal epithelial expansion and maintenance in the adult gland, whereas the second model proposes that only unipotent MaSCs identified by lineage tracing contribute to these processes. Through clonal cell-fate mapping studies using a stochastic multicolour cre reporter combined with a new three-dimensional imaging strategy, we provide evidence for the existence of bipotent MaSCs as well as distinct long-lived progenitor cells. The cellular dynamics at different developmental stages support a model in which both stem and progenitor cells drive morphogenesis during puberty, whereas bipotent MaSCs coordinate ductal homeostasis and remodelling of the mouse adult gland.

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Keywords:bip[otent,stem cells,mammary glands

Geriatric muscle stem cells switch reversible quiescence into senescence

Pedro Sousa-Victor,     Susana Gutarra,     Laura García-Prat,     Javier Rodriguez-Ubreva,     Laura Ortet,     Vanessa Ruiz-Bonilla,     Mercè Jardí,     Esteban Ballestar,     Susana González,     Antonio L. Serrano,     Eusebio Perdiguero     & Pura Muñoz-Cánoves

                                                                                      

Abstract:

Regeneration of skeletal muscle depends on a population of adult stem cells (satellite cells) that remain quiescent throughout life. Satellite cell regenerative functions decline with ageing. Here we report that geriatric satellite cells are incapable of maintaining their normal quiescent state in muscle homeostatic conditions, and that this irreversibly affects their intrinsic regenerative and self-renewal capacities. In geriatric mice, resting satellite cells lose reversible quiescence by switching to an irreversible pre-senescence state, caused by derepression of p16INK4a (also called Cdkn2a). On injury, these cells fail to activate and expand, undergoing accelerated entry into a full senescence state (geroconversion), even in a youthful environment. p16INK4a silencing in geriatric satellite cells restores quiescence and muscle regenerative functions. Our results demonstrate that maintenance of quiescence in adult life depends on the active repression of senescence pathways. As p16INK4a is dysregulated in human geriatric satellite cells, these findings provide the basis for stem-cell rejuvenation in sarcopenic muscles.

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Keywords:geriatric,stem cells,quiescence,senescence

A Crohn’s disease variant in Atg16l1 enhances its degradation by caspase 3

Aditya Murthy,     Yun Li,     Ivan Peng,     Mike Reichelt,     Anand Kumar Katakam,     Rajkumar Noubade,     Merone Roose-Girma,     Jason DeVoss,     Lauri Diehl,     Robert R. Graham     & Menno van Lookeren Campagne

                                                                                                                                                                                                               

Abstract:

Crohn’s disease is a debilitating inflammatory bowel disease (IBD) that can involve the entire digestive tract. A single-nucleotide polymorphism (SNP) encoding a missense variant in the autophagy gene ATG16L1 (rs2241880, Thr300Ala) is strongly associated with the incidence of Crohn’s disease. Numerous studies have demonstrated the effect of ATG16L1 deletion or deficiency; however, the molecular consequences of the Thr300Ala (T300A) variant remains unknown. Here we show that amino acids 296–299 constitute a caspase cleavage motif in ATG16L1 and that the T300A variant (T316A in mice) significantly increases ATG16L1 sensitization to caspase-3-mediated processing. We observed that death-receptor activation or starvation-induced metabolic stress in human and murine macrophages increased degradation of the T300A or T316A variants of ATG16L1, respectively, resulting in diminished autophagy. Knock-in mice harbouring the T316A variant showed defective clearance of the ileal pathogen Yersinia enterocolitica and an elevated inflammatory cytokine response. In turn, deletion of the caspase-3-encoding gene, Casp3, or elimination of the caspase cleavage site by site-directed mutagenesis rescued starvation-induced autophagy and pathogen clearance, respectively. These findings demonstrate that caspase 3 activation in the presence of a common risk allele leads to accelerated degradation of ATG16L1, placing cellular stress, apoptotic stimuli and impaired autophagy in a unified pathway that predisposes to Crohn’s disease.

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Keywords:Atg1611,autophagy,caspase 3,yersinia enterocolitica

C11orf95–RELA fusions drive oncogenic NF-κB signalling in ependymoma

Matthew Parker,     Kumarasamypet M. Mohankumar,     Chandanamali Punchihewa,     Ricardo Weinlich,     James D. Dalton,     Yongjin Li,     Ryan Lee,     Ruth G. Tatevossian,     Timothy N. Phoenix, Radhika Thiruvenkatam,     Elsie White,     Bo Tang,     Wilda Orisme,     Kirti Gupta,     Michael Rusch, Xiang Chen,     Yuxin Li,     Panduka Nagahawhatte,     Erin Hedlund,     David Finkelstein,     Gang Wu, Sheila Shurtleff,     John Easton,     Kristy Boggs,     Donald Yergeau     et al.

                                                                                     

Abstract:

Members of the nuclear factor-κB (NF-κB) family of transcriptional regulators are central mediators of the cellular inflammatory response. Although constitutive NF-κB signalling is present in most human tumours, mutations in pathway members are rare, complicating efforts to understand and block aberrant NF-κB activity in cancer. Here we show that more than two-thirds of supratentorial ependymomas contain oncogenic fusions between RELA, the principal effector of canonical NF-κB signalling, and an uncharacterized gene, C11orf95. In each case, C11orf95–RELA fusions resulted from chromothripsis involving chromosome 11q13.1. C11orf95–RELA fusion proteins translocated spontaneously to the nucleus to activate NF-κB target genes, and rapidly transformed neural stem cells—the cell of origin of ependymoma—to form these tumours in mice. Our data identify a highly recurrent genetic alteration of RELA in human cancer, and the C11orf95–RELA fusion protein as a potential therapeutic target in supratentorial ependymoma.

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Keywords:C11,f95,fusion drive,ependymoma

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

S. C. Mack,     H. Witt,     R. M. Piro,     L. Gu,     S. Zuyderduyn,     A. M. Stütz,     X. Wang,     M. Gallo,     L. Garzia,     K. Zayne,     X. Zhang,     V. Ramaswamy,     N. Jäger,     D. T. W. Jones,     M. Sill,     T. J. Pugh,     M. Ryzhova,     K. M. Wani,     D. J. H. Shih,     R. Head,     M. Remke,     S. D. Bailey,     T. Zichner,     C. C. Faria, M. Barszczyk     et al.

                                                                                      

Abstract:

Ependymomas are common childhood brain tumours that occur throughout the nervous system, but are most common in the paediatric hindbrain. Current standard therapy comprises surgery and radiation, but not cytotoxic chemotherapy as it does not further increase survival. Whole-genome and whole-exome sequencing of 47 hindbrain ependymomas reveals an extremely low mutation rate, and zero significant recurrent somatic single nucleotide variants. Although devoid of recurrent single nucleotide variants and focal copy number aberrations, poor-prognosis hindbrain ependymomas exhibit a CpG island methylator phenotype. Transcriptional silencing driven by CpG methylation converges exclusively on targets of the Polycomb repressive complex 2 which represses expression of differentiation genes through trimethylation of H3K27. CpG island methylator phenotype-positive hindbrain ependymomas are responsive to clinical drugs that target either DNA or H3K27 methylation both in vitro and in vivo. We conclude that epigenetic modifiers are the first rational therapeutic candidates for this deadly malignancy, which is epigenetically deregulated but genetically bland.

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Keywords:epigenomic,tumours,methylator,ependymomas

Crystal structure of the plant dual-affinity nitrate transporter NRT1.1

Ji Sun,     John R. Bankston,     Jian Payandeh,     Thomas R. Hinds,     William N. Zagotta     & Ning Zheng

                                                                         

Abstract:

Nitrate is a primary nutrient for plant growth, but its levels in soil can fluctuate by several orders of magnitude. Previous studies have identified Arabidopsis NRT1.1 as a dual-affinity nitrate transporter that can take up nitrate over a wide range of concentrations. The mode of action of NRT1.1 is controlled by phosphorylation of a key residue, Thr 101; however, how this post-translational modification switches the transporter between two affinity states remains unclear. Here we report the crystal structure of unphosphorylated NRT1.1, which reveals an unexpected homodimer in the inward-facing conformation. In this low-affinity state, the Thr 101 phosphorylation site is embedded in a pocket immediately adjacent to the dimer interface, linking the phosphorylation status of the transporter to its oligomeric state. Using a cell-based fluorescence resonance energy transfer assay, we show that functional NRT1.1 dimerizes in the cell membrane and that the phosphomimetic mutation of Thr 101 converts the protein into a monophasic high-affinity transporter by structurally decoupling the dimer. Together with analyses of the substrate transport tunnel, our results establish a phosphorylation-controlled dimerization switch that allows NRT1.1 to uptake nitrate with two distinct affinity modes.

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Keywords:arabidopsis,phosphorylation,oligomeric,homodimer

Molecular basis of nitrate uptake by the plant nitrate transporter NRT1.1

Joanne L. Parker     & Simon Newstead

                                                                             

Abstract:

The NRT1/PTR family of proton-coupled transporters are responsible for nitrogen assimilation in eukaryotes and bacteria through the uptake of peptides. However, in most plant species members of this family have evolved to transport nitrate as well as additional secondary metabolites and hormones. In response to falling nitrate levels, NRT1.1 is phosphorylated on an intracellular threonine that switches the transporter from a low-affinity to high-affinity state. Here we present both the apo and nitrate-bound crystal structures of Arabidopsis thaliana NRT1.1, which together with in vitro binding and transport data identify a key role for His 356 in nitrate binding. Our data support a model whereby phosphorylation increases structural flexibility and in turn the rate of transport. Comparison with peptide transporters further reveals how the NRT1/PTR family has evolved to recognize diverse nitrogenous ligands, while maintaining elements of a conserved coupling mechanism within this superfamily of nutrient transporters.

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Keywords:nitrate,transporter NRT1.1,plantphosphorylation

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

Samuel H. Sternberg,     Sy Redding,     Martin Jinek,     Eric C. Greene     & Jennifer A. Doudna

                                                       

Abstract:

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA–DNA base-pairing to target foreign DNA in bacteria. Cas9–guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9–RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9–RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9–RNA. Competition assays provide evidence that DNA strand separation and RNA–DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.

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Keywords:dna,endonuclease,Cas9,paliundromic

A predictive fitness model for influenza

Marta Łuksza     & Michael Lässig

                                                                           

Abstract:

The seasonal human influenza A/H3N2 virus undergoes rapid evolution, which produces significant year-to-year sequence turnover in the population of circulating strains. Adaptive mutations respond to human immune challenge and occur primarily in antigenic epitopes, the antibody-binding domains of the viral surface protein haemagglutinin. Here we develop a fitness model for haemagglutinin that predicts the evolution of the viral population from one year to the next. Two factors are shown to determine the fitness of a strain: adaptive epitope changes and deleterious mutations outside the epitopes. We infer both fitness components for the strains circulating in a given year, using population-genetic data of all previous strains. From fitness and frequency of each strain, we predict the frequency of its descendent strains in the following year. This fitness model maps the adaptive history of influenza A and suggests a principled method for vaccine selection. Our results call for a more comprehensive epidemiology of influenza and other fast-evolving pathogens that integrates antigenic phenotypes with other viral functions coupled by genetic linkage.

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Keywords:influenza,epitope,haemeagglutination

Disclinations provide the missing mechanism for deforming olivine-rich rocks in the mantle

Patrick Cordier,     Sylvie Demouchy,     Benoît Beausir,     Vincent Taupin,     Fabrice Barou     & Claude Fressengeas

                                                                                             

Abstract:

Mantle flow involves large strains of polymineral aggregates. The strongly anisotropic plastic response of each individual grain in the aggregate results from the interactions between neighbouring grains and the continuity of material displacement across the grain boundaries. Orthorhombic olivine, which is the dominant mineral phase of the Earth’s upper mantle, does not exhibit enough slip systems to accommodate a general deformation state by intracrystalline slip without inducing damage. Here we show that a more general description of the deformation process that includes the motion of rotational defects referred to as disclinations can solve the olivine deformation paradox. We use high-resolution electron backscattering diffraction (EBSD) maps of deformed olivine aggregates to resolve the disclinations. The disclinations are found to decorate grain boundaries in olivine samples deformed experimentally and in nature. We present a disclination-based model of a high-angle tilt boundary in olivine, which demonstrates that an applied shear induces grain-boundary migration through disclination motion. This new approach clarifies grain-boundary-mediated plasticity in polycrystalline aggregates. By providing the missing mechanism for describing plastic flow in olivine, this work will permit multiscale modelling of the rheology of the upper mantle, from the atomic scale to the scale of the flow.

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Keywords:Mantle,intracrystalline,disclinations,grain boundry migration

Proof of principle for epitope-focused vaccine design

Bruno E. Correia,     John T. Bates,     Rebecca J. Loomis,     Gretchen Baneyx,     Chris Carrico, Joseph G. Jardine,     Peter Rupert,     Colin Correnti,     Oleksandr Kalyuzhniy,     Vinayak Vittal, Mary J. Connell,     Eric Stevens,     Alexandria Schroeter,     Man Chen,     Skye MacPherson, Andreia M. Serra,     Yumiko Adachi,     Margaret A. Holmes,     Yuxing Li,     Rachel E. Klevit,     Barney S. Graham,     Richard T. Wyatt,     David Baker,     Roland K. Strong,     James E. Crowe     et al

                                                                              

Abstract:

Vaccines prevent infectious disease largely by inducing protective neutralizing antibodies against vulnerable epitopes. Several major pathogens have resisted traditional vaccine development, although vulnerable epitopes targeted by neutralizing antibodies have been identified for several such cases. Hence, new vaccine design methods to induce epitope-specific neutralizing antibodies are needed. Here we show, with a neutralization epitope from respiratory syncytial virus, that computational protein design can generate small, thermally and conformationally stable protein scaffolds that accurately mimic the viral epitope structure and induce potent neutralizing antibodies. These scaffolds represent promising leads for the research and development of a human respiratory syncytial virus vaccine needed to protect infants, young children and the elderly. More generally, the results provide proof of principle for epitope-focused and scaffold-based vaccine design, and encourage the evaluation and further development of these strategies for a variety of other vaccine targets, including antigenically highly variable pathogens such as human immunodeficiency virus and influenza.

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Keywords:epitope,vaccine,syncytial virus

C9orf72 nucleotide repeat structures initiate molecular cascades of disease

Aaron R. Haeusler,     Christopher J. Donnelly,     Goran Periz,     Eric A. J. Simko,     Patrick G. Shaw, Min-Sik Kim,     Nicholas J. Maragakis,     Juan C. Troncoso,     Akhilesh Pandey,     Rita Sattler, Jeffrey D. Rothstein     & Jiou Wang

                                                                            

Abstract:

A hexanucleotide repeat expansion (HRE), (GGGGCC)n, in C9orf72 is the most common genetic cause of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here we identify a molecular mechanism by which structural polymorphism of the HRE leads to ALS/FTD pathology and defects. The HRE forms DNA and RNA G-quadruplexes with distinct structures and promotes RNA•DNA hybrids (R-loops). The structural polymorphism causes a repeat-length-dependent accumulation of transcripts aborted in the HRE region. These transcribed repeats bind to ribonucleoproteins in a conformation-dependent manner. Specifically, nucleolin, an essential nucleolar protein, preferentially binds the HRE G-quadruplex, and patient cells show evidence of nucleolar stress. Our results demonstrate that distinct C9orf72 HRE structural polymorphism at both DNA and RNA levels initiates molecular cascades leading to ALS/FTD pathologies, and provide the basis for a mechanistic model for repeat-associated neurodegenerative diseases

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Keywords:C9,f72,ribonucleoprotein

Alveolar progenitor and stem cells in lung development, renewal and cancer

Tushar J. Desai,     Douglas G. Brownfield     & Mark A. Krasnow

                                                                                    

Abstract:

Alveoli are gas-exchange sacs lined by squamous alveolar type (AT) 1 cells and cuboidal, surfactant-secreting AT2 cells. Classical studies suggested that AT1 arise from AT2 cells, but recent studies propose other sources. Here we use molecular markers, lineage tracing and clonal analysis to map alveolar progenitors throughout the mouse lifespan. We show that, during development, AT1 and AT2 cells arise directly from a bipotent progenitor, whereas after birth new AT1 cells derive from rare, self-renewing, long-lived, mature AT2 cells that produce slowly expanding clonal foci of alveolar renewal. This stem-cell function is broadly activated by AT1 injury, and AT2 self-renewal is selectively induced by EGFR (epidermal growth factor receptor) ligands in vitro and oncogenic Kras(G12D) in vivo, efficiently generating multifocal, clonal adenomas. Thus, there is a switch after birth, when AT2 cells function as stem cells that contribute to alveolar renewal, repair and cancer. We propose that local signals regulate AT2 stem-cell activity: a signal transduced by EGFR-KRAS controls self-renewal and is hijacked during oncogenesis, whereas another signal controls reprogramming to AT1 fate.

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Keywords:alveoli,clonal analysis,AT1,AT2oncogenic Kras

Unexpected link between an antibiotic, pannexin channels and apoptosis

Ivan K. H. Poon,     Yu-Hsin Chiu,     Allison J. Armstrong,     Jason M. Kinchen,     Ignacio J. Juncadella,     Douglas A. Bayliss     & Kodi S. Ravichandran

                                                                        

Abstract:

Plasma membrane pannexin 1 channels (PANX1) release nucleotide find-me signals from apoptotic cells to attract phagocytes. Here we show that the quinolone antibiotic trovafloxacin is a novel PANX1 inhibitor, by using a small-molecule screen. Although quinolones are widely used to treat bacterial infections, some quinolones have unexplained side effects, including deaths among children. PANX1 is a direct target of trovafloxacin at drug concentrations seen in human plasma, and its inhibition led to dysregulated fragmentation of apoptotic cells. Genetic loss of PANX1 phenocopied trovafloxacin effects, revealing a non-redundant role for pannexin channels in regulating cellular disassembly during apoptosis. Increase in drug-resistant bacteria worldwide and the dearth of new antibiotics is a major human health challenge. Comparing different quinolone antibiotics suggests that certain structural features may contribute to PANX1 blockade. These data identify a novel linkage between an antibiotic, pannexin channels and cellular integrity, and suggest that re-engineering certain quinolones might help develop newer antibacterials.

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Keywords:anitibiotic,pannexin,apoptosis,trovaflaxin,quinolones

Coupling of angiogenesis and osteogenesis by a specific vessel subtype in bone

                                                                                

Abstract:

The mammalian skeletal system harbours a hierarchical system of mesenchymal stem cells, osteoprogenitors and osteoblasts sustaining lifelong bone formation. Osteogenesis is indispensable for the homeostatic renewal of bone as well as regenerative fracture healing, but these processes frequently decline in ageing organisms, leading to loss of bone mass and increased fracture incidence. Evidence indicates that the growth of blood vessels in bone and osteogenesis are coupled, but relatively little is known about the underlying cellular and molecular mechanisms. Here we identify a new capillary subtype in the murine skeletal system with distinct morphological, molecular and functional properties. These vessels are found in specific locations, mediate growth of the bone vasculature, generate distinct metabolic and molecular microenvironments, maintain perivascular osteoprogenitors and couple angiogenesis to osteogenesis. The abundance of these vessels and associated osteoprogenitors was strongly reduced in bone from aged animals, and pharmacological reversal of this decline allowed the restoration of bone mass.

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Keywords:vessel,bone,osteoprogenitors,angiogenesis

Comprehensive molecular characterization of urothelial bladder carcinoma

                                                                     

Abstract:

Urothelial carcinoma of the bladder is a common malignancy that causes approximately 150,000 deaths per year worldwide. So far, no molecularly targeted agents have been approved for treatment of the disease. As part of The Cancer Genome Atlas project, we report here an integrated analysis of 131 urothelial carcinomas to provide a comprehensive landscape of molecular alterations. There were statistically significant recurrent mutations in 32 genes, including multiple genes involved in cell-cycle regulation, chromatin regulation, and kinase signalling pathways, as well as 9 genes not previously reported as significantly mutated in any cancer. RNA sequencing revealed four expression subtypes, two of which (papillary-like and basal/squamous-like) were also evident in microRNA sequencing and protein data. Whole-genome and RNA sequencing identified recurrent in-frame activating FGFR3–TACC3 fusions and expression or integration of several viruses (including HPV16) that are associated with gene inactivation. Our analyses identified potential therapeutic targets in 69% of the tumours, including 42% with targets in the phosphatidylinositol-3-OH kinase/AKT/mTOR pathway and 45% with targets (including ERBB2) in the RTK/MAPK pathway. Chromatin regulatory genes were more frequently mutated in urothelial carcinoma than in any other common cancer studied so far, indicating the future possibility of targeted therapy for chromatin abnormalities.

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Keywords:urothelial carcinoma,kinase signalling,tumours,mTOR

A promoter-level mammalian expression atlas

                                                                                  

Abstract:

Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly ‘housekeeping’, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research

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Keywords:cDNA,mammalian gene expression,promoter

An atlas of active enhancers across human cell types and tissues

Robin Andersson,     Claudia Gebhard,     Irene Miguel-Escalada,     Ilka Hoof,     Jette Bornholdt, Mette Boyd,     Yun Chen,     Xiaobei Zhao,     Christian Schmidl,     Takahiro Suzuki,     Evgenia Ntini, Erik Arner,     Eivind Valen,     Kang Li,     Lucia Schwarzfischer,     Dagmar Glatz,     Johanna Raithel, Berit Lilje,     Nicolas Rapin,     Frederik Otzen Bagger,     Mette Jørgensen,     Peter Refsing Andersen,     Nicolas Bertin,     Owen Rackham,     A. Maxwell Burroughs     et al.

                                                                                               

Abstract:

Enhancers control the correct temporal and cell-type-specific activation of gene expression in multicellular eukaryotes. Knowing their properties, regulatory activity and targets is crucial to understand the regulation of differentiation and homeostasis. Here we use the FANTOM5 panel of samples, covering the majority of human tissues and cell types, to produce an atlas of active, in vivo-transcribed enhancers. We show that enhancers share properties with CpG-poor messenger RNA promoters but produce bidirectional, exosome-sensitive, relatively short unspliced RNAs, the generation of which is strongly related to enhancer activity. The atlas is used to compare regulatory programs between different cells at unprecedented depth, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify cell-type-specific and ubiquitous enhancers. We further explore the utility of enhancer redundancy, which explains gene expression strength rather than expression patterns. The online FANTOM5 enhancer atlas represents a unique resource for studies on cell-type-specific enhancers and gene regulation.

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Keywords:tissue,polymorphism,gene expression,CpG