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  • Articles  (331)
  • Springer Nature  (331)
  • EMBO Reports  (331)
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  • Biology  (331)
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  • Articles  (331)
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  • Biology  (331)
  • Process Engineering, Biotechnology, Nutrition Technology
  • Medicine  (331)
  • 1
    Publication Date: 2019
    Description: The splicing factors U2AF65 and CAPERα engage multivalent interactions through their low complexity RS domains. The resulting assemblies can bridge the U2snRNP component SF3b155 with repeated polypyrimidine tracts in introns, to promote alternative splicing. Abstract The essential splicing factor U2AF65 is known to help anchoring U2 snRNP at the branch site. Its C‐terminal UHM domain interacts with ULM motifs of SF3b155, an U2 snRNP protein. Here, we report a cooperative binding of U2AF65 and the related protein CAPERα to the multi‐ULM domain of SF3b155. In addition, we show that the RS domain of U2AF65 drives a liquid–liquid phase separation that is amplified by intronic RNA with repeated pyrimidine tracts. In cells, knockdown of either U2AF65 or CAPERα improves the inclusion of cassette exons that are preceded by such repeated pyrimidine‐rich motifs. These results support a model in which liquid‐like assemblies of U2AF65 and CAPERα on repetitive pyrimidine‐rich RNA sequences are driven by their RS domains, and facilitate the recruitment of the multi‐ULM domain of SF3b155. We anticipate that posttranslational modifications and proteins recruited in dynamical U2AF65 and CAPERα condensates may further contribute to the complex mechanisms leading to specific splice site choice that occurs in cells.
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  • 2
    Publication Date: 2019
    Description: Biasing the sex ratio by genetic and non‐genetic approaches has been demonstrated for diverse organisms except higher vertebrates. This study provides proof of concept for a genetic system in mammals that allows biased sex production. Abstract Biasing the sex ratio of populations of different organisms, including plants, insects, crustacean, and fish, has been demonstrated by genetic and non‐genetic approaches. However, biasing the sex ratio of mammalian populations has not been demonstrated genetically. Here, we provide a first proof of concept for such a genetic system in mammals by crossing two genetically engineered mouse lines. The maternal line encodes a functional Cas9 protein on an autosomal chromosome, whereas the paternal line encodes guide RNAs on the Y chromosome targeting vital mouse genes. After fertilization, the presence of both the Y‐encoded guide RNAs from the paternal sperm and the Cas9 protein from the maternal egg targets the vital genes in males. We show that these genes are specifically targeted in males and that this breeding consequently self‐destructs solely males. Our results pave the way for a genetic system that allows biased sex production of livestock.
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  • 3
    Publication Date: 2019
    Description: A large survey of visitors at a science museum about the perception of biotechnology shows that names matter and that gender has an influence on people's attitude towards new technologies.
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  • 4
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    Springer Nature
    Publication Date: 2019
    Description: Art can challenge scientists and laypersons about controversial issues in research and bring reality and thoughtfulness from outside the lab into the lab.
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  • 5
    Publication Date: 2019
    Description: Plk1 inhibition compromises kinetochore integrity during chromosome segregation without activating mitotic checkpoint, thereby leading to formation of micronuclei. Abstract During mitosis, sister chromatids attach to microtubules which generate ~ 700 pN pulling force focused on the centromere. We report that chromatin‐localized signals generated by Polo‐like kinase 1 (Plk1) maintain the integrity of the kinetochore and centromere against this force. Without sufficient Plk1 activity, chromosomes become misaligned after normal condensation and congression. These chromosomes are silent to the mitotic checkpoint, and many lag and mis‐segregate in anaphase. Their centromeres and kinetochores lack CENP‐A, CENP‐C, CENP‐T, Hec1, Nuf2, and Knl1; however, CENP‐B is retained. CENP‐A loss occurs coincident with secondary misalignment and anaphase onset. This disruption occurs asymmetrically prior to anaphase and requires tension generated by microtubules. Mechanistically, centromeres highly recruit PICH DNA helicase and PICH depletion restores kinetochore disruption in pre‐anaphase cells. Furthermore, anaphase defects are significantly reduced by tethering Plk1 to chromatin, including H2B, and INCENP, but not to CENP‐A. Taken as a whole, this demonstrates that Plk1 signals are crucial for stabilizing centromeric architecture against tension.
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  • 6
    Publication Date: 2019
    Description: PPM family phosphatases are thought to act as monomers. This study shows that PPM1G forms a distinct holoenzyme complex with the PP2A regulatory subunit B56δ in the cytoplasm that functions in adherens junction assembly. Abstract Serine/threonine phosphatases achieve substrate diversity by forming distinct holoenzyme complexes in cells. Although the PPP family of serine/threonine phosphatase family members such as PP1 and PP2A are well known to assemble and function as holoenzymes, none of the PPM family members were so far shown to act as holoenzymes. Here, we provide evidence that PPM1G, a member of PPM family of serine/threonine phosphatases, forms a distinct holoenzyme complex with the PP2A regulatory subunit B56δ. B56δ promotes the re‐localization of PPM1G to the cytoplasm where the phosphatase can access a discrete set of substrates. Further, we unveil α‐catenin, a component of adherens junction, as a new substrate for the PPM1G‐B56 phosphatase complex in the cytoplasm. B56δ‐PPM1G dephosphorylates α‐catenin at serine 641, which is necessary for the appropriate assembly of adherens junctions and the prevention of aberrant cell migration. Collectively, we reveal a new holoenzyme with PPM1G‐B56δ as integral components, in which the regulatory subunit provides accessibility to distinct substrates for the phosphatase by defining its cellular localization.
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  • 7
    Publication Date: 2019
    Description: Rab35 at the mammalian and zebrafish cilium regulates cilium length and left‐right asymmetry, and controls the ciliary levels of PI(4,5)P2 and regulators of the Sonic hedgehog pathway. Abstract Rab and Arl guanine nucleotide‐binding (G) proteins regulate trafficking pathways essential for the formation, function and composition of primary cilia, which are sensory devices associated with Sonic hedgehog (Shh) signalling and ciliopathies. Here, using mammalian cells and zebrafish, we uncover ciliary functions for Rab35, a multitasking G protein with endocytic recycling, actin remodelling and cytokinesis roles. Rab35 loss via siRNAs, morpholinos or knockout reduces cilium length in mammalian cells and the zebrafish left‐right organiser (Kupffer's vesicle) and causes motile cilia‐associated left‐right asymmetry defects. Consistent with these observations, GFP‐Rab35 localises to cilia, as do GEF (DENND1B) and GAP (TBC1D10A) Rab35 regulators, which also regulate ciliary length and Rab35 ciliary localisation. Mammalian Rab35 also controls the ciliary membrane levels of Shh signalling regulators, promoting ciliary targeting of Smoothened, limiting ciliary accumulation of Arl13b and the inositol polyphosphate 5‐phosphatase (INPP5E). Rab35 additionally regulates ciliary PI(4,5)P2 levels and interacts with Arl13b. Together, our findings demonstrate roles for Rab35 in regulating cilium length, function and membrane composition and implicate Rab35 in pathways controlling the ciliary levels of Shh signal regulators.
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  • 8
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    Springer Nature
    Publication Date: 2019
    Description: The current crisis of liberal, secular democracies may have a biological cause: the dichotomy between humans’ biological and cultural evolution.
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  • 9
    Publication Date: 2019
    Description: Lysophagy, the selective autophagy of permeabilized lysosomes, requires extensive ubiquitination of the damaged organelle. The ubiquitin‐conjugating enzyme UBE2QL1 is a key coordinator of lysosome ubiquitination and lysophagy after lysosomal damage. Abstract The autophagic clearance of damaged lysosomes by lysophagy involves extensive modification of the organelle with ubiquitin, but the underlying ubiquitination machinery is still poorly characterized. Here, we use an siRNA screening approach and identify human UBE2QL1 as a major regulator of lysosomal ubiquitination, lysophagy, and cell survival after lysosomal damage. UBE2QL1 translocates to permeabilized lysosomes where it associates with damage sensors, ubiquitination targets, and lysophagy effectors. UBE2QL1 knockdown reduces ubiquitination and accumulation of the critical autophagy receptor p62 and abrogates recruitment of the AAA‐ATPase VCP/p97, which is essential for efficient lysophagy. Crucially, it affects association of LC3B with damaged lysosomes indicating that autophagosome formation was impaired. Already in unchallenged cells, depletion of UBE2QL1 leads to increased lysosomal damage, mTOR dissociation from lysosomes, and TFEB activation pointing to a role in lysosomal homeostasis. In line with this, mutation of the homologue ubc‐25 in Caenorhabditis elegans exacerbates lysosome permeability in worms lacking the lysosome stabilizing protein SCAV‐3/LIMP2. Thus, UBE2QL1 coordinates critical steps in the acute endolysosomal damage response and is essential for maintenance of lysosomal integrity.
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  • 10
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    Springer Nature
    Publication Date: 2019
    Description: An interview with Yossi Shiloh about the hunt for the gene that causes ataxia‐telangiectasia, its clinical implications and about science in Israel.
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  • 11
    Publication Date: 2019
    Description: This review discusses communication and key messengers between peripheral metabolic organs and the central nervous system that crosstalk for the maintenance of whole body energy homeostasis in health and disease. Abstract Multidirectional interactions between metabolic organs in the periphery and the central nervous system have evolved concomitantly with multicellular organisms to maintain whole‐body energy homeostasis and ensure the organism's adaptation to external cues. These interactions are altered in pathological conditions such as obesity and type 2 diabetes. Bioactive peptides and proteins, such as hormones and cytokines, produced by both peripheral organs and the central nervous system, are key messengers in this inter‐organ communication. Despite the early discovery of the first hormones more than 100 years ago, recent studies taking advantage of novel technologies have shed light on the multiple ways used by cells in the body to communicate and maintain energy balance. This review briefly summarizes well‐established concepts and focuses on recent advances describing how specific proteins and peptides mediate the crosstalk between gut, brain, and other peripheral metabolic organs in order to maintain energy homeostasis. Additionally, this review outlines how the improved knowledge about these inter‐organ networks is helping us to redefine therapeutic strategies in an effort to promote healthy living and fight metabolic disorders and other diseases.
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  • 12
    Publication Date: 2019
    Description: This review analyzes dynamic interactions between mitochondria and other organelles, the effects of metabolic alterations on these interactions and the impact of deficient organelle tethering on cellular and organelle metabolism. Abstract Cellular organelles are not static but show dynamism—a property that is likely relevant for their function. In addition, they interact with other organelles in a highly dynamic manner. In this review, we analyze the proteins involved in the interaction between mitochondria and other cellular organelles, especially the endoplasmic reticulum, lipid droplets, and lysosomes. Recent results indicate that, on one hand, metabolic alterations perturb the interaction between mitochondria and other organelles, and, on the other hand, that deficiency in proteins involved in the tethering between mitochondria and the ER or in specific functions of the interaction leads to metabolic alterations in a variety of tissues. The interaction between organelles is an emerging field that will permit to identify key proteins, to delineate novel modulation pathways, and to elucidate their implications in human disease.
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  • 13
    Publication Date: 2019
    Description: The crystal structure of human MICU2 with three calcium ions bound in combination with biochemical analyses reveals the interaction interface between MICU1 and MICU2 in both Ca2+‐free and Ca2+‐bound conditions. Abstract The mitochondrial calcium uniporter (MCU) complex mediates the uptake of Ca2+ into mitochondria. Its activity is regulated by a heterodimer of MICU1 and MICU2, two EF‐hand‐containing proteins that act as the main gatekeeper of the uniporter. Herein we report the crystal structure of human MICU2 at 1.96 Å resolution. Our structure reveals a dimeric architecture of MICU2, in which each monomer adopts the canonical two‐lobe structure with a pair of EF‐hands in each lobe. Both Ca2+‐bound and Ca2+‐free EF‐hands are observed in our structure. Moreover, we characterize the interaction sites within the MICU2 homodimer, as well as the MICU1–MICU2 heterodimer in both Ca2+‐free and Ca2+‐bound conditions. Glu242 in MICU1 and Arg352 in MICU2 are crucial for apo heterodimer formation, while Phe383 in MICU1 and Glu196 in MICU2 significantly contribute to the interaction in the Ca2+‐bound state. Based on our structural and biochemical analyses, we propose a model for MICU1–MICU2 heterodimer formation and its conformational transition from apo to a more compact Ca2+‐bound state, which expands our understanding of this co‐regulatory mechanism critical for MCU's mitochondrial calcium uptake function.
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  • 14
    Publication Date: 2019
    Description: The Mxl‐1 transcription factor promotes axon regeneration in C. elegans via inhibition of TDPT‐1, which reduces ETS‐4 SUMOylation and increases svh‐2 transcription. Abstract In Caenorhabditis elegans, the JNK MAP kinase (MAPK) pathway is important for axon regeneration. The JNK pathway is activated by a signaling cascade consisting of the growth factor SVH‐1 and its receptor tyrosine kinase SVH‐2. Expression of the svh‐2 gene is induced by axonal injury in a process involving the transcription factors ETS‐4 and CEBP‐1. Here, we find that svh‐14/mxl‐1, a gene encoding a Max‐like transcription factor, is required for activation of svh‐2 expression in response to axonal injury. We show that MXL‐1 binds to and inhibits the function of TDPT‐1, a C. elegans homolog of mammalian tyrosyl‐DNA phosphodiesterase 2 [TDP2; also called Ets1‐associated protein II (EAPII)]. Deletion of tdpt‐1 suppresses the mxl‐1 defect, but not the ets‐4 defect, in axon regeneration. TDPT‐1 induces SUMOylation of ETS‐4, which inhibits ETS‐4 transcriptional activity, and MXL‐1 counteracts this effect. Thus, TDPT‐1 interacts with two different transcription factors in axon regeneration.
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  • 15
    Publication Date: 2019
    Description: Cyclin C promotes Bax activation, recruitment to mitochondria and mitochondrial fragmentation, thereby initiating apoptosis in response to stress. Abstract Intrinsic apoptosis requires mitochondrial outer membrane disruption triggered by recruitment, activation, and oligomerization of the Bcl‐2 homology protein Bax. Following oxidative stress, we demonstrated that the transcriptional regulator cyclin C is released into the cytosol where it directs mitochondrial fragmentation and efficient apoptotic induction. This study reveals that cytoplasmic cyclin C is required for both normal Bax activation and its efficient mitochondrial localization. This activity appears direct as cyclin C co‐immunoprecipitates with active Bax in stressed cells and binds recombinant Bax in vitro. In addition, stable cyclin C–Bax association requires the fission complex. Pharmacologically stimulating cyclin C nuclear release is sufficient for Bax association and their mitochondrial localization in the absence of any stress signals. However, these cells do not undergo cell death as Bax fails to oligomerize. These data support a model that cyclin C association defines an initial step in Bax mitochondrial recruitment and provides a physical connection between the fission and apoptotic factors. This strategy allows the cell to discriminate stress‐induced fission able to recruit Bax from other types of mitochondrial divisions.
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  • 16
    Publication Date: 2019
    Description: Cell membrane localized DHHC5 palmitoylates components of desmosomes and promotes cell adhesion. Abstract S‐acylation (palmitoylation) is the only fully reversible lipid modification of proteins; however, little is known about how protein S‐acyltransferases (PATs) that mediate it are regulated. DHHC5 is a PAT that is mainly localised at the plasma membrane with roles in synaptic plasticity, massive endocytosis and cancer cell growth/invasion. Here, we demonstrate that DHHC5 binds to and palmitoylates a novel accessory protein Golga7b. Palmitoylation of Golga7b prevents clathrin‐mediated endocytosis of DHHC5 and stabilises it at the plasma membrane. Proteomic analysis of the composition of DHHC5/Golga7b‐associated protein complexes reveals a striking enrichment in adhesion proteins, particularly components of desmosomes. We show that desmoglein‐2 and plakophilin‐3 are substrates of DHHC5 and that DHHC5 and Golga7b are required for localisation of desmoglein‐2 to the plasma membrane and for desmosomal patterning. Loss of DHHC5/Golga7b causes functional impairments in cell adhesion, suggesting these proteins have a wider role in cell adhesion beyond desmosome assembly. This work uncovers a novel mechanism of DHHC5 regulation by Golga7b and demonstrates a role for the DHHC5/Golga7b complex in the regulation of cell adhesion.
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  • 17
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    Springer Nature
    Publication Date: 2019
    Description: Ancient retrovirus infections played a role in human evolution and are still involved in innate immunity and neural plasticity.
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  • 18
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    Springer Nature
    Publication Date: 2019
    Description: A better understanding of the nature and causes of failure in research could inform policies to improve the reproducibility of biomedical research.
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  • 19
    Publication Date: 2019
    Description: Cryo‐electron microscopy and atomistic simulations of SecYEG in the lipid environment reveal an early stage of membrane protein insertion. The flexible nascent chain triggers a conformational change that pre‐opens the translocon. Abstract The Sec translocon provides the lipid bilayer entry for ribosome‐bound nascent chains and thus facilitates membrane protein biogenesis. Despite the appreciated role of the native environment in the translocon:ribosome assembly, structural information on the complex in the lipid membrane is scarce. Here, we present a cryo‐electron microscopy‐based structure of bacterial translocon SecYEG in lipid nanodiscs and elucidate an early intermediate state upon insertion of the FtsQ anchor domain. Insertion of the short nascent chain causes initial displacements within the lateral gate of the translocon, where α‐helices 2b, 7, and 8 tilt within the membrane core to “unzip” the gate at the cytoplasmic side. Molecular dynamics simulations demonstrate that the conformational change is reversed in the absence of the ribosome, and suggest that the accessory α‐helices of SecE subunit modulate the lateral gate conformation. Site‐specific cross‐linking validates that the FtsQ nascent chain passes the lateral gate upon insertion. The structure and the biochemical data suggest that the partially inserted nascent chain remains highly flexible until it acquires the transmembrane topology.
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  • 20
    Publication Date: 2019
    Description: The non‐canonical inflammasome mediates pyroptotic cell death in response to bacterial LPS. A study in this issue of EMBO Reports identifies IRF2 as important player in the human non‐canonical inflammasome activating caspase‐4. The non‐canonical inflammasome mediates pyroptotic cell death in response to bacterial lipopolysaccharide (LPS) found in the cytosol. Understanding the mechanism and regulation of this system is of great interest, given its central role in mouse models of bacterial septic shock. In this issue of EMBO Reports, Benaoudia and colleagues sought to discover extra players in the human non‐canonical inflammasome using a CRISPR library screen; the only strongly positive hit apart from the known components caspase‐4 and gasdermin D was interferon regulatory factor‐2 (IRF2) [1]. IRF2 was found to be a transcriptional activator of caspase‐4, and in its absence, induction of IRF1 could substitute to maintain caspase‐4 expression.
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  • 21
    Publication Date: 2019
    Description: Nuclear flattening at late G1 activates TEAD and AP1, which in turn induces transcription of genes that promotes G1/S transition. Abstract The shape of the cell nucleus can vary considerably during developmental and pathological processes; however, the impact of nuclear morphology on cell behavior is not known. Here, we observed that the nuclear envelope flattens as cells transit from G1 to S phase and inhibition of myosin II prevents nuclear flattening and impedes progression to S phase. Strikingly, we show that applying compressive force on the nucleus in the absence of myosin II‐mediated tension is sufficient to restore G1 to S transition. Using a combination of tools to manipulate nuclear morphology, we observed that nuclear flattening activates a subset of transcription factors, including TEAD and AP1, leading to transcriptional induction of target genes that promote G1 to S transition. In addition, we found that nuclear flattening mediates TEAD and AP1 activation in response to ROCK‐generated contractility or cell spreading. Our results reveal that the nuclear envelope can operate as a mechanical sensor whose deformation controls cell growth in response to tension.
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  • 22
    Publication Date: 2019
    Description: Diflunisal, which is a drug in use in the clinic, selectively inhibits the chemotactic activity of HMGB1/CXCL12 complex. Abstract Extracellular HMGB1 triggers inflammation following infection or injury and supports tumorigenesis in inflammation‐related malignancies. HMGB1 has several redox states: reduced HMGB1 recruits inflammatory cells to injured tissues forming a heterocomplex with CXCL12 and signaling via its receptor CXCR4; disulfide‐containing HMGB1 binds to TLR4 and promotes inflammatory responses. Here we show that diflunisal, an aspirin‐like nonsteroidal anti‐inflammatory drug (NSAID) that has been in clinical use for decades, specifically inhibits in vitro and in vivo the chemotactic activity of HMGB1 at nanomolar concentrations, at least in part by binding directly to both HMGB1 and CXCL12 and disrupting their heterocomplex. Importantly, diflunisal does not inhibit TLR4‐dependent responses. Our findings clarify the mode of action of diflunisal and open the way to the rational design of functionally specific anti‐inflammatory drugs.
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  • 23
    Publication Date: 2019
    Description: The activation of MLKL by RIPK3 controls the execution of necroptosis. During the early stages of necroptotic cell death, MLKL oligomers promote the activation of Pannexin‐1 channels, which constricts the production of proinflammatory cytokines. Abstract The activation of mixed lineage kinase‐like (MLKL) by receptor‐interacting protein kinase‐3 (RIPK3) controls the execution of necroptosis, a regulated form of necrosis that occurs in apoptosis‐deficient conditions. Active oligomerized MLKL triggers the exposure of phosphatidylserine residues on the cell surface and disrupts the plasma membrane integrity by forming lytic pores. MLKL also governs endosomal trafficking and biogenesis of small extracellular vesicles as well as the production of proinflammatory cytokines during the early steps of necroptosis; however, the molecular basis continues to be elucidated. Here, we find that MLKL oligomers activate Pannexin‐1 (PANX1) channels, concomitantly to the loss of phosphatidylserine asymmetry. This plasma membrane “leakiness” requires the small GTPase RAB27A and RAB27B isoforms, which regulate intracellular vesicle trafficking, docking, and fusion with the plasma membrane. Although cells in which PANX1 is silenced or inhibited normally undergo necroptotic death, they display enhanced production of cytokines such as interleukin‐8, indicating that PANX1 may tamper with inflammation. These data identify a novel signaling nexus between MLKL, RAB27, and PANX1 and propose ways to interfere with inflammation associated with necroptosis.
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  • 24
    Publication Date: 2019
    Description: Trehalose‐6‐phosphate is a signaling molecule coordinating endogenous sugar availability and plant growth at high temperatures. Abstract Growth plasticity is a key mechanism by which plants adapt to the ever‐changing environmental conditions. Since growth is a high‐energy‐demanding and irreversible process, it is expected to be regulated by the integration of endogenous energy status as well as environmental conditions. Here, we show that trehalose‐6‐phosphate (T6P) functions as a sugar signaling molecule that coordinates thermoresponsive hypocotyl growth with endogenous sugar availability. We found that the loss of T6P SYNTHASE 1 (TPS1) in Arabidopsis thaliana impaired high‐temperature‐mediated hypocotyl growth. Consistently, the activity of PIF4, a transcription factor that positively regulates hypocotyl growth, was compromised in the tps1 mutant. We further show that, in the tps1 mutant, a sugar signaling kinase KIN10 directly phosphorylates and destabilizes PIF4. T6P inhibits KIN10 activity in a GRIK‐dependent manner, allowing PIF4 to promote hypocotyl growth at high temperatures. Together, our results demonstrate that T6P determines thermoresponsive growth through the KIN10‐PIF4 signaling module. Such regulation of PIF4 by T6P integrates the temperature‐signaling pathway with the endogenous sugar status, thus optimizing plant growth response to environmental stresses.
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  • 25
    Publication Date: 2019
    Description: EMBO reports, Volume 20, Issue 8, August 2019.
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  • 26
    Publication Date: 2019
    Description: Post‐transcriptional regulation by Lin28A and Lin28B enhances de novo fatty acid synthesis and metabolic conversion of saturated and unsaturated fatty acids via SREBP‐1, thereby promoting tumor progression. Abstract Lin28 plays an important role in promoting tumor development, whereas its exact functions and underlying mechanisms are largely unknown. Here, we show that both human homologs of Lin28 accelerate de novo fatty acid synthesis and promote the conversion from saturated to unsaturated fatty acids via the regulation of SREBP‐1. By directly binding to the mRNAs of both SREBP‐1 and SCAP, Lin28A/B enhance the translation and maturation of SREBP‐1, and protect cancer cells from lipotoxicity. Lin28A/B‐stimulated tumor growth is abrogated by SREBP‐1 inhibition and by the impairment of the RNA binding properties of Lin28A/B, respectively. Collectively, our findings uncover that post‐transcriptional regulation by Lin28A/B enhances de novo fatty acid synthesis and metabolic conversion of saturated and unsaturated fatty acids via SREBP‐1, which is critical for cancer progression.
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  • 27
    Publication Date: 2019
    Description: A study in this issue provides evidence that PC1 functions as an ion channel pore‐forming subunit in the PC1/PC2 complex. The assembly with PC1 changes the channel properties compared to PC2 homotetrameric channels. The functions of polycystin 1 and polycystin 2 (PC1 and PC2) have been surprisingly difficult to establish. PC1 and PC2 are encoded by the Pkd1 and Pkd2 genes that are implicated in autosomal dominant polycystic kidney disease (ADPKD). ADPKD is the most common potentially lethal genetic disorder, affecting ~1 in 1,000 people. Over the course of decades, ADPKD patients’ kidneys acquire numerous fluid‐filled cysts whose expansion compresses the surrounding parenchyma, leading to end‐stage renal disease in ~50% of afflicted individuals [1]. Identification of the genes encoding the PC proteins 20 years ago led to the hypothesis that they form an ion channel, since the sequence of PC2 marks it as a member of the TRP family of cation channels. In the ensuing 2 decades, tremendous effort has been devoted to determining whether this is indeed true and, if so, what characteristics that channel might manifest. A recent paper by Wang et al in this issue of EMBO Reports [2] demonstrates that assembly with PC1 changes the properties of the polycystin channel in ways that may help explain the complex behaviors that have been attributed to it.
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  • 28
    Publication Date: 2019
    Description: The SecYEG translocon provides the major route for co‐translational membrane protein insertion in bacteria. A cryo‐electron microscopy structure of SecYEG in lipid nanodiscs bound to a translating ribosome reveals an intermediate stage of protein insertion. The cytoplasm is the main place for protein translation from where nascent proteins are transported to their working areas, including the inside, outside, and membrane of the cell. The majority of newly synthesized membrane proteins is co‐translationally inserted into the membrane by the evolutionary conserved Sec translocon. In this issue of EMBO Reports, Kater et al [1] use single‐particle cryo‐electron microscopy to visualize a high‐resolution structure of the E. coli SecYEG translocon:ribosome‐nascent chain complex in a lipid environment constituted by nanodiscs. This snapshot represents an early intermediate state in membrane protein insertion and provides important information for understanding the molecular mechanism of membrane protein biogenesis.
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  • 29
    Publication Date: 2019
    Description: Old data are like yesterday's leftovers: sapped of novelty and excitement. But revisiting old sequence data with a fresh mind and new techniques can yield new and unexpected results.
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  • 30
    Publication Date: 2019
    Description: This review focuses on how pericytes link cerebrovascular and neurodegenerative diseases, and how recent insight into pericyte function might potentially be used for therapy. Abstract Neurodegenerative and cerebrovascular diseases cause considerable human suffering, and therapy options for these two disease categories are limited or non‐existing. It is an emerging notion that neurodegenerative and cerebrovascular diseases are linked in several ways, and in this review, we discuss the current status regarding vascular dysregulation in neurodegenerative disease, and conversely, how cerebrovascular diseases are associated with central nervous system (CNS) degeneration and dysfunction. The emerging links between neurodegenerative and cerebrovascular diseases are reviewed with a particular focus on pericytes—important cells that ensheath the endothelium in the microvasculature and which are pivotal for blood–brain barrier function and cerebral blood flow. Finally, we address how novel molecular and cellular insights into pericytes and other vascular cell types may open new avenues for diagnosis and therapy development for these important diseases.
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  • 31
    Publication Date: 2019
    Description: The bone marrow niche harbors cell populations that constitutively express heme oxygenase 1 (HO‐1). HO‐1 regulates the niche and protects HSCs from exhaustion in a cell extrinsic manner. Abstract While intrinsic changes in aging hematopoietic stem cells (HSCs) are well characterized, it remains unclear how extrinsic factors affect HSC aging. Here, we demonstrate that cells in the niche—endothelial cells (ECs) and CXCL12‐abundant reticular cells (CARs)—highly express the heme‐degrading enzyme, heme oxygenase 1 (HO‐1), but then decrease its expression with age. HO‐1‐deficient animals (HO‐1−/−) have altered numbers of ECs and CARs that produce less hematopoietic factors. HSCs co‐cultured in vitro with HO‐1−/− mesenchymal stromal cells expand, but have altered kinetic of growth and differentiation of derived colonies. HSCs from young HO‐1−/− animals have reduced quiescence and regenerative potential. Young HO‐1−/− HSCs exhibit features of premature exhaustion on the transcriptional and functional level. HO‐1+/+ HSCs transplanted into HO‐1−/− recipients exhaust their regenerative potential early and do not reconstitute secondary recipients. In turn, transplantation of HO‐1−/− HSCs to the HO‐1+/+ recipients recovers the regenerative potential of HO‐1−/− HSCs and reverses their transcriptional alterations. Thus, HSC‐extrinsic activity of HO‐1 prevents HSCs from premature exhaustion and may restore the function of aged HSCs.
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  • 32
    Publication Date: 2019
    Description: DOCK5 has been associated with obesity, however, the mechanism was not understood. This study reveals that DOCK5 reduces Raptor stability and mTORC1 activity in hepatocytes, thereby modulating hepatic insulin activity and glucose homeostasis. Abstract The dedicator of cytokinesis 5 (DOCK5) is associated with obesity. However, the mechanism by which DOCK5 contributes to obesity remains completely unknown. Here, we show that hepatic DOCK5 expression significantly decreases at a state of insulin resistance (IR). Deletion of DOCK5 in mice reduces energy expenditure, promotes obesity, augments IR, dysregulates glucose metabolism, and activates the mTOR (Raptor)/S6K1 pathway under a high‐fat diet (HFD). The overexpression of DOCK5 in hepatocytes inhibits gluconeogenic gene expression and increases the level of insulin receptor (InsR) and Akt phosphorylation. DOCK5 overexpression also inhibits mTOR/S6K1 phosphorylation and decreases the level of raptor protein expression. The opposite effects were observed in DOCK5‐deficient hepatocytes. Importantly, in liver‐specific Raptor knockout mice and associated hepatocytes, the effects of an adeno‐associated virus (AAV8)‐ or adenovirus‐mediated DOCK5 knockdown on glucose metabolism and insulin signaling are largely eliminated. Additionally, DOCK5–Raptor interaction is indispensable for the DOCK5‐mediated regulation of hepatic glucose production (HGP). Therefore, DOCK5 acts as a regulator of Raptor to control hepatic insulin activity and glucose homeostasis.
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  • 33
    Publication Date: 2019
    Description: CEP41 regulates cilia disassembly and angiogenesis through AURKA activation by modulating axonemal tubulin glutamylation in mammalian and zebrafish endothelial cells. Abstract The endothelial cilium is a microtubule‐based organelle responsible for blood flow‐induced mechanosensation and signal transduction during angiogenesis. The precise function and mechanisms by which ciliary mechanosensation occurs, however, are poorly understood. Although posttranslational modifications (PTMs) of cytoplasmic tubulin are known to be important in angiogenesis, the specific roles of ciliary tubulin PTMs play remain unclear. Here, we report that loss of centrosomal protein 41 (CEP41) results in vascular impairment in human cell lines and zebrafish, implying a previously unknown pro‐angiogenic role for CEP41. We show that proper control of tubulin glutamylation by CEP41 is necessary for cilia disassembly and that is involved in endothelial cell (EC) dynamics such as migration and tubulogenesis. We show that in ECs responding to shear stress or hypoxia, CEP41 activates Aurora kinase A (AURKA) and upregulates expression of VEGFA and VEGFR2 through ciliary tubulin glutamylation, as well as leads to the deciliation. We further show that in hypoxia‐induced angiogenesis, CEP41 is responsible for the activation of HIF1α to trigger the AURKA‐VEGF pathway. Overall, our results suggest the CEP41‐HIF1α‐AURKA‐VEGF axis as a key molecular mechanism of angiogenesis and demonstrate how important ciliary tubulin glutamylation is in mechanosense‐responded EC dynamics.
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  • 34
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    Springer Nature
    Publication Date: 2019
    Description: EMBO reports, EarlyView.
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  • 35
    Publication Date: 2019
    Description: Models describing the tethering mechanism of cohesin depend on either a monomeric cohesin ring or a dimer. Fluorescence correlation microscopy and photon counting histogram analysis now show that cohesin exists mostly as a monomer. Abstract The cohesin complex plays an important role in the maintenance of genome stability. Cohesin is composed of four core subunits and a set of regulatory subunits that interact with the core subunits. Less is known about cohesin dynamics in live cells and on the contribution of individual subunits to the overall complex. Understanding the tethering mechanism of cohesin is still a challenge, especially because the proposed mechanisms are still not conclusive. Models proposed to describe tethering depend on either the monomeric cohesin ring or a cohesin dimer. Here, we investigate the role of cohesin dynamics and stoichiometry in live yeast cells at single‐molecule resolution. We explore the effect of regulatory subunit deletion on cohesin mobility and found that depletion of different regulatory subunits has opposing effects. Finally, we show that cohesin exists mostly as a canonical monomer throughout the cell cycle, and its monomeric form is independent of its regulatory factors. Our results demonstrate that single‐molecule tools have the potential to provide new insights into the cohesin mechanism of action in live cells.
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  • 36
    Publication Date: 2019
    Description: Msp1 removes mislocalized tail‐anchored proteins to safeguard mitochondrial function. Msp1 recognizes substrates through a dual recognition mechanism involving hydrophobic interactions in the cytoplasm and electrostatic interactions in the intermembrane space. Abstract The conserved AAA‐ATPase Msp1 is embedded in the outer mitochondrial membrane and removes mislocalized tail‐anchored (TA) proteins upon dysfunction of the guided entry of tail‐anchored (GET) pathway. It remains unclear how Msp1 recognizes its substrates. Here, we extensively characterize Msp1 and its substrates, including the mitochondrially targeted Pex15Δ30, and full‐length Pex15, which mislocalizes to mitochondria upon dysfunction of Pex19 but not the GET pathway. Moreover, we identify two new substrates, Frt1 and Ysy6. Our results suggest that mislocalized TA proteins expose hydrophobic surfaces in the cytoplasm and are recognized by Msp1 through conserved hydrophobic residues. Introducing a hydrophobic patch into mitochondrial TA proteins transforms them into Msp1 substrates. In addition, Pex15Δ30 and Frt1 contain basic inter‐membrane space (IMS) residues critical for their mitochondrial mistargeting. Remarkably, Msp1 recognizes this feature through the acidic D12 residue in its IMS domain. This dual‐recognition mechanism involving interactions at the cytoplasmic and IMS domains of Msp1 and substrates greatly facilitates substrate recognition and is required by Msp1 to safeguard mitochondrial functions.
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  • 37
    Publication Date: 2019
    Description: A combination of gene‐editing, lineage tracing and human stem cell technologies identifies human nephron progenitors in kidney organoids and shows that human kidney organoids lack a progenitor niche capable of self‐renewal and ongoing nephrogenesis. Abstract Nephron formation continues throughout kidney morphogenesis in both mice and humans. Lineage tracing studies in mice identified a self‐renewing Six2‐expressing nephron progenitor population able to give rise to the full complement of nephrons throughout kidney morphogenesis. To investigate the origin of nephrons within human pluripotent stem cell‐derived kidney organoids, we performed a similar fate‐mapping analysis of the SIX2‐expressing lineage in induced pluripotent stem cell (iPSC)‐derived kidney organoids to explore the feasibility of investigating lineage relationships in differentiating iPSCs in vitro. Using CRISPR/Cas9 gene‐edited lineage reporter lines, we show that SIX2‐expressing cells give rise to nephron epithelial cell types but not to presumptive ureteric epithelium. The use of an inducible (CreERT2) line revealed a declining capacity for SIX2+ cells to contribute to nephron formation over time, but retention of nephron‐forming capacity if provided an exogenous WNT signal. Hence, while human iPSC‐derived kidney tissue appears to maintain lineage relationships previously identified in developing mouse kidney, unlike the developing kidney in vivo, kidney organoids lack a nephron progenitor niche capable of both self‐renewal and ongoing nephrogenesis.
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  • 38
    Publication Date: 2019
    Description: Parkin, a key protein in mitochondrial homeostasis, promotes the adaptive physiological plasticity of brown adipose tissue in response to thermogenic challenges. Abstract Parkin is an ubiquitin‐E3 ligase that acts as a key component of the cellular machinery for mitophagy. We show here that Parkin expression is reciprocally regulated in brown adipose tissue in relation to thermogenic activity. Thermogenic stimuli repress Parkin gene expression via transcriptional mechanisms that are elicited by noradrenergic and PPARα‐mediated pathways that involve intracellular lipolysis in brown adipocytes. Parkin‐KO mice show over‐activated brown adipose tissue thermogenic activity and exhibit improved metabolic parameters, especially when fed a high‐fat diet. Deacclimation, which is the return of a cold‐adapted mouse to a thermoneutral temperature, dramatically induces mitophagy in brown adipocytes, with a concomitant induction of Parkin levels. We further reveal that Parkin‐KO mice exhibit defects in the degradative processing of mitochondrial proteins in brown adipose tissue in response to deacclimation. These results suggest that the transcriptional control of Parkin in brown adipose tissue may contribute to modulating the mitochondrial mass and activity for adaptation to thermogenic requirements.
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  • 39
    Publication Date: 2019
    Description: Condensin I has a central role in mitotic chromosome assembly and segregation. The crystal structure of a human condensin I subcomplex reveals that the interaction between hCAP‐G and hCAP‐H is essential for mitotic chromosome assembly and DNA binding. Abstract Condensin I is a multi‐protein complex that plays an essential role in mitotic chromosome assembly and segregation in eukaryotes. It is composed of five subunits: two SMC (SMC2 and SMC4), a kleisin (CAP‐H), and two HEAT‐repeat (CAP‐D2 and CAP‐G) subunits. Although balancing acts of the two HEAT‐repeat subunits have been demonstrated to enable this complex to support the dynamic assembly of chromosomal axes in vertebrate cells, its underlying mechanisms remain poorly understood. Here, we report the crystal structure of a human condensin I subcomplex comprising hCAP‐G and hCAP‐H. hCAP‐H binds to the concave surfaces of a harp‐shaped HEAT‐repeat domain of hCAP‐G. Physical interaction between hCAP‐G and hCAP‐H is indeed essential for mitotic chromosome assembly recapitulated in Xenopus egg cell‐free extracts. Furthermore, this study reveals that the human CAP‐G‐H subcomplex has the ability to interact with not only double‐stranded DNA, but also single‐stranded DNA, suggesting functional divergence of the vertebrate condensin I complex in proper mitotic chromosome assembly.
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  • 40
    Publication Date: 2019
    Description: The increasing number of corrections in the scientific record and the debate about reproducibility affect journalists’ reporting about science and thereby public opinion on scientists and research.
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  • 41
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    Springer Nature
    Publication Date: 2019
    Description: Evolution had been puzzled scholars for centuries until Lamarck and Darwin proposed their general theories of evolution. While Lamarck was shown to be wrong, Darwin's insights revolutionized biology.
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  • 42
    Publication Date: 2019
    Description: EHMTs methylate LMNB1 to regulate its stability and localization and to promote heterochromatin assembly at the nuclear periphery. Depletion of EHMTs during physiological aging results in loss of heterochromatin organization in aged cells. Abstract Euchromatic histone methyltransferases (EHMTs), members of the KMT1 family, methylate histone and non‐histone proteins. Here, we uncover a novel role for EHMTs in regulating heterochromatin anchorage to the nuclear periphery (NP) via non‐histone methylation. We show that EHMTs methylate and stabilize LaminB1 (LMNB1), which associates with the H3K9me2‐marked peripheral heterochromatin. Loss of LMNB1 methylation or EHMTs abrogates heterochromatin anchorage at the NP. We further demonstrate that the loss of EHMTs induces many hallmarks of aging including global reduction of H3K27methyl marks and altered nuclear morphology. Consistent with this, we observe a gradual depletion of EHMTs, which correlates with loss of methylated LMNB1 and peripheral heterochromatin in aging human fibroblasts. Restoration of EHMT expression reverts peripheral heterochromatin defects in aged cells. Collectively, our work elucidates a new mechanism by which EHMTs regulate heterochromatin domain organization and reveals their impact on fundamental changes associated with the intrinsic aging process.
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  • 43
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    Springer Nature
    Publication Date: 2019
    Description: Biomedical research and clinical studies provide evidence that a healthy diet and lifestyle along with psychological support could be more efficient in treating and managing metabolic disorders than medication.
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  • 44
    Publication Date: 2019
    Description: The endothelial cells of the cranial vasculature in zebrafish extrude transient spherical structures termed “kugeln” after the German for sphere. Kugeln only form on cerebral vessels and are highly reactive for nitric oxide but their function is currently unknown. Abstract We identify a novel endothelial membrane behaviour in transgenic zebrafish. Cerebral blood vessels extrude large transient spherical structures that persist for an average of 23 min before regressing into the parent vessel. We term these structures “kugeln”, after the German for sphere. Kugeln are only observed arising from the cerebral vessels and are present as late as 28 days post fertilization. Kugeln do not communicate with the vessel lumen and can form in the absence of blood flow. They contain little or no cytoplasm, but the majority are highly positive for nitric oxide reactivity. Kugeln do not interact with brain lymphatic endothelial cells (BLECs) and can form in their absence, nor do they perform a scavenging role or interact with macrophages. Inhibition of actin polymerization, Myosin II, or Notch signalling reduces kugel formation, while inhibition of VEGF or Wnt dysregulation (either inhibition or activation) increases kugel formation. Kugeln represent a novel Notch‐dependent NO‐containing endothelial organelle restricted to the cerebral vessels, of currently unknown function.
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  • 45
    Publication Date: 2019
    Description: Acute myeloid leukemia functionally remodels the bone marrow niche. AML cells constitutively release extracellular vesicles enriched in miR‐1246, that traffic to long‐term hematopoietic stem cells and induce quiescence and DNA damage. Abstract Progressive remodeling of the bone marrow microenvironment is recognized as an integral aspect of leukemogenesis. Expanding acute myeloid leukemia (AML) clones not only alter stroma composition, but also actively constrain hematopoiesis, representing a significant source of patient morbidity and mortality. Recent studies revealed the surprising resistance of long‐term hematopoietic stem cells (LT‐HSC) to elimination from the leukemic niche. Here, we examine the fate and function of residual LT‐HSC in the BM of murine xenografts with emphasis on the role of AML‐derived extracellular vesicles (EV). AML‐EV rapidly enter HSC, and their trafficking elicits protein synthesis suppression and LT‐HSC quiescence. Mechanistically, AML‐EV transfer a panel of miRNA, including miR‐1246, that target the mTOR subunit Raptor, causing ribosomal protein S6 hypo‐phosphorylation, which in turn impairs protein synthesis in LT‐HSC. While HSC functionally recover from quiescence upon transplantation to an AML‐naive environment, they maintain relative gains in repopulation capacity. These phenotypic changes are accompanied by DNA double‐strand breaks and evidence of a sustained DNA‐damage response. In sum, AML‐EV contribute to niche‐dependent, reversible quiescence and elicit persisting DNA damage in LT‐HSC.
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  • 46
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    Springer Nature
    Publication Date: 2019
    Description: An interview with Dame Anne Glover on Brexit, science in politics and science policy.
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  • 47
    Publication Date: 2019
    Description: Machine learning systems are increasingly applied in health care and the life sciences with great potential for cancer diagnostics and optical microscopy.
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  • 48
    Publication Date: 2019
    Description: Checkpoint kinase 1 is needed for hematopoietic stem cell expansion and survival in the fetal liver. Conditional deletion of Chk1 in hematopoietic cells of adult mice selects cells retaining CHK1, suggesting an essential role in functional hematopoiesis. Abstract Checkpoint kinase 1 (CHK1) is critical for S‐phase fidelity and preventing premature mitotic entry in the presence of DNA damage. Tumor cells have developed a strong dependence on CHK1 for survival, and hence, this kinase has developed into a promising drug target. Chk1 deficiency in mice results in blastocyst death due to G2/M checkpoint failure showing that it is an essential gene and may be difficult to target therapeutically. Here, we show that chemical inhibition of CHK1 kills murine and human hematopoietic stem and progenitor cells (HSPCs) by the induction of BCL2‐regulated apoptosis. Cell death in HSPCs is independent of p53 but requires the BH3‐only proteins BIM, PUMA, and NOXA. Moreover, Chk1 is essential for definitive hematopoiesis in the embryo. Noteworthy, cell death inhibition in HSPCs cannot restore blood cell formation as HSPCs lacking CHK1 accumulate DNA damage and stop dividing. Moreover, conditional deletion of Chk1 in hematopoietic cells of adult mice selects for blood cells retaining CHK1, suggesting an essential role in maintaining functional hematopoiesis. Our findings establish a previously unrecognized role for CHK1 in establishing and maintaining hematopoiesis.
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  • 49
    Publication Date: 2019
    Description: Transfer RNA‐derived small RNAs are important regulators of protein translation. A set of tsRNAs is upregulated during induced differentiation of mESCs and regulates their stem cell‐state by modulating transcript stability and translation of the pluripotency factor c‐Myc. Abstract Transfer RNA (tRNA)‐derived small RNAs (tsRNAs) have recently emerged as important regulators of protein translation and shown to have diverse biological functions. However, the underlying cellular and molecular mechanisms of tsRNA function in the context of dynamic cell‐state transitions remain unclear. Expression analysis of tsRNAs in distinct heterologous cell and tissue models of stem vs. differentiated states revealed a differentiation‐dependent enrichment of 5′‐tsRNAs. We report the identification of a set of 5′‐tsRNAs that is upregulated in differentiating mouse embryonic stem cells (mESCs). Notably, interactome studies with differentially enriched 5′‐tsRNAs revealed a switch in their association with “effector” RNPs and “target” mRNAs in different cell states. We demonstrate that specific 5′‐tsRNAs can preferentially interact with the RNA‐binding protein, Igf2bp1, in the RA‐induced differentiated state. This association influences the transcript stability and thereby translation of the pluripotency‐promoting factor, c‐Myc, thus providing a mechanistic basis for how 5′‐tsRNAs can modulate stem cell states in mESCs. Together our study highlights the role of 5′‐tsRNAs in defining distinct cell states.
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  • 50
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    Springer Nature
    Publication Date: 2019
    Description: The term interdisciplinarity is frequently used to describe the nature of new research fields. But it is not always clear what these terms mean and whether new research fields do fulfill the criteria for truly interdisciplinary research.
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  • 51
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    Springer Nature
    Publication Date: 2019
    Description: Labmates are colleagues, friends, comforters…and competitors.
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  • 52
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    Springer Nature
    Publication Date: 2019
    Description: Experiments in space and on free‐fall platforms have yielded important insights into plant's reaction to low gravity with potential applications for space research and exploration.
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  • 53
    Publication Date: 2019
    Description: Tau accumulation, one hallmark of Alzheimer's disease, induces synaptic impairment by activating JAK2/STAT1 signaling, which transcriptionally suppresses N‐methyl‐D‐aspartate receptors. Downregulation of STAT1 ameliorates synaptic function and memory performance in mice. Abstract Intracellular tau accumulation forming neurofibrillary tangles is hallmark pathology of Alzheimer's disease (AD), but how tau accumulation induces synapse impairment is elusive. By overexpressing human full‐length wild‐type tau (termed hTau) to mimic tau abnormality as seen in the brain of sporadic AD patients, we find that hTau accumulation activates JAK2 to phosphorylate STAT1 (signal transducer and activator of transcription 1) at Tyr701 leading to STAT1 dimerization, nuclear translocation, and its activation. STAT1 activation suppresses expression of N‐methyl‐D‐aspartate receptors (NMDARs) through direct binding to the specific GAS element of GluN1, GluN2A, and GluN2B promoters, while knockdown of STAT1 by AAV‐Cre in STAT1flox/flox mice or expressing dominant negative Y701F‐STAT1 efficiently rescues hTau‐induced suppression of NMDAR expression with amelioration of synaptic functions and memory performance. These findings indicate that hTau accumulation impairs synaptic plasticity through JAK2/STAT1‐induced suppression of NMDAR expression, revealing a novel mechanism for hTau‐associated synapse and memory deficits.
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  • 54
    Publication Date: 2019
    Description: A study in this issue shows that high intracellular levels of lactate activate mTORC1 in KRAS transformed cells independently of growth factor input, thereby supporting oncogenic growth and proliferation. The kinase mammalian target of rapamycin (mTOR) is a major regulatory hub that senses and integrates nutrient, energy, and growth factor inputs to promote cell growth. In this issue of EMBO Reports, Byun et al [1] report that high intracellular levels of lactate activate mTORC1 in KRAS transformed cells independently of a growth factor input. This suggests a mechanism for how mTORC1 can be co‐opted to support oncogenic growth and proliferation.
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  • 55
    Publication Date: 2019
    Description: PfPH2 is a pan‐apicomplexan phosphoinositide‐binding protein important to attach and invade a red blood cell by the malaria parasite Plasmodium falciparum. It is implicated in the exocytosis of the micronemes secretory organelles. Abstract Invasion of human red blood cells by the malaria parasite Plasmodium falciparum is an essential step in the development of the disease. Consequently, the molecular players involved in host cell invasion represent important targets for inhibitor design and vaccine development. The process of merozoite invasion is a succession of steps underlined by the sequential secretion of the organelles of the apical complex. However, little is known with regard to how their contents are exocytosed. Here, we identify a phosphoinositide‐binding protein conserved in apicomplexan parasites and show that it is important for the attachment and subsequent invasion of the erythrocyte by the merozoite. Critically, removing the protein from its site of action by knock sideways preferentially prevents the secretion of certain types of micronemes. Our results therefore provide evidence for a role of phosphoinositide lipids in the malaria invasion process and provide further insight into the secretion of microneme organelle populations, which is potentially applicable to diverse apicomplexan parasites.
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  • 56
    Publication Date: 2019
    Description: Inflammasomes are intracellular multi‐protein complexes that act as signalling hubs of the innate immune system by inducing pyroptosis and by promoting the secretion of pro‐inflammatory cytokines. This review discusses the diverging roles of inflammasome‐produced cytokines in cancer. Abstract In addition to the genomic alterations that occur in malignant cells, the immune system is increasingly appreciated as a critical axis that regulates the rise of neoplasms and the development of primary tumours and metastases. The interaction between inflammatory cell infiltrates and stromal cells in the tumour microenvironment is complex, with inflammation playing both pro‐ and anti‐tumorigenic roles. Inflammasomes are intracellular multi‐protein complexes that act as key signalling hubs of the innate immune system. They respond to cellular stress and trauma by promoting activation of caspase‐1, a protease that induces a pro‐inflammatory cell death mode termed pyroptosis along with the maturation and secretion of the pro‐inflammatory cytokines interleukin (IL)‐1β and IL‐18. Here, we will briefly introduce inflammasome biology with a focus on the dual roles of inflammasome‐produced cytokines in cancer development. Despite emerging insight that inflammasomes may promote and suppress cancer development according to the tumour stage and the tumour microenvironment, much remains to be uncovered. Further exploration of inflammasome biology in tumorigenesis should enable the development of novel immunotherapies for cancer patients.
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  • 57
    Publication Date: 2019
    Description: A study in this issue reports on an alternative variant of TAZ, called cTAZ, which fine‐tunes type I interferon‐induced JAK‐STAT signalling, thereby contributing to the tight control of antiviral innate immune responses. The antiviral response is a tightly regulated process that follows specific patterns of timing and duration. The type I interferon‐induced antiviral pathway is driven by JAK‐STAT signalling. This is characterized by the dimerization of the receptor upon ligand binding, inducing cytoplasmic protein–protein interactions between phosphorylated STAT1 and STAT2, dimerization and nuclear translocation, which leads to the formation of a trimeric transcriptional competent complex, followed by INF‐inducible gene expression. Aberrant activation and timing of JAK‐STAT signalling might result in autoimmune disease. This implies that the strict regulation of this signalling pathway is essential to prevent pathological consequences. In this issue of EMBO Reports, Fang et al [1] describe an alternative variant of TAZ, called cTAZ, which fine‐tunes JAK‐STAT signalling, thereby contributing to the tight control of antiviral responses.
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  • 58
    Publication Date: 2019
    Description: The mitochondrial transcription elongation factor TEFM provides primers for mtDNA replication and is required for mtDNA transcription and also for RNA processing. Abstract Regulation of replication and expression of mitochondrial DNA (mtDNA) is essential for cellular energy conversion via oxidative phosphorylation. The mitochondrial transcription elongation factor (TEFM) has been proposed to regulate the switch between transcription termination for replication primer formation and processive, near genome‐length transcription for mtDNA gene expression. Here, we report that Tefm is essential for mouse embryogenesis and that levels of promoter‐distal mitochondrial transcripts are drastically reduced in conditional Tefm‐knockout hearts. In contrast, the promoter‐proximal transcripts are much increased in Tefm knockout mice, but they mostly terminate before the region where the switch from transcription to replication occurs, and consequently, de novo mtDNA replication is profoundly reduced. Unexpectedly, deep sequencing of RNA from Tefm knockouts revealed accumulation of unprocessed transcripts in addition to defective transcription elongation. Furthermore, a proximity‐labeling (BioID) assay showed that TEFM interacts with multiple RNA processing factors. Our data demonstrate that TEFM acts as a general transcription elongation factor, necessary for both gene transcription and replication primer formation, and loss of TEFM affects RNA processing in mammalian mitochondria.
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  • 59
    Publication Date: 2019
    Description: How the nucleus acquires its size is a fundamental cell biological question. This study identifies a novel mammalian nuclear size effector, and shows that pore complex number and transport factor levels tune nuclear import capacity and size. Abstract How intracellular organelles acquire their characteristic sizes is a fundamental question in cell biology. Given stereotypical changes in nuclear size in cancer, it is important to understand the mechanisms that control nuclear size in human cells. Using a high‐throughput imaging RNAi screen, we identify and mechanistically characterize ELYS, a nucleoporin required for post‐mitotic nuclear pore complex (NPC) assembly, as a determinant of nuclear size in mammalian cells. ELYS knockdown results in small nuclei, reduced nuclear lamin B2 localization, lower NPC density, and decreased nuclear import. Increasing nuclear import by importin α overexpression rescues nuclear size and lamin B2 import, while inhibiting importin α/β‐mediated nuclear import decreases nuclear size. Conversely, ELYS overexpression increases nuclear size, enriches nuclear lamin B2 at the nuclear periphery, and elevates NPC density and nuclear import. Consistent with these observations, knockdown or inhibition of exportin 1 increases nuclear size. Thus, we identify ELYS as a novel positive effector of mammalian nuclear size and propose that nuclear size is sensitive to NPC density and nuclear import capacity.
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  • 60
    Publication Date: 2019
    Description: The RNA binding protein IGF2BP1/IMP1 is upregulated in patients with Crohn's disease and ulcerative colitis. Imp1 deletion increases autophagy and recovery from colonic epithelial damage, suggesting that IMP1 modulates colonic inflammation and epithelial homeostasis. Abstract RNA binding proteins, including IMP1/IGF2BP1, are essential regulators of intestinal development and cancer. Imp1 hypomorphic mice exhibit gastrointestinal growth defects, yet the specific role for IMP1 in colon epithelial repair is unclear. Our prior work revealed that intestinal epithelial cell‐specific Imp1 deletion (Imp1ΔIEC) was associated with better regeneration in mice after irradiation. Here, we report increased IMP1 expression in patients with Crohn's disease and ulcerative colitis. We demonstrate that Imp1ΔIEC mice exhibit enhanced recovery following dextran sodium sulfate (DSS)‐mediated colonic injury. Imp1ΔIEC mice exhibit Paneth cell granule changes, increased autophagy flux, and upregulation of Atg5. In silico and biochemical analyses revealed direct binding of IMP1 to MAP1LC3B, ATG3, and ATG5 transcripts. Genetic deletion of essential autophagy gene Atg7 in Imp1ΔIEC mice revealed increased sensitivity of double‐mutant mice to colonic injury compared to control or Atg7 single mutant mice, suggesting a compensatory relationship between Imp1 and the autophagy pathway. The present study defines a novel interplay between IMP1 and autophagy, where IMP1 may be transiently induced during damage to modulate colonic epithelial cell responses to damage.
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  • 61
    Publication Date: 2019
    Description: The orphan nuclear receptor COUP‐TFII transmits KRAS‐induced oncogenic signals to promote glycolysis in cancer. KRAS/MEK‐dependent upregulation of COUP‐TFII increases LDHA expression, resulting in lactate production and mTORC1 activation. Abstract Oncogenic signals contribute to enhanced glycolysis and mTORC1 activity, leading to rapid cell proliferation in cancer. Regulation of glycolysis and mTORC1 by PI3K/Akt signaling is well established, but how KRAS‐induced MEK signaling regulates these pathways remains poorly understood. Here, we report a role for MEK‐driven lactate production in mTORC1 activation in KRAS‐activated cells. KRAS/MEK‐induced upregulation of the chicken ovalbumin upstream promoter transcriptional factor II (COUP‐TFII) increases the expression of lactate dehydrogenase A (LDHA), resulting in lactate production and mTORC1 activation. Further, lactate inhibits the interaction of TSC2 and Rheb, leading to the cellular activation of mTORC1 irrespective of growth factor stimulation. These findings suggest that COUP‐TFII is a novel oncogenic mediator, connecting KRAS signaling and glycolysis, and leading to mTORC1 activation and cellular growth.
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  • 62
    Publication Date: 2019
    Description: Aerobic exercise leads to skeletal muscle remodelling. This study reveals that dietary succinate is sufficient to elicit muscle remodelling and increased endurance in sedentary mice. Abstract The conversion of skeletal muscle fiber from fast twitch to slow‐twitch is important for sustained and tonic contractile events, maintenance of energy homeostasis, and the alleviation of fatigue. Skeletal muscle remodeling is effectively induced by endurance or aerobic exercise, which also generates several tricarboxylic acid (TCA) cycle intermediates, including succinate. However, whether succinate regulates muscle fiber‐type transitions remains unclear. Here, we found that dietary succinate supplementation increased endurance exercise ability, myosin heavy chain I expression, aerobic enzyme activity, oxygen consumption, and mitochondrial biogenesis in mouse skeletal muscle. By contrast, succinate decreased lactate dehydrogenase activity, lactate production, and myosin heavy chain IIb expression. Further, by using pharmacological or genetic loss‐of‐function models generated by phospholipase Cβ antagonists, SUNCR1 global knockout, or SUNCR1 gastrocnemius‐specific knockdown, we found that the effects of succinate on skeletal muscle fiber‐type remodeling are mediated by SUNCR1 and its downstream calcium/NFAT signaling pathway. In summary, our results demonstrate succinate induces transition of skeletal muscle fiber via SUNCR1 signaling pathway. These findings suggest the potential beneficial use of succinate‐based compounds in both athletic and sedentary populations.
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  • 63
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    Unknown
    Springer Nature
    Publication Date: 2019
    Description: Journalistic impartiality is a laudable aim, but overly rigid application of unbiased reporting may do more harm than good. The issue of false balance in science reporting has severe consequences for health and the environment.
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  • 64
    Publication Date: 2019
    Description: Dosage compensation to overcome X chromosome monosomy in Drosophila is established progressively during embryo development. Gradual dissemination of the active H4K16ac mark from DCC binding sites suggests that maturation of the X chromosome compartment is required for this process. Abstract In Drosophila melanogaster males, X‐chromosome monosomy is compensated by chromosome‐wide transcription activation. We found that complete dosage compensation during embryogenesis takes surprisingly long and is incomplete even after 10 h of development. Although the activating dosage compensation complex (DCC) associates with the X‐chromosome and MOF acetylates histone H4 early, many genes are not compensated. Acetylation levels on gene bodies continue to increase for several hours after gastrulation in parallel with progressive compensation. Constitutive genes are compensated earlier than developmental genes. Remarkably, later compensation correlates with longer distances to DCC binding sites. This time–space relationship suggests that DCC action on target genes requires maturation of the active chromosome compartment.
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  • 65
    Publication Date: 2019
    Description: Loss of the Elongator subunit Elp3 in the inner ear results in enhanced protein misfolding and aggregation. Impaired proteostasis negatively affects neuron survival and sensory cell polarity and results in deafness. Abstract Protein homeostasis is essential to cell function, and a compromised ability to reduce the load of misfolded and aggregated proteins is linked to numerous age‐related diseases, including hearing loss. Here, we show that altered proteostasis consequent to Elongator complex deficiency also impacts the proper development of the cochlea and results in deafness. In the absence of the catalytic subunit Elp3, differentiating spiral ganglion neurons display large aggresome‐like structures and undergo apoptosis before birth. The cochlear mechanosensory cells are able to survive proteostasis disruption but suffer defects in polarity and stereociliary bundle morphogenesis. We demonstrate that protein aggregates accumulate at the apical surface of hair cells, where they cause a local slowdown of microtubular trafficking, altering the distribution of intrinsic polarity proteins and affecting kinocilium position and length. Alleviation of protein misfolding using the chemical chaperone 4‐phenylbutyric acid during embryonic development ameliorates hair cell polarity in Elp3‐deficient animals. Our study highlights the importance of developmental proteostasis in the cochlea and unveils an unexpected link between proteome integrity and polarized organization of cellular components.
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  • 66
    Publication Date: 2019
    Description: The use of GM animals to produce human recombinant therapeutic proteins has progressed only slowly. But recent successes and new technologies could speed up development.
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  • 67
    Publication Date: 2019
    Description: Biological materials are a rich resource for nanoscale engineering. Their structure is easily accessible via their DNA and they were optimised through evolution to fulfill their function.
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  • 68
    Publication Date: 2019
    Description: 3D chromosome dynamics analysis of live mouse oocytes reveals a striking difference in the frequencies of erroneous kinetochore attachments during metaphase II, lagging chromosomes during anaphase II and aneuploidy in eggs. Abstract The accuracy of the two sequential meiotic divisions in oocytes is essential for creating a haploid gamete with a normal chromosomal content. Here, we have analysed the 3D dynamics of chromosomes during the second meiotic division in live mouse oocytes. We find that chromosomes form stable kinetochore–microtubule attachments at the end of prometaphase II stage that are retained until anaphase II onset. Remarkably, we observe that more than 20% of the kinetochore–microtubule attachments at the metaphase II stage are merotelic or lateral. However, 〈 1% of all chromosomes at onset of anaphase II are found to lag at the spindle equator and 〈 10% of the laggards missegregate and give rise to aneuploid gametes. Our results demonstrate that aberrant kinetochore–microtubule attachments are not corrected at the metaphase stage of the second meiotic division. Thus, the accuracy of the chromosome segregation process in mouse oocytes during meiosis II is ensured by an efficient correction process acting at the anaphase stage.
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  • 69
    Publication Date: 2019
    Description: Plant plasmodesmata are pore‐like cell‐to‐cell junctions containing a strand of endoplasmic reticulum in close contact to the plasma membrane. The MCTP protein family regulates these contact sites by acting as ER‐plasma membrane tethers. Abstract In eukaryotes, membrane contact sites (MCS) allow direct communication between organelles. Plants have evolved a unique type of MCS, inside intercellular pores, the plasmodesmata, where endoplasmic reticulum (ER)–plasma membrane (PM) contacts coincide with regulation of cell‐to‐cell signalling. The molecular mechanism and function of membrane tethering within plasmodesmata remain unknown. Here, we show that the multiple C2 domains and transmembrane region protein (MCTP) family, key regulators of cell‐to‐cell signalling in plants, act as ER‐PM tethers specifically at plasmodesmata. We report that MCTPs are plasmodesmata proteins that insert into the ER via their transmembrane region while their C2 domains dock to the PM through interaction with anionic phospholipids. A Atmctp3/Atmctp4 loss of function mutant induces plant developmental defects, impaired plasmodesmata function and composition, while MCTP4 expression in a yeast Δtether mutant partially restores ER‐PM tethering. Our data suggest that MCTPs are unique membrane tethers controlling both ER‐PM contacts and cell‐to‐cell signalling.
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  • 70
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    Unknown
    Springer Nature
    Publication Date: 2019
    Description: A subset of γδ T cells with limited clonal diversity strongly expands in lymph nodes of ageing mice, indicating a link between the aging‐dependent composition of γδ T cells and increased cancer risk in aged mice. Progressive susceptibility to tumors and infectious diseases in the elderly are a serious threat to public health in aging societies. For this reason, there is growing interest in mechanisms and predictive biomarkers that accompany and potentially cause this process. In this issue of EMBO Reports, Chen et al [1] report the surprising finding that a specific subset of γδ T cells with very limited clonal diversity strongly expands in lymph nodes of aging mice. These T cells uniformly express a T‐cell receptor (TCR) composed of a Vγ6 and a Vδ1 chain and show an effector T‐cell phenotype characterized by the swift production of the pro‐inflammatory cytokine interleukin‐17 (IL‐17) upon ex vivo stimulation (γδT17 cells). Since γδT17 cells are suspected to be pro‐tumorigenic [2], the authors next compared how mice of different age coped with an experimental lung cancer challenge and found impaired anti‐tumor responses in old mice. Based on these observations, they propose a link between changes of the composition of γδ T cells in the aging lymph nodes and increased risk of cancer development in aged mice.
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  • 71
    Publication Date: 2019
    Description: Upon ageing, γδ17 T cells expand at the expense of γδ1 T cells in response to increased IL‐7 in the peripheral lymph nodes. This leads to enhanced infiltration of γδ17 T cells into the tumour microenvironment, promoting faster tumour growth. Abstract How the age‐associated decline of immune function leads to increased cancer incidence is poorly understood. Here, we have characterised the cellular composition of the γδ T‐cell pool in peripheral lymph nodes (pLNs) upon ageing. We find that ageing has minimal cell‐intrinsic effects on function and global gene expression of γδ T cells, and γδTCR diversity remains stable. However, ageing alters TCRδ chain usage and clonal structure of γδ T‐cell subsets. Importantly, IL‐17‐producing γδ17 T cells dominate the γδ T‐cell pool of aged mice—mainly due to the selective expansion of Vγ6+ γδ17 T cells and augmented γδ17 polarisation of Vγ4+ T cells. Expansion of the γδ17 T‐cell compartment is mediated by increased IL‐7 expression in the T‐cell zone of old mice. In a Lewis lung cancer model, pro‐tumourigenic Vγ6+ γδ17 T cells are exclusively activated in the tumour‐draining LN and their infiltration into the tumour correlates with increased tumour size in aged mice. Thus, upon ageing, substantial compositional changes in γδ T‐cell pool in the pLN lead to an unbalanced γδ T‐cell response in the tumour that is associated with accelerated tumour growth.
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  • 72
    Publication Date: 2019
    Description: The EU Data Protection Regulation has wide‐ranging implications for research based on anonymized personal genomic and genetic data given the realistic risk of re‐identification.
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  • 73
    Publication Date: 2019
    Description: CDK12‐dependent RNAPII processivity on core DNA replication genes is a rate limiting factor for G1/S progression. CDK12 inhibition leads to premature termination and transcript shortening of a subset of genes. Abstract CDK12 is a kinase associated with elongating RNA polymerase II (RNAPII) and is frequently mutated in cancer. CDK12 depletion reduces the expression of homologous recombination (HR) DNA repair genes, but comprehensive insight into its target genes and cellular processes is lacking. We use a chemical genetic approach to inhibit analog‐sensitive CDK12, and find that CDK12 kinase activity is required for transcription of core DNA replication genes and thus for G1/S progression. RNA‐seq and ChIP‐seq reveal that CDK12 inhibition triggers an RNAPII processivity defect characterized by a loss of mapped reads from 3′ends of predominantly long, poly(A)‐signal‐rich genes. CDK12 inhibition does not globally reduce levels of RNAPII‐Ser2 phosphorylation. However, individual CDK12‐dependent genes show a shift of P‐Ser2 peaks into the gene body approximately to the positions where RNAPII occupancy and transcription were lost. Thus, CDK12 catalytic activity represents a novel link between regulation of transcription and cell cycle progression. We propose that DNA replication and HR DNA repair defects as a consequence of CDK12 inactivation underlie the genome instability phenotype observed in many cancers.
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  • 74
    Publication Date: 2019
    Description: The protein p62/Sequestosome 1 has dual activities in selective autophagy and in inflammatory signaling. The kinase TAK1 directs p62 action away from autophagy and relocalizes it to cytoplasmic “signalosomes” where p62 can promote signaling. Abstract The protein p62/Sequestosome 1 (p62) has been described as a selective autophagy receptor and independently as a platform for pro‐inflammatory and other intracellular signaling. How these seemingly disparate functional roles of p62 are coordinated has not been resolved. Here, we show that TAK1, a kinase involved in immune signaling, negatively regulates p62 action in autophagy. TAK1 reduces p62 localization to autophagosomes, dampening the autophagic degradation of both p62 and p62‐directed autophagy substrates. TAK1 also relocalizes p62 into dynamic cytoplasmic bodies, a phenomenon that accompanies the stabilization of TAK1 complex components. On the other hand, p62 facilitates the assembly and activation of TAK1 complexes, suggesting a connection between p62's signaling functions and p62 body formation. Thus, TAK1 governs p62 action, switching it from an autophagy receptor to a signaling platform. This ability of TAK1 to disable p62 as an autophagy receptor may allow certain autophagic substrates to accumulate when needed for cellular functions.
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  • 75
    Publication Date: 2019
    Description: FXTAS is caused by CGG repeat‐associated non‐AUG (RAN) translation that initiates within the 5′UTR of FMR1. A candidate‐based screen identified several initiation factors—DDX3X/Belle, eIF4B, eIF4H, eIF1, and eIF5—critical for FMR1 RAN translation. Abstract A CGG trinucleotide repeat expansion in the 5′ UTR of FMR1 causes the neurodegenerative disorder Fragile X‐associated tremor/ataxia syndrome (FXTAS). This repeat supports a non‐canonical mode of protein synthesis known as repeat‐associated, non‐AUG (RAN) translation. The mechanism underlying RAN translation at CGG repeats remains unclear. To identify modifiers of RAN translation and potential therapeutic targets, we performed a candidate‐based screen of eukaryotic initiation factors and RNA helicases in cell‐based assays and a Drosophila melanogaster model of FXTAS. We identified multiple modifiers of toxicity and RAN translation from an expanded CGG repeat in the context of the FMR1 5′UTR. These include the DEAD‐box RNA helicase belle/DDX3X, the helicase accessory factors EIF4B/4H, and the start codon selectivity factors EIF1 and EIF5. Disrupting belle/DDX3X selectively inhibited FMR1 RAN translation in Drosophila in vivo and cultured human cells, and mitigated repeat‐induced toxicity in Drosophila and primary rodent neurons. These findings implicate RNA secondary structure and start codon fidelity as critical elements mediating FMR1 RAN translation and identify potential targets for treating repeat‐associated neurodegeneration.
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  • 76
    Publication Date: 2019
    Description: Sensing of cytosolic LPS by caspase‐4 triggers non‐canonical inflammasome activation. Interferon‐Regulatory Factor 2 (IRF2) is a transcription factor controlling caspase‐4 expression and LPS‐mediated pyroptosis in human cells. Abstract Caspase‐4, the cytosolic LPS sensor, and gasdermin D, its downstream effector, constitute the non‐canonical inflammasome, which drives inflammatory responses during Gram‐negative bacterial infections. It remains unclear whether other proteins regulate cytosolic LPS sensing, particularly in human cells. Here, we conduct a genome‐wide CRISPR/Cas9 screen in a human monocyte cell line to identify genes controlling cytosolic LPS‐mediated pyroptosis. We find that the transcription factor, IRF2, is required for pyroptosis following cytosolic LPS delivery and functions by directly regulating caspase‐4 levels in human monocytes and iPSC‐derived monocytes. CASP4, GSDMD, and IRF2 are the only genes identified with high significance in this screen highlighting the simplicity of the non‐canonical inflammasome. Upon IFN‐γ priming, IRF1 induction compensates IRF2 deficiency, leading to robust caspase‐4 expression. Deficiency in IRF2 results in dampened inflammasome responses upon infection with Gram‐negative bacteria. This study emphasizes the central role of IRF family members as specific regulators of the non‐canonical inflammasome.
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  • 77
    Publication Date: 2019
    Description: The lncRNA CALIC associates with hnRNP‐L to induce AXL expression and to enhance the metastatic potential of colon cancer cells. Abstract Long non‐coding RNAs (lncRNAs) are aberrantly expressed in many disease conditions, including cancer. Accumulating evidence indicates that some lncRNAs may play critical roles in cancer progression and metastasis. Here, we identify a set of lncRNAs that are upregulated in metastatic subpopulations isolated from colon cancer HCT116 cells in vivo and show that one of these lncRNAs, which we name CALIC, is required for the metastatic activity of colon cancer cells. We show that CALIC associates with the RNA‐binding protein hnRNP‐L and imparts specificity to hnRNP‐L‐mediated gene expression. Furthermore, we demonstrate that the CALIC/hnRNP‐L complex upregulates the tyrosine kinase receptor AXL and that knockdown of CALIC or AXL using shRNA in colon cancer cells attenuates their ability to form metastases in mice. These results suggest that the CALIC/hnRNP‐L complex enhances the metastatic potential of colon cancer cells.
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  • 78
    Publication Date: 2019
    Description: Repositioning of nucleosomes occurs as human iPSC develop into neural progenitor cells, but a small number of nucleosome arrays remain in place at regulatory sites that control long‐range chromatin organisation. Abstract Nucleosome positioning is important for neurodevelopment, and genes mediating chromatin remodelling are strongly associated with human neurodevelopmental disorders. To investigate changes in nucleosome positioning during neural differentiation, we generate genome‐wide nucleosome maps from an undifferentiated human‐induced pluripotent stem cell (hiPSC) line and after its differentiation to the neural progenitor cell (NPC) stage. We find that nearly 3% of nucleosomes are highly positioned in NPC, but significantly, there are eightfold fewer positioned nucleosomes in pluripotent cells, indicating increased positioning during cell differentiation. Positioned nucleosomes do not strongly correlate with active chromatin marks or gene transcription. Unexpectedly, we find a small population of nucleosomes that occupy similar positions in pluripotent and neural progenitor cells and are found at binding sites of the key gene regulators NRSF/REST and CTCF. Remarkably, the presence of these nucleosomes appears to be independent of the associated regulatory complexes. Together, these results present a scenario in human cells, where positioned nucleosomes are sparse and dynamic, but may act to alter gene expression at a distance via the structural conformation at sites of chromatin regulation.
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  • 79
    Publication Date: 2019
    Description: This review discusses diverse functions of the NSL complex and NSL‐catalyzed lysine acetylation in transcriptional and signaling networks in health and disease. Abstract The functionality of chromatin is tightly regulated by post‐translational modifications that modulate transcriptional output from target loci. Among the post‐translational modifications of chromatin, reversible ε‐lysine acetylation of histone proteins is prominent at transcriptionally active genes. Lysine acetylation is catalyzed by lysine acetyltransferases (KATs), which utilize the central cellular metabolite acetyl‐CoA as their substrate. Among the KATs that mediate lysine acetylation, males absent on the first (MOF/KAT8) is particularly notable for its ability to acetylate histone 4 lysine 16 (H4K16ac), a modification that decompacts chromatin structure. MOF and its non‐specific lethal (NSL) complex members have been shown to localize to gene promoters and enhancers in the nucleus, as well as to microtubules and mitochondria to regulate key cellular processes. Highlighting their importance, mutations or deregulation of NSL complex members has been reported in both human neurodevelopmental disorders and cancer. Based on insight gained from studies in human, mouse, and Drosophila model systems, this review discusses the role of NSL‐mediated lysine acetylation in a myriad of cellular functions in both health and disease. Through these studies, the importance of the NSL complex in regulating core transcriptional and signaling networks required for normal development and cellular homeostasis is beginning to emerge.
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  • 80
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    Unknown
    Springer Nature
    Publication Date: 2019
    Description: A growing number of amateur biologists tinker with DNA at home or in community labs. This do‐it‐yourself movement helps to improve science literacy but it also creates some security concerns.
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  • 81
    Publication Date: 2019
    Description: The RNA‐binding protein Gadd45α controls aversive learning and synaptic plasticity by post‐transcriptional regulation of a set of memory‐related transcripts, containing long 3′UTR extensions. Abstract Learning is essential for survival and is controlled by complex molecular mechanisms including regulation of newly synthesized mRNAs that are required to modify synaptic functions. Despite the well‐known role of RNA‐binding proteins (RBPs) in mRNA functionality, their detailed regulation during memory consolidation is poorly understood. This study focuses on the brain function of the RBP Gadd45α (growth arrest and DNA damage‐inducible protein 45 alpha, encoded by the Gadd45a gene). Here, we find that hippocampal memory and long‐term potentiation are strongly impaired in Gadd45a‐deficient mice, a phenotype accompanied by reduced levels of memory‐related mRNAs. The majority of the Gadd45α‐regulated transcripts show unusually long 3′ untranslated regions (3′UTRs) that are destabilized in Gadd45a‐deficient mice via a transcription‐independent mechanism, leading to reduced levels of the corresponding proteins in synaptosomes. Moreover, Gadd45α can bind specifically to these memory‐related mRNAs. Our study reveals a new function for extended 3′UTRs in memory consolidation and identifies Gadd45α as a novel regulator of mRNA stability.
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  • 82
    Publication Date: 2019
    Description: ULK1 phosphorylates ATG16L1 on S278 to promote autophagic activity of wild‐type ATG16L1. In contrast, this regulation enhances caspase‐mediated degradation of Crohn‐associated (T300A) ATG16L1, thereby reducing xenophagy and bacterial clearance. Abstract Autophagy is a highly regulated catabolic pathway that is potently induced by stressors including starvation and infection. An essential component of the autophagy pathway is an ATG16L1‐containing E3‐like enzyme, which is responsible for lipidating LC3B and driving autophagosome formation. ATG16L1 polymorphisms have been linked to the development of Crohn's disease (CD), and phosphorylation of CD‐associated ATG16L1 T300A (caATG16L1) has been hypothesized to contribute to cleavage and autophagy dysfunction. Here we show that ULK1 kinase directly phosphorylates ATG16L1 in response to infection and starvation. Phosphorylated ATG16L1 localizes to the site of internalized bacteria and stable cell lines harbouring a phospho‐dead mutant of ATG16L1 have impaired xenophagy, indicating a role for ATG16L1 phosphorylation in the promotion of anti‐bacterial autophagy. In contrast to wild‐type ATG16L1, ULK1‐mediated phosphorylation of caATG16L1 drives its destabilization in response to stress. In summary, our results show that ATG16L1 is a novel target of ULK1 kinase and that ULK1 signalling to ATG16L1 is a double‐edged sword, enhancing the function of the wild‐type ATG16L1, but promoting degradation of caATG16L1.
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  • 83
    Publication Date: 2019
    Description: Thioperamide selectively increases the levels of the endosomal phospholipid lysobisphosphatidic acid and reduces the endosomal cholesterol overload in Niemann‐Pick type C patient fibroblasts or the livers of Npc1‐deficient mice. Abstract Most cells acquire cholesterol by endocytosis of circulating low‐density lipoproteins (LDLs). After cholesteryl ester de‐esterification in endosomes, free cholesterol is redistributed to intracellular membranes via unclear mechanisms. Our previous work suggested that the unconventional phospholipid lysobisphosphatidic acid (LBPA) may play a role in modulating the cholesterol flux through endosomes. In this study, we used the Prestwick library of FDA‐approved compounds in a high‐content, image‐based screen of the endosomal lipids, lysobisphosphatidic acid and LDL‐derived cholesterol. We report that thioperamide maleate, an inverse agonist of the histamine H3 receptor HRH3, increases highly selectively the levels of lysobisphosphatidic acid, without affecting any endosomal protein or function that we tested. Our data also show that thioperamide significantly reduces the endosome cholesterol overload in fibroblasts from patients with the cholesterol storage disorder Niemann–Pick type C (NPC), as well as in liver of Npc1−/− mice. We conclude that LBPA controls endosomal cholesterol mobilization and export to cellular destinations, perhaps by fluidifying or buffering cholesterol in endosomal membranes, and that thioperamide has repurposing potential for the treatment of NPC.
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  • 84
    Publication Date: 2019
    Description: p53 recruits USP7 to the regulatory region of SLC7A11 to reduce H2B monoubiquitination, resulting in transcriptional repression of SCL7A11 and ferroptosis induction. These results uncover an epigenetic regulatory mechanism for the control of ferroptosis. Abstract Monoubiquitination of histone H2B on lysine 120 (H2Bub1) is an epigenetic mark generally associated with transcriptional activation, yet the global functions of H2Bub1 remain poorly understood. Ferroptosis is a form of non‐apoptotic cell death characterized by the iron‐dependent overproduction of lipid hydroperoxides, which can be inhibited by the antioxidant activity of the solute carrier family member 11 (SLC7A11/xCT), a component of the cystine/glutamate antiporter. Whether nuclear events participate in the regulation of ferroptosis is largely unknown. Here, we show that the levels of H2Bub1 are decreased during erastin‐induced ferroptosis and that loss of H2Bub1 increases the cellular sensitivity to ferroptosis. H2Bub1 epigenetically activates the expression of SLC7A11. Additionally, we show that the tumor suppressor p53 negatively regulates H2Bub1 levels independently of p53's transcription factor activity by promoting the nuclear translocation of the deubiquitinase USP7. Moreover, our studies reveal that p53 decreases H2Bub1 occupancy on the SLC7A11 gene regulatory region and represses the expression of SLC7A11 during erastin treatment. These data not only suggest a noncanonical role of p53 in chromatin regulation but also link p53 to ferroptosis via an H2Bub1‐mediated epigenetic pathway. Overall, our work uncovers a previously unappreciated epigenetic mechanism for the regulation of ferroptosis.
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  • 85
    Publication Date: 2019
    Description: JAK‐STAT signaling drives the expression of IFN‐stimulated genes to mediate antiviral immunity. A short TAZ variant, cTAZ, represses JAK‐STAT signaling and cellular antiviral responses in a Hippo pathway independent manner. Abstract Type I interferon (IFN)‐induced Janus kinase (JAK)–signal transducer and activator of transcription (STAT) signaling drives the expression of IFN‐stimulated genes (ISGs) to mediate antiviral response. The strength and duration of JAK‐STAT signaling are tightly regulated to ensure effective antiviral defense while avoiding pathological inflammation and autoimmunity. Here, we report that cTAZ, an isoform of the Hippo pathway effector TAZ, is transcribed by an alternative promoter. Although majority of C‐terminal sequences of TAZ is retained, cTAZ is not regulated by the Hippo signaling and does not mediate its growth‐inhibitory functions. Instead, cTAZ negatively regulates JAK‐STAT signaling by inhibiting STAT1/2 nuclear localization and ISG expression, and its expression is induced by type I IFN. Thus, cTAZ functions as a modulator of JAK‐STAT signaling and may play a role in fine‐tuning cellular antiviral response.
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  • 86
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    Springer Nature
    Publication Date: 2019
    Description: Scanning and other non‐invasive technologies not only help to address relatives’ concerns over invasive autopsy, but can even yield more information about the cause of death when used in combination.
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  • 87
    Publication Date: 2019
    Description: The CRL4‐DCAF12 E3 ubiquitin ligase controls MAGE‐A3/6 protein abundance to tune autophagy in response to cellular starvation. Abstract Melanoma antigen genes (MAGEs) are emerging as important oncogenic drivers that are normally restricted to expression in male germ cells but are aberrantly expressed in cancers and promote tumorigenesis. Mechanistically, MAGEs function as substrate specifying subunits of E3 ubiquitin ligases. Thus, the activation of germline‐specific genes in cancer can drive metabolic and signaling pathways through altered ubiquitination to promote tumorigenesis. However, the mechanisms regulating MAGE expression and activity are unclear. Here, we describe how the MAGE‐A3/6 proteins that function as repressors of autophagy are downregulated in response to nutrient deprivation. Short‐term cellular starvation promotes rapid MAGE‐A3/6 degradation in a proteasome‐dependent manner. Proteomic analysis reveals that degradation of MAGE‐A3/6 is controlled by the CRL4‐DCAF12 E3 ubiquitin ligase. Importantly, the degradation of MAGE‐A3/6 by CRL4‐DCAF12 is required for starvation‐induced autophagy. These findings suggest that oncogenic MAGEs can be dynamically controlled in response to stress to allow cellular adaptation, autophagy regulation, and tumor growth and that CRL4‐DCAF12 activity is responsive to nutrient status.
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  • 88
    Publication Date: 2019
    Description: Inflammation‐induced vascular permeability is suppressed by inhibiting the endothelial tyrosine phosphatase VE‐PTP. FGD5, a GEF for Cdc42, is essential for this effect and acts as a direct substrate of VE‐PTP, which stabilizes endothelial junctions. Abstract Inhibition of VE‐PTP, an endothelial receptor‐type tyrosine phosphatase, triggers phosphorylation of the tyrosine kinase receptor Tie‐2, which leads to the suppression of inflammation‐induced vascular permeability. Analyzing the underlying mechanism, we show here that inhibition of VE‐PTP and activation of Tie‐2 induce tyrosine phosphorylation of FGD5, a GTPase exchange factor (GEF) for Cdc42, and stimulate its translocation to cell contacts. Interfering with the expression of FGD5 blocks the junction‐stabilizing effect of VE‐PTP inhibition in vitro and in vivo. Likewise, FGD5 is required for strengthening cortical actin bundles and inhibiting radial stress fiber formation, which are each stimulated by VE‐PTP inhibition. We identify Y820 of FGD5 as the direct substrate for VE‐PTP. The phosphorylation of FGD5‐Y820 is required for the stabilization of endothelial junctions and for the activation of Cdc42 by VE‐PTP inhibition but is dispensable for the recruitment of FGD5 to endothelial cell contacts. Thus, activation of FGD5 is a two‐step process that comprises membrane recruitment and phosphorylation of Y820. These steps are necessary for the junction‐stabilizing effect stimulated by VE‐PTP inhibition and Tie‐2 activation.
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  • 89
    Publication Date: 2019
    Description: A study in this issue shows that phosphorylation of NICD by CDKs suppresses Notch activity by promoting NICD turnover, linking Notch pathway activity to the cell cycle and the embryonic segmentation clock. The Notch signaling pathway is tightly controlled via post‐transcriptional regulatory mechanisms that promote or terminate pathway activity. In this issue, Carrieri et al [1] show that phosphorylation of the Notch intracellular domain (NICD) by cyclin‐dependent kinases (CDKs) suppresses Notch activity by promoting NICD turnover. These findings link Notch pathway activity to the cell cycle, and the authors propose connections between this regulation and the segmentation clock that times embryonic somitogenesis.
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  • 90
    Publication Date: 2019
    Description: Yb bodies are membraneless organelles central for piRNA biogenesis in Drosophila ovarian somatic cells. Yb body formation depends on all three domains of Yb (RNA helicase, Hel‐C and eTud), and is specifically required for efficient production of transposon‐repressing piRNAs. Abstract Female sterile (1) Yb (Yb) is a primary component of Yb bodies, perinuclear foci considered to be the site of PIWI‐interacting RNA (piRNA) biogenesis in Drosophila ovarian somatic cells (OSCs). Yb consists of three domains: Helicase C‐terminal (Hel‐C), RNA helicase, and extended Tudor (eTud) domains. We previously showed that the RNA helicase domain is necessary for Yb–RNA interaction, Yb body formation, and piRNA biogenesis. Here, we investigate the functions of Hel‐C and eTud and reveal that Hel‐C is dedicated to Yb–Yb homotypic interaction, while eTud is necessary for Yb–RNA association, as is the RNA helicase domain. All of these domains are indispensable for Yb body formation and transposon‐repressing piRNA production. Strikingly, however, genic piRNAs unrelated to transposon silencing are produced in OSCs where Yb bodies are disassembled. We also reveal that Yb bodies are liquid‐like multivalent condensates whose assembly depends on Yb–Yb homotypic interaction and Yb binding particularly with flamenco RNA transcripts, the source of transposon‐repressing piRNAs. New insights into Yb body assembly and biological relevance of Yb bodies in transposon silencing have emerged.
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  • 91
    Publication Date: 2019
    Description: Enteroviruses hijack host PI4KB and GBF1 to build replication organelles. This study reveals that the direct interaction between c10orf76 and PI4KB is required for c10orf76 recruitment to the Golgi and the replication of c10orf76‐dependent enteroviruses. Abstract The lipid kinase PI4KB, which generates phosphatidylinositol 4‐phosphate (PI4P), is a key enzyme in regulating membrane transport and is also hijacked by multiple picornaviruses to mediate viral replication. PI4KB can interact with multiple protein binding partners, which are differentially manipulated by picornaviruses to facilitate replication. The protein c10orf76 is a PI4KB‐associated protein that increases PI4P levels at the Golgi and is essential for the viral replication of specific enteroviruses. We used hydrogen–deuterium exchange mass spectrometry to characterize the c10orf76‐PI4KB complex and reveal that binding is mediated by the kinase linker of PI4KB, with formation of the heterodimeric complex modulated by PKA‐dependent phosphorylation. Complex‐disrupting mutations demonstrate that PI4KB is required for membrane recruitment of c10orf76 to the Golgi, and that an intact c10orf76‐PI4KB complex is required for the replication of c10orf76‐dependent enteroviruses. Intriguingly, c10orf76 also contributed to proper Arf1 activation at the Golgi, providing a putative mechanism for the c10orf76‐dependent increase in PI4P levels at the Golgi.
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  • 92
    Publication Date: 2019
    Description: The current focus on biomedical research has led to dearth of funding for basic research in evolution or ecology with the aim to better understand life.
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  • 93
    Publication Date: 2019
    Description: Peer review to allocate funding for researchers and projects has faced difficulties lately and come under criticism. Various alternatives and improvements are being tested to address these problems.
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  • 94
    Publication Date: 2019
    Description: The RNA binding protein Mip6 interacts with the ubiquitin‐associated domain of Mex67 and attenuates the nuclear export of mRNAs regulated by the stress response Msn2/4 transcription factors. Abstract RNA‐binding proteins (RBPs) participate in all steps of gene expression, underscoring their potential as regulators of RNA homeostasis. We structurally and functionally characterize Mip6, a four‐RNA recognition motif (RRM)‐containing RBP, as a functional and physical interactor of the export factor Mex67. Mip6‐RRM4 directly interacts with the ubiquitin‐associated (UBA) domain of Mex67 through a loop containing tryptophan 442. Mip6 shuttles between the nucleus and the cytoplasm in a Mex67‐dependent manner and concentrates in cytoplasmic foci under stress. Photoactivatable ribonucleoside‐enhanced crosslinking and immunoprecipitation experiments show preferential binding of Mip6 to mRNAs regulated by the stress‐response Msn2/4 transcription factors. Consistent with this binding, MIP6 deletion affects their export and expression levels. Additionally, Mip6 interacts physically and/or functionally with proteins with a role in mRNA metabolism and transcription such as Rrp6, Xrn1, Sgf73, and Rpb1. These results reveal a novel role for Mip6 in the homeostasis of Msn2/4‐dependent transcripts through its direct interaction with the Mex67 UBA domain.
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  • 95
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    Springer Nature
    Publication Date: 2019
    Description: Anxiety is the most common mental disorder. New insights into the underlying neural patterns and new drug candidates offer prospects for long‐lasting relief.
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  • 96
    Publication Date: 2019
    Description: A comment on “The Sense of Social Influence: Pluralistic Ignorance in Climate Change” by Esther M Kjeldahl & Vincent F. Hendricks.
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  • 97
    Publication Date: 2019
    Description: The mycobacterial Sec2 secretion system regulates the loading of bacterial RNA into macrophage‐derived extracellular vesicles. Secreted vesicles with mycobacterial RNA promote IFN‐β production upon entry into target cells, and induce bacterial clearance. Tuberculosis remains one of the deadliest infectious diseases worldwide. Mycobacterium tuberculosis (M.tb) has developed various mechanisms to manipulate the human host, in particular by disrupting the host phagosome and the immune response. It is becoming evident that secreted extracellular vesicles (EVs) are involved in the dynamic crosstalk between M.tb and the host cells. These vesicles shuttle different cargo components, such as RNA, lipids, and proteins, between cells. In this issue of EMBO Reports, Cheng and Schorey describe a previously unknown EV‐mediated process, regulating M.tb RNA loading into EVs and their internalization by naïve macrophages. They identify the mycobacterial Sec2 secretion system as involved in RNA loading into EVs and show that secreted vesicles contain bacterial RNA that not only promotes IFN‐β production upon entry into target cells, but also leads to M.tb clearance via the activation of the host's RIG‐I/MAVS signaling pathway. Importantly, combined treatment with secreted EVs and antibiotics decreases bacterial load in a mouse model, improving lung pathology compared to treatment with antibiotics alone.
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  • 98
    Publication Date: 2019
    Description: The G‐protein coupled receptor SRD‐1 mediates male attraction to volatile sex pheromones in Caenorhabditis elegans AWA neurons. The characterization of receptors for sex pheromones provides important clues for understanding the mechanisms controlling animal mating and reproduction. In this issue, Wan et al identify a putative sex pheromone receptor, the G protein‐coupled receptor SRD‐1, acting in a single Caenorhabditis elegans olfactory neuron class, called AWA, to mediate male attraction to volatile sex pheromones. Like in other systems, C. elegans sex pheromone elicits sex‐specific responses even though sex pheromone activates sensory neurons of both sexes.
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  • 99
    Publication Date: 2019
    Description: The G‐protein coupled receptor SRD‐1 shows male‐specific expression in AWA neurons and acts as receptor for volatile sex pheromones in Caenorhabditis elegans and Caenorhabditis remanei. Abstract Pheromones are critical cues for attracting mating partners for successful reproduction. Sexually mature Caenorhabditis remanei virgin females and self‐sperm‐depleted Caenorhabditis elegans hermaphrodites produce volatile sex pheromones to attract adult males of both species from afar. The chemoresponsive receptor in males has remained unknown. Here, we show that the male chemotactic behavior requires amphid sensory neurons (AWA neurons) and the G‐protein‐coupled receptor SRD‐1. SRD‐1 expression in AWA neurons is sexually dimorphic, with the levels being high in males but undetectable in hermaphrodites. Notably, srd‐1 mutant males lack the chemotactic response and pheromone‐induced excitation of AWA neurons, both of which can be restored in males and hermaphrodites by AWA‐specific srd‐1 expression, and ectopic expression of srd‐1 in AWB neurons in srd‐1 mutants results in a repulsive behavioral response in both sexes. Furthermore, we show that the C‐terminal region of SRD‐1 confers species‐specific differences in the ability to perceive sex pheromones between C. elegans and C. remanei. These findings offer an excellent model for dissecting how a single G‐protein‐coupled receptor expressed in a dimorphic neural system contributes to sex‐specific behaviors in animals.
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  • 100
    Publication Date: 2019
    Description: EMBO reports, Volume 20, Issue 2, February 2019.
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