Continual removal of H3K9 promoter methylation by Jmjd2 demethylases is vital for ESC self-renewal and early development
We report that while individual Jmjd2 family members are dispensable for ESC maintenance and embryogenesis, combined deficiency for specifically Jmjd2a and Jmjd2c leads to early embryonic lethality and impaired ESC self-renewal, with spontaneous differentiation towards primitive endoderm under permissive culture conditions. We further show that Jmjd2a and Jmjd2c both localize to H3K4me3-positive promoters, where they have widespread and redundant roles in preventing accumulation of H3K9me3 and H3K36me3. Jmjd2 catalytic activity is required for ESC maintenance, and increased H3K9me3 levels in knockout ESCs compromise the ex...
Source: EMBO Journal - July 15, 2016 Category: Molecular Biology Authors: Pedersen, M. T., Kooistra, S. M., Radzisheuskaya, A., Laugesen, A., Johansen, J. V., Hayward, D. G., Nilsson, J., Agger, K., Helin, K. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Stem Cells, Transcription Articles Source Type: research

DnaJ/Hsc70 chaperone complexes control the extracellular release of neurodegenerative-associated proteins
It is now known that proteins associated with neurodegenerative disease can spread throughout the brain in a prionlike manner. However, the mechanisms regulating the trans-synaptic spread propagation, including the neuronal release of these proteins, remain unknown. The interaction of neurodegenerative disease-associated proteins with the molecular chaperone Hsc70 is well known, and we hypothesized that much like disaggregation, refolding, degradation, and even normal function, Hsc70 may dictate the extracellular fate of these proteins. Here, we show that several proteins, including TDP-43, α-synuclein, and the micro...
Source: EMBO Journal - July 15, 2016 Category: Molecular Biology Authors: Fontaine, S. N., Zheng, D., Sabbagh, J. J., Martin, M. D., Chaput, D., Darling, A., Trotter, J. H., Stothert, A. R., Nordhues, B. A., Lussier, A., Baker, J., Shelton, L., Kahn, M., Blair, L. J., Stevens, S. M., Dickey, C. A. Tags: Neuroscience Articles Source Type: research

Ubiquitin-like domains can target to the proteasome but proteolysis requires a disordered region
Ubiquitin and some of its homologues target proteins to the proteasome for degradation. Other ubiquitin-like domains are involved in cellular processes unrelated to the proteasome, and proteins containing these domains remain stable in the cell. We find that the 10 yeast ubiquitin-like domains tested bind to the proteasome, and that all 11 identified domains can target proteins for degradation. Their apparent proteasome affinities are not directly related to their stabilities or functions. That is, ubiquitin-like domains in proteins not part of the ubiquitin proteasome system may bind the proteasome more tightly than domai...
Source: EMBO Journal - July 15, 2016 Category: Molecular Biology Authors: Yu, H., Kago, G., Yellman, C. M., Matouschek, A. Tags: Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Minor intron splicing is regulated by FUS and affected by ALS-associated FUS mutants
Fused in sarcoma (FUS) is a ubiquitously expressed RNA-binding protein proposed to function in various RNA metabolic pathways, including transcription regulation, pre-mRNA splicing, RNA transport and microRNA processing. Mutations in the FUS gene were identified in patients with amyotrophic lateral sclerosis (ALS), but the pathomechanisms by which these mutations cause ALS are not known. Here, we show that FUS interacts with the minor spliceosome constituent U11 snRNP, binds preferentially to minor introns and directly regulates their removal. Furthermore, a FUS knockout in neuroblastoma cells strongly disturbs the splicin...
Source: EMBO Journal - July 15, 2016 Category: Molecular Biology Authors: Reber, S., Stettler, J., Filosa, G., Colombo, M., Jutzi, D., Lenzken, S. C., Schweingruber, C., Bruggmann, R., Bachi, A., Barabino, S. M., Mühlemann, O., Ruepp, M.-D. Tags: Neuroscience, RNA Biology Articles Source Type: research

SIRT7 promotes genome integrity and modulates non-homologous end joining DNA repair
Sirtuins, a family of protein deacetylases, promote cellular homeostasis by mediating communication between cells and environment. The enzymatic activity of the mammalian sirtuin SIRT7 targets acetylated lysine in the N-terminal tail of histone H3 (H3K18Ac), thus modulating chromatin structure and transcriptional competency. SIRT7 deletion is associated with reduced lifespan in mice through unknown mechanisms. Here, we show that SirT7-knockout mice suffer from partial embryonic lethality and a progeroid-like phenotype. Consistently, SIRT7-deficient cells display increased replication stress and impaired DNA repair. SIRT7 i...
Source: EMBO Journal - July 15, 2016 Category: Molecular Biology Authors: Vazquez, B. N., Thackray, J. K., Simonet, N. G., Kane-Goldsmith, N., Martinez-Redondo, P., Nguyen, T., Bunting, S., Vaquero, A., Tischfield, J. A., Serrano, L. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

The minor spliceosome could be the major key for FUS/TLS mutants in ALS
Despite its name, minor spliceosome alterations are often involved in human disease origin. Work by Reber et al (2016) in this issue of The EMBO Journal now demonstrates a connection between minor spliceosome components and FUS/TLS, one of the major proteins aggregating in the brain of patients affected by amyotrophic lateral sclerosis (ALS). This finding has important implications as it extends the spectrum of diseases where minor spliceosome plays a role. It may also represent a new opportunity for specific therapeutic targets. (Source: EMBO Journal)
Source: EMBO Journal - July 15, 2016 Category: Molecular Biology Authors: Buratti, E. Tags: Neuroscience, RNA Biology News [amp ] Views Source Type: research

SIRT7 clears the way for DNA repair
Histone modification by reversible lysine acetylation is a key regulatory mechanism in chromatin and nuclear signaling, whose deregulation is linked to aging, cancer, and other diseases. New work by Vazquez et al (2016) uncovers a role for the sirtuin family deacetylase SIRT7, which controls epigenetic maintenance of oncogenic gene expression programs, mitochondrial homeostasis, and ribosome biogenesis, in promoting genomic stability and DNA repair via site-specific deacetylation of a damage-associated histone mark, H3K18Ac. (Source: EMBO Journal)
Source: EMBO Journal - July 15, 2016 Category: Molecular Biology Authors: Paredes, S., Chua, K. F. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

Structural evidence for Nap1-dependent H2A-H2B deposition and nucleosome assembly
Nap1 is a histone chaperone involved in the nuclear import of H2A–H2B and nucleosome assembly. Here, we report the crystal structure of Nap1 bound to H2A–H2B together with in vitro and in vivo functional studies that elucidate the principles underlying Nap1-mediated H2A–H2B chaperoning and nucleosome assembly. A Nap1 dimer provides an acidic binding surface and asymmetrically engages a single H2A–H2B heterodimer. Oligomerization of the Nap1–H2A–H2B complex results in burial of surfaces required for deposition of H2A–H2B into nucleosomes. Chromatin immunoprecipitation-exon...
Source: EMBO Journal - July 1, 2016 Category: Molecular Biology Authors: Aguilar-Gurrieri, C., Larabi, A., Vinayachandran, V., Patel, N. A., Yen, K., Reja, R., Ebong, I.-O., Schoehn, G., Robinson, C. V., Pugh, B. F., Panne, D. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Structural Biology Articles Source Type: research

Histone H3.3 promotes IgV gene diversification by enhancing formation of AID-accessible single-stranded DNA
Immunoglobulin diversification is driven by activation-induced deaminase (AID), which converts cytidine to uracil within the Ig variable (IgV) regions. Central to the recruitment of AID to the IgV genes are factors that regulate the generation of single-stranded DNA (ssDNA), the enzymatic substrate of AID. Here, we report that chicken DT40 cells lacking variant histone H3.3 exhibit reduced IgV sequence diversification. We show that this results from impairment of the ability of AID to access the IgV genes due to reduced formation of ssDNA during IgV transcription. Loss of H3.3 also diminishes IgV R-loop formation. However,...
Source: EMBO Journal - July 1, 2016 Category: Molecular Biology Authors: Romanello, M., Schiavone, D., Frey, A., Sale, J. E. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination, Immunology Articles Source Type: research

WRNIP1 protects stalled forks from degradation and promotes fork restart after replication stress
Accurate handling of stalled replication forks is crucial for the maintenance of genome stability. RAD51 defends stalled replication forks from nucleolytic attack, which otherwise can threaten genome stability. However, the identity of other factors that can collaborate with RAD51 in this task is poorly elucidated. Here, we establish that human Werner helicase interacting protein 1 (WRNIP1) is localized to stalled replication forks and cooperates with RAD51 to safeguard fork integrity. We show that WRNIP1 is directly involved in preventing uncontrolled MRE11-mediated degradation of stalled replication forks by promoting RA...
Source: EMBO Journal - July 1, 2016 Category: Molecular Biology Authors: Leuzzi, G., Marabitti, V., Pichierri, P., Franchitto, A. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Novel function of Tau in regulating the effects of external stimuli on adult hippocampal neurogenesis
Tau is a microtubule-associated neuronal protein found mainly in axons. However, its presence in dendrites and dendritic spines is particularly relevant due to its involvement in synaptic plasticity and neurodegeneration. Here, we show that Tau plays a novel in vivo role in the morphological and synaptic maturation of newborn hippocampal granule neurons under basal conditions. Furthermore, we reveal that Tau is involved in the selective cell death of immature granule neurons caused by acute stress. Also, Tau deficiency protects newborn neurons from the stress-induced dendritic atrophy and loss of postsynaptic densitie...
Source: EMBO Journal - July 1, 2016 Category: Molecular Biology Authors: Pallas-Bazarra, N., Jurado-Arjona, J., Navarrete, M., Esteban, J. A., Hernandez, F., Avila, J., Llorens-Martin, M. Tags: Neuroscience Articles Source Type: research

SCF (Fbxl17) ubiquitylation of Sufu regulates Hedgehog signaling and medulloblastoma development
Skp1-Cul1-F-box protein (SCF) ubiquitin ligases direct cell survival decisions by controlling protein ubiquitylation and degradation. Sufu (Suppressor of fused) is a central regulator of Hh (Hedgehog) signaling and acts as a tumor suppressor by maintaining the Gli (Glioma-associated oncogene homolog) transcription factors inactive. Although Sufu has a pivotal role in Hh signaling, the players involved in controlling Sufu levels and their role in tumor growth are unknown. Here, we show that Fbxl17 (F-box and leucine-rich repeat protein 17) targets Sufu for proteolysis in the nucleus. The ubiquitylation of Sufu, mediated by ...
Source: EMBO Journal - July 1, 2016 Category: Molecular Biology Authors: Raducu, M., Fung, E., Serres, S., Infante, P., Barberis, A., Fischer, R., Bristow, C., Thezenas, M.-L., Finta, C., Christianson, J. C., Buffa, F. M., Kessler, B. M., Sibson, N. R., Di Marcotullio, L., Toftgard, R., D'Angiolella, V. Tags: Cancer, Post-translational Modifications, Proteolysis & Proteomics, Signal Transduction Articles Source Type: research

HSV-1 ICP27 targets the TBK1-activated STING signalsome to inhibit virus-induced type I IFN expression
Herpes simplex virus (HSV) 1 stimulates type I IFN expression through the cGAS–STING–TBK1 signaling axis. Macrophages have recently been proposed to be an essential source of IFN during viral infection. However, it is not known how HSV-1 inhibits IFN expression in this cell type. Here, we show that HSV-1 inhibits type I IFN induction through the cGAS–STING–TBK1 pathway in human macrophages, in a manner dependent on the conserved herpesvirus protein ICP27. This viral protein was expressed de novo in macrophages with early nuclear localization followed by later translocation to the cytoplasm where ICP...
Source: EMBO Journal - July 1, 2016 Category: Molecular Biology Authors: Christensen, M. H., Jensen, S. B., Miettinen, J. J., Luecke, S., Prabakaran, T., Reinert, L. S., Mettenleiter, T., Chen, Z. J., Knipe, D. M., Sandri-Goldin, R. M., Enquist, L. W., Hartmann, R., Mogensen, T. H., Rice, S. A., Nyman, T. A., Matikainen, S., P Tags: Immunology Articles Source Type: research

FUNDC1 regulates mitochondrial dynamics at the ER-mitochondrial contact site under hypoxic conditions
In hypoxic cells, dysfunctional mitochondria are selectively removed by a specialized autophagic process called mitophagy. The ER–mitochondrial contact site (MAM) is essential for fission of mitochondria prior to engulfment, and the outer mitochondrial membrane protein FUNDC1 interacts with LC3 to recruit autophagosomes, but the mechanisms integrating these processes are poorly understood. Here, we describe a new pathway mediating mitochondrial fission and subsequent mitophagy under hypoxic conditions. FUNDC1 accumulates at the MAM by associating with the ER membrane protein calnexin. As mitophagy proceeds, FUNDC1/ca...
Source: EMBO Journal - July 1, 2016 Category: Molecular Biology Authors: Wu, W., Lin, C., Wu, K., Jiang, L., Wang, X., Li, W., Zhuang, H., Zhang, X., Chen, H., Li, S., Yang, Y., Lu, Y., Wang, J., Zhu, R., Zhang, L., Sui, S., Tan, N., Zhao, B., Zhang, J., Li, L., Feng, D. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Metabolism Articles Source Type: research

Mitochondria just wanna have FUN(DC1)
A fascinating story is unfolding at the interface between mitochondria and the ER. Two new papers, one in this issue of The EMBO Journal (Wu et al, 2016) and one in the journal Autophagy (Chen et al, 2016), further clarify the role of mitochondrial outer membrane protein FUNDC1 in autophagy and connect it to mitochondrial fission occurring at the interface between mitochondria and the ER. (Source: EMBO Journal)
Source: EMBO Journal - July 1, 2016 Category: Molecular Biology Authors: van der Bliek, A. M. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Metabolism News [amp ] Views Source Type: research

Phosphorylation-dependent Akt-Inversin interaction at the basal body of primary cilia
A primary cilium is a microtubule-based sensory organelle that plays an important role in human development and disease. However, regulation of Akt in cilia and its role in ciliary development has not been demonstrated. Using yeast two-hybrid screening, we demonstrate that Inversin (INVS) interacts with Akt. Mutation in the INVS gene causes nephronophthisis type II (NPHP2), an autosomal recessive chronic tubulointerstitial nephropathy. Co-immunoprecipitation assays show that Akt interacts with INVS via the C-terminus. In vitro kinase assays demonstrate that Akt phosphorylates INVS at amino acids 864–866 that are requ...
Source: EMBO Journal - June 14, 2016 Category: Molecular Biology Authors: Suizu, F., Hirata, N., Kimura, K., Edamura, T., Tanaka, T., Ishigaki, S., Donia, T., Noguchi, H., Iwanaga, T., Noguchi, M. Tags: Cell Adhesion, Polarity & Cytoskeleton, Molecular Biology of Disease, Signal Transduction Articles Source Type: research

Phosphorylation of Cav1.2 on S1928 uncouples the L-type Ca2+ channel from the {beta}2 adrenergic receptor
Agonist-triggered downregulation of β-adrenergic receptors (ARs) constitutes vital negative feedback to prevent cellular overexcitation. Here, we report a novel downregulation of β2AR signaling highly specific for Cav1.2. We find that β2-AR binding to Cav1.2 residues 1923–1942 is required for β-adrenergic regulation of Cav1.2. Despite the prominence of PKA-mediated phosphorylation of Cav1.2 S1928 within the newly identified β2AR binding site, its physiological function has so far escaped identification. We show that phosphorylation of S1928 displaces the β2AR from Cav1.2 upon β-adre...
Source: EMBO Journal - June 14, 2016 Category: Molecular Biology Authors: Patriarchi, T., Qian, H., Di Biase, V., Malik, Z. A., Chowdhury, D., Price, J. L., Hammes, E. A., Buonarati, O. R., Westenbroek, R. E., Catterall, W. A., Hofmann, F., Xiang, Y. K., Murphy, G. G., Chen, C.-Y., Navedo, M. F., Hell, J. W. Tags: Neuroscience Articles Source Type: research

Redox regulation of SUMO enzymes is required for ATM activity and survival in oxidative stress
To sense and defend against oxidative stress, cells depend on signal transduction cascades involving redox-sensitive proteins. We previously identified SUMO (small ubiquitin-related modifier) enzymes as downstream effectors of reactive oxygen species (ROS). Hydrogen peroxide transiently inactivates SUMO E1 and E2 enzymes by inducing a disulfide bond between their catalytic cysteines. How important their oxidation is in light of many other redox-regulated proteins has however been unclear. To selectively disrupt this redox switch, we identified a catalytically fully active SUMO E2 enzyme variant (Ubc9 D100A) with strongly r...
Source: EMBO Journal - June 14, 2016 Category: Molecular Biology Authors: Stankovic-Valentin, N., Drzewicka, K., König, C., Schiebel, E., Melchior, F. Tags: DNA Replication, Repair & Recombination, Metabolism, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Parental epigenetic asymmetry of PRC2-mediated histone modifications in the Arabidopsis endosperm
Parental genomes in the endosperm are marked by differential DNA methylation and are therefore epigenetically distinct. This epigenetic asymmetry is established in the gametes and maintained after fertilization by unknown mechanisms. In this manuscript, we have addressed the key question whether parentally inherited differential DNA methylation affects de novo targeting of chromatin modifiers in the early endosperm. Our data reveal that polycomb-mediated H3 lysine 27 trimethylation (H3K27me3) is preferentially localized to regions that are targeted by the DNA glycosylase DEMETER (DME), mechanistically linking DNA hypomethy...
Source: EMBO Journal - June 14, 2016 Category: Molecular Biology Authors: Moreno-Romero, J., Jiang, H., Santos-Gonzalez, J., Köhler, C. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Plant Biology Articles Source Type: research

Loss of C9ORF72 impairs autophagy and synergizes with polyQ Ataxin-2 to induce motor neuron dysfunction and cell death
An intronic expansion of GGGGCC repeats within the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). Ataxin-2 with intermediate length of polyglutamine expansions (Ataxin-2 Q30x) is a genetic modifier of the disease. Here, we found that C9ORF72 forms a complex with the WDR41 and SMCR8 proteins to act as a GDP/GTP exchange factor for RAB8a and RAB39b and to thereby control autophagic flux. Depletion of C9orf72 in neurons partly impairs autophagy and leads to accumulation of aggregates of TDP-43 and P62 proteins, which are histopathological hallmarks of ALS-...
Source: EMBO Journal - June 14, 2016 Category: Molecular Biology Authors: Sellier, C., Campanari, M.-L., Julie Corbier, C., Gaucherot, A., Kolb-Cheynel, I., Oulad-Abdelghani, M., Ruffenach, F., Page, A., Ciura, S., Kabashi, E., Charlet-Berguerand, N. Tags: Neuroscience Articles Source Type: research

Higher-order oligomerization promotes localization of SPOP to liquid nuclear speckles
Membrane-less organelles in cells are large, dynamic protein/protein or protein/RNA assemblies that have been reported in some cases to have liquid droplet properties. However, the molecular interactions underlying the recruitment of components are not well understood. Herein, we study how the ability to form higher-order assemblies influences the recruitment of the speckle-type POZ protein (SPOP) to nuclear speckles. SPOP, a cullin-3-RING ubiquitin ligase (CRL3) substrate adaptor, self-associates into higher-order oligomers; that is, the number of monomers in an oligomer is broadly distributed and can be large. While wild...
Source: EMBO Journal - June 14, 2016 Category: Molecular Biology Authors: Marzahn, M. R., Marada, S., Lee, J., Nourse, A., Kenrick, S., Zhao, H., Ben-Nissan, G., Kolaitis, R.-M., Peters, J. L., Pounds, S., Errington, W. J., Prive, G. G., Taylor, J. P., Sharon, M., Schuck, P., Ogden, S. K., Mittag, T. Tags: Post-translational Modifications, Proteolysis & Proteomics, Protein Biosynthesis & Quality Control, Structural Biology Articles Source Type: research

Lost & found: C9ORF72 and the autophagy pathway in ALS/FTD
C9ORF72 expression is reduced in a substantial number of patients with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), which may contribute to disease pathogenesis. However, its normal molecular function remains unknown. In this issue of The EMBO Journal, Sellier et al (2016) identified a novel protein complex consisting of C9ORF72, WDR41, and SMCR8 that acts as a GDP-GTP exchange factor (GEF) for RAB8a and RAB39b and is regulated by TBK1, whose partial loss of function also causes ALS and FTD. They further reveal a potential modulatory role for this novel complex in macroautophagy (autophagy), ...
Source: EMBO Journal - June 14, 2016 Category: Molecular Biology Authors: Almeida, S., Gao, F.-B. Tags: Neuroscience News [amp ] Views Source Type: research

Presynaptic inhibition upon CB1 or mGlu2/3 receptor activation requires ERK/MAPK phosphorylation of Munc18-1
Presynaptic cannabinoid (CB1R) and metabotropic glutamate receptors (mGluR2/3) regulate synaptic strength by inhibiting secretion. Here, we reveal a presynaptic inhibitory pathway activated by extracellular signal-regulated kinase (ERK) that mediates CB1R- and mGluR2/3-induced secretion inhibition. This pathway is triggered by a variety of events, from foot shock-induced stress to intense neuronal activity, and induces phosphorylation of the presynaptic protein Munc18-1. Mimicking constitutive phosphorylation of Munc18-1 results in a drastic decrease in synaptic transmission. ERK-mediated phosphorylation of Munc18-1 ultima...
Source: EMBO Journal - May 31, 2016 Category: Molecular Biology Authors: Schmitz, S. K., King, C., Kortleven, C., Huson, V., Kroon, T., Kevenaar, J. T., Schut, D., Saarloos, I., Hoetjes, J. P., de Wit, H., Stiedl, O., Spijker, S., Li, K. W., Mansvelder, H. D., Smit, A. B., Cornelisse, L. N., Verhage, M., Toonen, R. F. Tags: Neuroscience Articles Source Type: research

The retinal pigment epithelium as a gateway for monocyte trafficking into the eye
The choroid plexus epithelium within the brain ventricles orchestrates blood-derived monocyte entry to the central nervous system under injurious conditions, including when the primary injury site is remote from the brain. Here, we hypothesized that the retinal pigment epithelium (RPE) serves a parallel role, as a gateway for monocyte trafficking to the retina following direct or remote injury. We found elevated expression of genes encoding leukocyte trafficking determinants in mouse RPE as a consequence of retinal glutamate intoxication or optic nerve crush (ONC). Blocking VCAM-1 after ONC interfered with monocyte infiltr...
Source: EMBO Journal - May 31, 2016 Category: Molecular Biology Authors: Benhar, I., Reemst, K., Kalchenko, V., Schwartz, M. Tags: Neuroscience Articles Source Type: research

Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity
TRIM E3 ubiquitin ligases regulate a wide variety of cellular processes and are particularly important during innate immune signalling events. They are characterized by a conserved tripartite motif in their N-terminal portion which comprises a canonical RING domain, one or two B-box domains and a coiled-coil region that mediates ligase dimerization. Self-association via the coiled-coil has been suggested to be crucial for catalytic activity of TRIMs; however, the precise molecular mechanism underlying this observation remains elusive. Here, we provide a detailed characterization of the TRIM ligases TRIM25 and TRIM32 and sh...
Source: EMBO Journal - May 31, 2016 Category: Molecular Biology Authors: Koliopoulos, M. G., Esposito, D., Christodoulou, E., Taylor, I. A., Rittinger, K. Tags: Post-translational Modifications, Proteolysis & Proteomics, Structural Biology Articles Source Type: research

miRISC and the CCR4-NOT complex silence mRNA targets independently of 43S ribosomal scanning
miRNAs associate with Argonaute (AGO) proteins to silence the expression of mRNA targets by inhibiting translation and promoting deadenylation, decapping, and mRNA degradation. A current model for silencing suggests that AGOs mediate these effects through the sequential recruitment of GW182 proteins, the CCR4–NOT deadenylase complex and the translational repressor and decapping activator DDX6. An alternative model posits that AGOs repress translation by interfering with eIF4A function during 43S ribosomal scanning and that this mechanism is independent of GW182 and the CCR4–NOT complex in Drosophila melanogaste...
Source: EMBO Journal - May 31, 2016 Category: Molecular Biology Authors: Kuzuoglu-Öztürk, D., Bhandari, D., Huntzinger, E., Fauser, M., Helms, S., Izaurralde, E. Tags: Protein Biosynthesis & Quality Control, RNA Biology Articles Source Type: research

Tyrosination of {alpha}-tubulin controls the initiation of processive dynein-dynactin motility
Post-translational modifications (PTMs) of α/β-tubulin are believed to regulate interactions with microtubule-binding proteins. A well-characterized PTM involves in the removal and re-ligation of the C-terminal tyrosine on α-tubulin, but the purpose of this tyrosination–detyrosination cycle remains elusive. Here, we examined the processive motility of mammalian dynein complexed with dynactin and BicD2 (DDB) on tyrosinated versus detyrosinated microtubules. Motility was decreased ~fourfold on detyrosinated microtubules, constituting the largest effect of a tubulin PTM on motor function observed to dat...
Source: EMBO Journal - May 31, 2016 Category: Molecular Biology Authors: McKenney, R. J., Huynh, W., Vale, R. D., Sirajuddin, M. Tags: Cell Adhesion, Polarity & Cytoskeleton, Membrane & Intracellular Transport Articles Source Type: research

Rac1-Rab11-FIP3 regulatory hub coordinates vesicle traffic with actin remodeling and T-cell activation
The immunological synapse generation and function is the result of a T-cell polarization process that depends on the orchestrated action of the actin and microtubule cytoskeleton and of intracellular vesicle traffic. However, how these events are coordinated is ill defined. Since Rab and Rho families of GTPases control intracellular vesicle traffic and cytoskeleton reorganization, respectively, we investigated their possible interplay. We show here that a significant fraction of Rac1 is associated with Rab11-positive recycling endosomes. Moreover, the Rab11 effector FIP3 controls Rac1 intracellular localization and Rac1 ta...
Source: EMBO Journal - May 31, 2016 Category: Molecular Biology Authors: Bouchet, J., del Rio-Iniguez, I., Lasserre, R., Agüera-Gonzalez, S., Cuche, C., Danckaert, A., McCaffrey, M. W., Di Bartolo, V., Alcover, A. Tags: Cell Adhesion, Polarity & Cytoskeleton, Immunology, Membrane & Intracellular Transport Articles Source Type: research

Scanning for a unified model for translational repression by microRNAs
MicroRNAs (miRNAs) silence target mRNAs by inhibiting translation and subsequently initiating mRNA decay. The mechanism by which miRNAs silence translation is still poorly understood, with a number of competing models proposed. In this issue of The EMBO Journal, Kuzuoğlu-Öztürk et al (2016) investigated miRNA silencing in human and insect cells. Their data support a model whereby miRNAs inhibit translation initiation. However, in contrast to several recent reports, their data suggest that translational inhibition is independent of 43S ribosomal subunit scanning, eIF4A translation factor activity, and 5'UTR second...
Source: EMBO Journal - May 31, 2016 Category: Molecular Biology Authors: Nishimura, T., Fabian, M. R. Tags: Protein Biosynthesis & Quality Control, RNA Biology News [amp ] Views Source Type: research

A tale of two {alpha}-tubulin tails
Post-translational modifications of tubulin, such as the removal of the C-terminal tyrosine of α-tubulin, have long been proposed to influence the ability of microtubule motors to walk along the microtubule surface. This hypothesis has now been tested for cytoplasmic dynein-1 (dynein), revealing that active dynein–dynactin–adaptor complexes prefer to start moving on tyrosinated microtubules. This choice is governed by the p150 subunit of dynactin. Once moving, however, dynein is not choosy about whether the microtubule is tyrosinated or not. (Source: EMBO Journal)
Source: EMBO Journal - May 31, 2016 Category: Molecular Biology Authors: Allan, V. J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Membrane & Intracellular Transport News [amp ] Views Source Type: research

Considerations for a European animal welfare standard to evaluate adverse phenotypes in teleost fish
(Source: EMBO Journal)
Source: EMBO Journal - May 31, 2016 Category: Molecular Biology Authors: Bert, B., Chmielewska, J., Bergmann, S., Busch, M., Driever, W., Finger-Baier, K., Hössler, J., Köhler, A., Leich, N., Misgeld, T., Nöldner, T., Reiher, A., Schartl, M., Seebach-Sproedt, A., Thumberger, T., Schönfelder, G., Tags: Commentary Source Type: research

Regulators of complement activity mediate inhibitory mechanisms through a common C3b-binding mode
We present crystal structures of human RCA (MCP, DAF, and CR1) and a smallpox virus homolog (SPICE) bound to complement component C3b. Our structural data reveal that up to four consecutive homologous CCP domains (i–iv), responsible for inhibition, bind in the same orientation and extended arrangement at a shared binding platform on C3b. Large sequence variations in CCP domains explain the diverse C3b-binding patterns, with limited or no contribution of some individual domains, while all regulators show extensive contacts with C3b for the domains at the third site. A variation of ~100° rotation around the lo...
Source: EMBO Journal - May 16, 2016 Category: Molecular Biology Authors: Forneris, F., Wu, J., Xue, X., Ricklin, D., Lin, Z., Sfyroera, G., Tzekou, A., Volokhina, E., Granneman, J. C., Hauhart, R., Bertram, P., Liszewski, M. K., Atkinson, J. P., Lambris, J. D., Gros, P. Tags: Immunology, Structural Biology Articles Source Type: research

Nucleosomal arrays self-assemble into supramolecular globular structures lacking 30-nm fibers
The existence of a 30-nm fiber as a basic folding unit for DNA packaging has remained a topic of active discussion. Here, we characterize the supramolecular structures formed by reversible Mg2+-dependent self-association of linear 12-mer nucleosomal arrays using microscopy and physicochemical approaches. These reconstituted chromatin structures, which we call "oligomers", are globular throughout all stages of cooperative assembly and range in size from ~50 nm to a maximum diameter of ~1,000 nm. The nucleosomal arrays were packaged within the oligomers as interdigitated 10-nm fibers, rather than folded 3...
Source: EMBO Journal - May 16, 2016 Category: Molecular Biology Authors: Maeshima, K., Rogge, R., Tamura, S., Joti, Y., Hikima, T., Szerlong, H., Krause, C., Herman, J., Seidel, E., DeLuca, J., Ishikawa, T., Hansen, J. C. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics Articles Source Type: research

How to make a synaptic ribbon: RIBEYE deletion abolishes ribbons in retinal synapses and disrupts neurotransmitter release
Synaptic ribbons are large proteinaceous scaffolds at the active zone of ribbon synapses that are specialized for rapid sustained synaptic vesicles exocytosis. A single ribbon-specific protein is known, RIBEYE, suggesting that ribbons may be constructed from RIBEYE protein. RIBEYE knockdown in zebrafish, however, only reduced but did not eliminate ribbons, indicating a more ancillary role. Here, we show in mice that full deletion of RIBEYE abolishes all presynaptic ribbons in retina synapses. Using paired recordings in acute retina slices, we demonstrate that deletion of RIBEYE severely impaired fast and sustained neurotra...
Source: EMBO Journal - May 16, 2016 Category: Molecular Biology Authors: Maxeiner, S., Luo, F., Tan, A., Schmitz, F., Südhof, T. C. Tags: Neuroscience Articles Source Type: research

Toxic gain of function from mutant FUS protein is crucial to trigger cell autonomous motor neuron loss
FUS is an RNA-binding protein involved in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Cytoplasmic FUS-containing aggregates are often associated with concomitant loss of nuclear FUS. Whether loss of nuclear FUS function, gain of a cytoplasmic function, or a combination of both lead to neurodegeneration remains elusive. To address this question, we generated knockin mice expressing mislocalized cytoplasmic FUS and complete FUS knockout mice. Both mouse models display similar perinatal lethality with respiratory insufficiency, reduced body weight and length, and largely similar alterations in gene ...
Source: EMBO Journal - May 16, 2016 Category: Molecular Biology Authors: Scekic-Zahirovic, J., Sendscheid, O., El Oussini, H., Jambeau, M., Sun, Y., Mersmann, S., Wagner, M., Dieterle, S., Sinniger, J., Dirrig-Grosch, S., Drenner, K., Birling, M.-C., Qiu, J., Zhou, Y., Li, H., Fu, X.-D., Rouaux, C., Shelkovnikova, T., Witting, Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research

eIF4A inactivates TORC1 in response to amino acid starvation
This study identifies specific components of the translation machinery as important mediators of TORC1 inactivation upon amino acid removal. (Source: EMBO Journal)
Source: EMBO Journal - May 16, 2016 Category: Molecular Biology Authors: Tsokanos, F.-F., Albert, M.-A., Demetriades, C., Spirohn, K., Boutros, M., Teleman, A. A. Tags: Metabolism, Protein Biosynthesis & Quality Control, Signal Transduction Articles Source Type: research

The mitochondrial outer membrane protein MDI promotes local protein synthesis and mtDNA replication
Early embryonic development features rapid nuclear DNA replication cycles, but lacks mtDNA replication. To meet the high-energy demands of embryogenesis, mature oocytes are furnished with vast amounts of mitochondria and mtDNA. However, the cellular machinery driving massive mtDNA replication in ovaries remains unknown. Here, we describe a Drosophila AKAP protein, MDI that recruits a translation stimulator, La-related protein (Larp), to the mitochondrial outer membrane in ovaries. The MDI-Larp complex promotes the synthesis of a subset of nuclear-encoded mitochondrial proteins by cytosolic ribosomes on the mitochondrial su...
Source: EMBO Journal - May 16, 2016 Category: Molecular Biology Authors: Zhang, Y., Chen, Y., Gucek, M., Xu, H. Tags: Development & Differentiation, DNA Replication, Repair & Recombination, Protein Biosynthesis & Quality Control Articles Source Type: research

Cerebral cortex expansion and folding: what have we learned?
One of the most prominent features of the human brain is the fabulous size of the cerebral cortex and its intricate folding. Cortical folding takes place during embryonic development and is important to optimize the functional organization and wiring of the brain, as well as to allow fitting a large cortex in a limited cranial volume. Pathological alterations in size or folding of the human cortex lead to severe intellectual disability and intractable epilepsy. Hence, cortical expansion and folding are viewed as key processes in mammalian brain development and evolution, ultimately leading to increased intellectual perform...
Source: EMBO Journal - May 16, 2016 Category: Molecular Biology Authors: Fernandez, V., Llinares-Benadero, C., Borrell, V. Tags: Neuroscience Review Source Type: research

Eyes without a ribbon
Eye and ear employ specialized glutamatergic synapses that feature an elaborate electron-dense projection—the synaptic ribbon. Despite major efforts, the function of the synaptic ribbon has remained enigmatic, because its brick-stone-like core-component RIBEYE has remained hard to crack genetically. In an elegant study, Maxeiner et al (2016) genetically deleted RIBEYE in mice. This abolished retinal ribbons and impaired exocytosis at the presynaptic active zone of bipolar cells. (Source: EMBO Journal)
Source: EMBO Journal - May 16, 2016 Category: Molecular Biology Authors: Moser, T. Tags: Neuroscience News [amp ] Views Source Type: research

FUScinating insights into motor neuron degeneration
Point mutations in FUS cause amyotrophic lateral sclerosis (ALS), a devastating neurodegenerative disease—but do they do that by a loss of the protein's normal function, or by endowing it with novel toxic functions, or both? In this issue of The EMBO Journal, Scekic-Zahirovic et al (2016) report that mutant FUS, but not the complete loss of FUS, triggers motor neuron degeneration in mice, arguing for a toxic gain-of-function mechanism. (Source: EMBO Journal)
Source: EMBO Journal - May 16, 2016 Category: Molecular Biology Authors: Dormann, D. Tags: Molecular Biology of Disease, Neuroscience News [amp ] Views Source Type: research

eIF4A moonlights as an off switch for TORC1
TORC1 is actively inhibited upon amino acid withdrawal. Tsokanos et al (2016) shed light on the underlying molecular mechanism. They demonstrate that upon removal of exogenous amino acids, eIF4A inhibits TORC1 via TSC2. Thus, whereas it is well known that TORC1 regulates the translation machinery, we now know the inverse is also true. (Source: EMBO Journal)
Source: EMBO Journal - May 16, 2016 Category: Molecular Biology Authors: Swierczynska, M. M., Hall, M. N. Tags: Metabolism, Protein Biosynthesis & Quality Control, Signal Transduction News [amp ] Views Source Type: research

Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo
The molecular roles of many RNA-binding proteins in bacterial post-transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP-seq) have begun to revolutionize the transcriptome-wide mapping of eukaryotic RNA-binding protein target sites. We have applied CLIP-seq to chart the target landscape of two major bacterial post-transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. By detecting binding sites at single-nucleotide resolution, we identify RNA preferences and structural constraints of Hfq and CsrA during thei...
Source: EMBO Journal - May 2, 2016 Category: Molecular Biology Authors: Holmqvist, E., Wright, P. R., Li, L., Bischler, T., Barquist, L., Reinhardt, R., Backofen, R., Vogel, J. Tags: Methods & Resources, Microbiology, Virology & Host Pathogen Interaction, RNA Biology Source Type: research

Distinct modes of recruitment of the CCR4-NOT complex by Drosophila and vertebrate Nanos
Nanos proteins repress the expression of target mRNAs by recruiting effector complexes through non-conserved N-terminal regions. In vertebrates, Nanos proteins interact with the NOT1 subunit of the CCR4–NOT effector complex through a NOT1 interacting motif (NIM), which is absent in Nanos orthologs from several invertebrate species. Therefore, it has remained unclear whether the Nanos repressive mechanism is conserved and whether it also involves direct interactions with the CCR4–NOT deadenylase complex in invertebrates. Here, we identify an effector domain (NED) that is necessary for the Drosophila melanogaster...
Source: EMBO Journal - May 2, 2016 Category: Molecular Biology Authors: Raisch, T., Bhandari, D., Sabath, K., Helms, S., Valkov, E., Weichenrieder, O., Izaurralde, E. Tags: RNA Biology, Structural Biology Articles Source Type: research

Phosphopeptide binding by Sld3 links Dbf4-dependent kinase to MCM replicative helicase activation
The initiation of eukaryotic DNA replication requires the assembly of active CMG (Cdc45-MCM-GINS) helicases at replication origins by a set of conserved and essential firing factors. This process is controlled during the cell cycle by cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK), and in response to DNA damage by the checkpoint kinase Rad53/Chk1. Here we show that Sld3, previously shown to be an essential CDK and Rad53 substrate, is recruited to the inactive MCM double hexamer in a DDK-dependent manner. Sld3 binds specifically to DDK-phosphorylated peptides from two MCM subunits (Mcm4, 6) and then recruits ...
Source: EMBO Journal - May 2, 2016 Category: Molecular Biology Authors: Deegan, T. D., Yeeles, J. T., Diffley, J. F. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

GEMC1 is a critical regulator of multiciliated cell differentiation
The generation of multiciliated cells (MCCs) is required for the proper function of many tissues, including the respiratory tract, brain, and germline. Defects in MCC development have been demonstrated to cause a subclass of mucociliary clearance disorders termed reduced generation of multiple motile cilia (RGMC). To date, only two genes, Multicilin (MCIDAS) and cyclin O (CCNO) have been identified in this disorder in humans. Here, we describe mice lacking GEMC1 (GMNC), a protein with a similar domain organization as Multicilin that has been implicated in DNA replication control. We have found that GEMC1-deficient mice are...
Source: EMBO Journal - May 2, 2016 Category: Molecular Biology Authors: Terre, B., Piergiovanni, G., Segura-Bayona, S., Gil-Gomez, G., Youssef, S. A., Attolini, C. S.-O., Wilsch-Bräuninger, M., Jung, C., Rojas, A. M., Marjanovic, M., Knobel, P. A., Palenzuela, L., Lopez-Rovira, T., Forrow, S., Huttner, W. B., Valverde Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation Articles Source Type: research

Relief of hypoxia by angiogenesis promotes neural stem cell differentiation by targeting glycolysis
Blood vessels are part of the stem cell niche in the developing cerebral cortex, but their in vivo role in controlling the expansion and differentiation of neural stem cells (NSCs) in development has not been studied. Here, we report that relief of hypoxia in the developing cerebral cortex by ingrowth of blood vessels temporo-spatially coincided with NSC differentiation. Selective perturbation of brain angiogenesis in vessel-specific Gpr124 null embryos, which prevented the relief from hypoxia, increased NSC expansion at the expense of differentiation. Conversely, exposure to increased oxygen levels rescued NSC differ...
Source: EMBO Journal - May 2, 2016 Category: Molecular Biology Authors: Lange, C., Turrero Garcia, M., Decimo, I., Bifari, F., Eelen, G., Quaegebeur, A., Boon, R., Zhao, H., Boeckx, B., Chang, J., Wu, C., Le Noble, F., Lambrechts, D., Dewerchin, M., Kuo, C. J., Huttner, W. B., Carmeliet, P. Tags: Neuroscience, Vascular Biology & Angiogenesis Articles Source Type: research

Interplay between Fanconi anemia and homologous recombination pathways in genome integrity
The Fanconi anemia (FA) pathway plays a central role in the repair of DNA interstrand crosslinks (ICLs) and regulates cellular responses to replication stress. Homologous recombination (HR), the error-free pathway for double-strand break (DSB) repair, is required during physiological cell cycle progression for the repair of replication-associated DNA damage and protection of stalled replication forks. Substantial crosstalk between the two pathways has recently been unravelled, in that key HR proteins such as the RAD51 recombinase and the tumour suppressors BRCA1 and BRCA2 also play important roles in ICL repair. Consistent...
Source: EMBO Journal - May 2, 2016 Category: Molecular Biology Authors: Michl, J., Zimmer, J., Tarsounas, M. Tags: Cancer, DNA Replication, Repair & Recombination, Molecular Biology of Disease Reviews Source Type: research

Elucidating the DDK-dependent step in replication initiation
By phosphorylating specific replication factors, cell cycle kinases ensure that eukaryotic DNA replication is initiated once and only once per mitotic cell division. New work in The EMBO Journal now reveals how DDK-mediated phosphorylation of Mcm2-7 helicase subunits is read out by Sld3, which provides further integration with CDK phosphorylation. (Source: EMBO Journal)
Source: EMBO Journal - May 2, 2016 Category: Molecular Biology Authors: Araki, H. Tags: DNA Replication, Repair & Recombination News [amp ] Views Source Type: research

It's a family act: the geminin triplets take center stage in motile ciliogenesis
The balance between proliferation and differentiation is a fundamental aspect of multicellular life. Perhaps nowhere is this delicate balance more palpable than in the multiciliated cells (MCCs) that line the respiratory tract, the ependyma, and the oviduct. These cells contain dozens to hundreds of motile cilia that beat in a concerted fashion to generate directed fluid flow over the tissue surface. Although MCCs have exited the cell cycle, remarkably, they retain the ability to duplicate their centrioles and to mature those centrioles into ciliary basal bodies—two features, which are known to be normally under stri...
Source: EMBO Journal - May 2, 2016 Category: Molecular Biology Authors: Vladar, E. K., Mitchell, B. J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation News [amp ] Views Source Type: research

Fetal neurogenesis: breathe HIF you can
Microvascular circulation creates a supporting niche for neurogenesis through the secretion of angiocrine factors. The emerging concept that energy balance and metabolic status play a role in the modulation of stem cells suggests that oxygen delivery by nearby capillary vascular beds could also regulate neurogenesis. Blood vessel formation and neuron production proceed in a coordinated fashion in the developing cerebral cortex, providing a unique opportunity to test the possibility that oxygen supply regulates cell fate decisions in neurogenic niches. The interesting study by the Carmeliet laboratory yields evidence that t...
Source: EMBO Journal - May 2, 2016 Category: Molecular Biology Authors: Morante-Redolat, J. M., Farinas, I. Tags: Neuroscience, Vascular Biology & Angiogenesis News [amp ] Views Source Type: research