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

UCP2 regulates energy metabolism and differentiation potential of human pluripotent stem cells
(Source: EMBO Journal)
Source: EMBO Journal - April 15, 2016 Category: Molecular Biology Authors: Zhang, J., Khvorostov, I., Hong, J. S., Oktay, Y., Vergnes, L., Nuebel, E., Wahjudi, P. N., Setoguchi, K., Wang, G., Do, A., Jung, H.-J., McCaffery, J. M., Kurland, I. J., Reue, K., Lee, W.-N. P., Koehler, C. M., Teitell, M. A. Tags: Corrigendum Source Type: research

The transcriptional coactivator Bob1 promotes the development of follicular T helper cells via Bcl6
Follicular T helper (Tfh) cells are key regulators of the germinal center reaction and long-term humoral immunity. Tfh cell differentiation requires the sustained expression of the transcriptional repressor Bcl6; however, its regulation in CD4+ T cells is incompletely understood. Here, we report that the transcriptional coactivator Bob1, encoded by the Pou2af1 gene, promotes Bcl6 expression and Tfh cell development. We found that Bob1 together with the octamer transcription factors Oct1/Oct2 can directly bind to and transactivate the Bcl6 and Btla promoters. Mixed bone marrow chimeras revealed that Bob1 is required for the...
Source: EMBO Journal - April 15, 2016 Category: Molecular Biology Authors: Stauss, D., Brunner, C., Berberich-Siebelt, F., Höpken, U. E., Lipp, M., Müller, G. Tags: Immunology Articles Source Type: research

USP19 modulates autophagy and antiviral immune responses by deubiquitinating Beclin-1
Autophagy, mediated by a number of autophagy-related (ATG) proteins, plays an important role in the bulk degradation of cellular constituents. Beclin-1 (also known as Atg6 in yeast) is a core protein essential for autophagic initiation and other biological processes. The activity of Beclin-1 is tightly regulated by multiple post-translational modifications, including ubiquitination, yet the molecular mechanism underpinning its reversible deubiquitination remains poorly defined. Here, we identified ubiquitin-specific protease 19 (USP19) as a positive regulator of autophagy, but a negative regulator of type I interferon (IFN...
Source: EMBO Journal - April 15, 2016 Category: Molecular Biology Authors: Jin, S., Tian, S., Chen, Y., Zhang, C., Xie, W., Xia, X., Cui, J., Wang, R.-F. Tags: Autophagy & Cell Death, Immunology, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

ALS-linked protein disulfide isomerase variants cause motor dysfunction
This study identifies ER proteostasis imbalance as a risk factor for ALS, driving initial stages of the disease. (Source: EMBO Journal)
Source: EMBO Journal - April 15, 2016 Category: Molecular Biology Authors: Woehlbier, U., Colombo, A., Saaranen, M. J., Perez, V., Ojeda, J., Bustos, F. J., Andreu, C. I., Torres, M., Valenzuela, V., Medinas, D. B., Rozas, P., Vidal, R. L., Lopez-Gonzalez, R., Salameh, J., Fernandez-Collemann, S., Munoz, N., Matus, S., Armisen, Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research

Ribonuclease H2 mutations induce a cGAS/STING-dependent innate immune response
Aicardi–Goutières syndrome (AGS) provides a monogenic model of nucleic acid-mediated inflammation relevant to the pathogenesis of systemic autoimmunity. Mutations that impair ribonuclease (RNase) H2 enzyme function are the most frequent cause of this autoinflammatory disorder of childhood and are also associated with systemic lupus erythematosus. Reduced processing of either RNA:DNA hybrid or genome-embedded ribonucleotide substrates is thought to lead to activation of a yet undefined nucleic acid-sensing pathway. Here, we establish Rnaseh2bA174T/A174T knock-in mice as a subclinical model of disease, identifyi...
Source: EMBO Journal - April 15, 2016 Category: Molecular Biology Authors: Mackenzie, K. J., Carroll, P., Lettice, L., Tarnauskaite, Z., Reddy, K., Dix, F., Revuelta, A., Abbondati, E., Rigby, R. E., Rabe, B., Kilanowski, F., Grimes, G., Fluteau, A., Devenney, P. S., Hill, R. E., Reijns, M. A., Jackson, A. P. Tags: Immunology Articles Source Type: research

Molecular basis of ion permeability in a voltage-gated sodium channel
Voltage-gated sodium channels are essential for electrical signalling across cell membranes. They exhibit strong selectivities for sodium ions over other cations, enabling the finely tuned cascade of events associated with action potentials. This paper describes the ion permeability characteristics and the crystal structure of a prokaryotic sodium channel, showing for the first time the detailed locations of sodium ions in the selectivity filter of a sodium channel. Electrostatic calculations based on the structure are consistent with the relative cation permeability ratios (Na+  Li+ >> K+, Ca2+, ...
Source: EMBO Journal - April 15, 2016 Category: Molecular Biology Authors: Naylor, C. E., Bagneris, C., DeCaen, P. G., Sula, A., Scaglione, A., Clapham, D. E., Wallace, B. Tags: Membrane & Intracellular Transport, Structural Biology Articles Source Type: research

CPAP promotes timely cilium disassembly to maintain neural progenitor pool
A mutation in the centrosomal-P4.1-associated protein (CPAP) causes Seckel syndrome with microcephaly, which is suggested to arise from a decline in neural progenitor cells (NPCs) during development. However, mechanisms of NPCs maintenance remain unclear. Here, we report an unexpected role for the cilium in NPCs maintenance and identify CPAP as a negative regulator of ciliary length independent of its role in centrosome biogenesis. At the onset of cilium disassembly, CPAP provides a scaffold for the cilium disassembly complex (CDC), which includes Nde1, Aurora A, and OFD1, recruited to the ciliary base for timely cilium di...
Source: EMBO Journal - April 15, 2016 Category: Molecular Biology Authors: Gabriel, E., Wason, A., Ramani, A., Gooi, L. M., Keller, P., Pozniakovsky, A., Poser, I., Noack, F., Telugu, N. S., Calegari, F., Saric, T., Hescheler, J., Hyman, A. A., Gottardo, M., Callaini, G., Alkuraya, F. S., Gopalakrishnan, J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation, Molecular Biology of Disease Articles Source Type: research

When Myc's asleep, embryonic stem cells are dormant
Myc is one of the original reprogramming factors used to produce induced pluripotent stem cells. However, it is not necessary, instead its main role is to increase the efficiency of the reprogramming. The article by Scognamiglio et al (2016) helps clarify how. The authors show that Myc depletion leads to a reversible dormant state consistent with diapause. In this state, the cell sees its proliferation potential diminished but its pluripotency unchanged. The ability to coordinate the induction of this state should have important implications in cell differentiation. (Source: EMBO Journal)
Source: EMBO Journal - April 15, 2016 Category: Molecular Biology Authors: Nakagawa, M., Karagiannis, P., Yamanaka, S. Tags: Development & Differentiation, Stem Cells News [amp ] Views Source Type: research

ER strikes again: Proteostasis Dysfunction In ALS
The precise contribution of endoplasmic reticulum (ER) chaperone protein disulfide isomerase (PDI) variants in human amyotrophic lateral sclerosis (ALS) patients to the pathogenesis of ALS remained unclear. In the present study, Woehlbier et al (2016) demonstrated that these PDI variants are capable of altering motor neuron morphology, impairing the expression of synaptic proteins, and compromising neuromuscular junction (NMJ) integrity. (Source: EMBO Journal)
Source: EMBO Journal - April 15, 2016 Category: Molecular Biology Authors: Maharjan, N., Saxena, S. Tags: Molecular Biology of Disease, Neuroscience News [amp ] Views Source Type: research

cGAS-STING do it again: pivotal role in RNase H2 genetic disease
RNase H2 is a susceptibility gene for the Aicardi–Goutières syndrome (AGS), a genetic auto-inflammatory disease. Mackenzie and colleagues now report a tractable mouse model for the disease, implicating the cGAS-STING pathway. (Source: EMBO Journal)
Source: EMBO Journal - April 15, 2016 Category: Molecular Biology Authors: Gentili, M., Manel, N. Tags: Immunology News [amp ] Views Source Type: research

Three in a row--how sodium ions cross the channel
Sodium channels are central to a host of fundamental cellular processes, including sensory perception, pain, and muscle contraction. In order to understand any of these processes in detail, it is necessary to know the atomic structure of the channel proteins both with and without bound sodium ions. In this issue, Naylor et al (2016) present the structure of a bacterial sodium channel tetramer. The three bound, partially hydrated sodium ions line up neatly in a row inside the selectivity filter, providing us with the first detailed insights into ion conduction in sodium channels, and the mechanisms by which sodium and ...
Source: EMBO Journal - April 15, 2016 Category: Molecular Biology Authors: Kühlbrandt, W. Tags: Membrane & Intracellular Transport, Structural Biology News [amp ] Views Source Type: research

ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling
(Source: EMBO Journal)
Source: EMBO Journal - March 31, 2016 Category: Molecular Biology Authors: Deshpande, R. A., Williams, G. J., Limbo, O., Williams, R. S., Kuhnlein, J., Lee, J.-H., Classen, S., Guenther, G., Russell, P., Tainer, J. A., Paull, T. T. Tags: Corrigendum Source Type: research

Intraflagellar transport proteins 172, 80, 57, 54, 38, and 20 form a stable tubulin-binding IFT-B2 complex
Intraflagellar transport (IFT) relies on the IFT complex and is required for ciliogenesis. The IFT-B complex consists of 9–10 stably associated core subunits and six "peripheral" subunits that were shown to dissociate from the core structure at moderate salt concentration. We purified the six "peripheral" IFT-B subunits of Chlamydomonas reinhardtii as recombinant proteins and show that they form a stable complex independently of the IFT-B core. We suggest a nomenclature of IFT-B1 (core) and IFT-B2 (peripheral) for the two IFT-B subcomplexes. We demonstrate that IFT88, together with the N-terminal ...
Source: EMBO Journal - March 31, 2016 Category: Molecular Biology Authors: Taschner, M., Weber, K., Mourao, A., Vetter, M., Awasthi, M., Stiegler, M., Bhogaraju, S., Lorentzen, E. Tags: Cell Adhesion, Polarity & Cytoskeleton Articles Source Type: research

Structural mechanism of ATP-dependent DNA binding and DNA end bridging by eukaryotic Rad50
The Mre11–Rad50–Nbs1 (MRN) complex is a central factor in the repair of DNA double-strand breaks (DSBs). The ATP-dependent mechanisms of how MRN detects and endonucleolytically processes DNA ends for the repair by microhomology-mediated end-joining or further resection in homologous recombination are still unclear. Here, we report the crystal structures of the ATPS-bound dimer of the Rad50NBD (nucleotide-binding domain) from the thermophilic eukaryote Chaetomium thermophilum (Ct) in complex with either DNA or CtMre11RBD (Rad50-binding domain) along with small-angle X-ray scattering and cross-linking studies. Th...
Source: EMBO Journal - March 31, 2016 Category: Molecular Biology Authors: Seifert, F. U., Lammens, K., Stoehr, G., Kessler, B., Hopfner, K.-P. Tags: DNA Replication, Repair & Recombination, Structural Biology Articles Source Type: research

ATP-dependent DNA binding, unwinding, and resection by the Mre11/Rad50 complex
ATP-dependent DNA end recognition and nucleolytic processing are central functions of the Mre11/Rad50 (MR) complex in DNA double-strand break repair. However, it is still unclear how ATP binding and hydrolysis primes the MR function and regulates repair pathway choice in cells. Here, Methanococcus jannaschii MR-ATPS-DNA structure reveals that the partly deformed DNA runs symmetrically across central groove between two ATPS-bound Rad50 nucleotide-binding domains. Duplex DNA cannot access the Mre11 active site in the ATP-free full-length MR complex. ATP hydrolysis drives rotation of the nucleotide-binding domain and induces ...
Source: EMBO Journal - March 31, 2016 Category: Molecular Biology Authors: Liu, Y., Sung, S., Kim, Y., Li, F., Gwon, G., Jo, A., Kim, A.-K., Kim, T., Song, O.-k., Lee, S. E., Cho, Y. Tags: DNA Replication, Repair & Recombination, Structural Biology Articles Source Type: research

Mitochondria are required for pro-ageing features of the senescent phenotype
Cell senescence is an important tumour suppressor mechanism and driver of ageing. Both functions are dependent on the development of the senescent phenotype, which involves an overproduction of pro-inflammatory and pro-oxidant signals. However, the exact mechanisms regulating these phenotypes remain poorly understood. Here, we show the critical role of mitochondria in cellular senescence. In multiple models of senescence, absence of mitochondria reduced a spectrum of senescence effectors and phenotypes while preserving ATP production via enhanced glycolysis. Global transcriptomic analysis by RNA sequencing revealed that a ...
Source: EMBO Journal - March 31, 2016 Category: Molecular Biology Authors: Correia-Melo, C., Marques, F. D., Anderson, R., Hewitt, G., Hewitt, R., Cole, J., Carroll, B. M., Miwa, S., Birch, J., Merz, A., Rushton, M. D., Charles, M., Jurk, D., Tait, S. W., Czapiewski, R., Greaves, L., Nelson, G., Bohlooly-Y, M., Rodriguez-Cuenca, Tags: Ageing, Cell Cycle, Metabolism Articles Source Type: research

Upstream ORFs are prevalent translational repressors in vertebrates
Regulation of gene expression is fundamental in establishing cellular diversity and a target of natural selection. Untranslated mRNA regions (UTRs) are key mediators of post-transcriptional regulation. Previous studies have predicted thousands of ORFs in 5' UTRs, the vast majority of which have unknown function. Here, we present a systematic analysis of the translation and function of upstream open reading frames (uORFs) across vertebrates. Using high-resolution ribosome footprinting, we find that (i) uORFs are prevalent within vertebrate transcriptomes, (ii) the majority show signatures of active translation, and (iii) uO...
Source: EMBO Journal - March 31, 2016 Category: Molecular Biology Authors: Johnstone, T. G., Bazzini, A. A., Giraldez, A. J. Tags: Protein Biosynthesis & Quality Control, RNA Biology, Systems & Computational Biology Articles Source Type: research

DNA binding to SMC ATPases--trapped for release
The SMC/Rad50/RecN proteins are universal DNA-associated ABC-type ATPases with crucial functions in genome maintenance. New insights into Rad50–DNA complex structure and cohesin regulation inspire a speculative look at the entire superfamily. Identification of a continuous DNA binding site across the Rad50 dimer interface (Liu et al, 2016; Seifert et al, 2016) suggests a similar site in cohesin. The localization of this site hints a DNA-activated mechanism for cohesin removal from chromosomes. (Source: EMBO Journal)
Source: EMBO Journal - March 31, 2016 Category: Molecular Biology Authors: Schüler, H., Sjögren, C. Tags: Cell Cycle, DNA Replication, Repair & Recombination News [amp ] Views Source Type: research

Mitochondria and senescence: new actors for an old play
Mitochondrial dysfunction has been linked to both cellular senescence and ageing. Despite the relationship, it is still unclear whether mitochondria have a causal role in senescence. In this issue of The EMBO Journal, Correia-Melo et al (2016) combine targeted depletion of mitochondria with impairment of their biogenesis to demonstrate that decreased numbers of mitochondria impair the senescence response. Their results suggest that targeting mitochondria could reduce the detrimental effects of senescence during ageing. (Source: EMBO Journal)
Source: EMBO Journal - March 31, 2016 Category: Molecular Biology Authors: Herranz, N., Gil, J. Tags: Ageing, Cell Cycle, Metabolism News [amp ] Views Source Type: research

Starting too soon: upstream reading frames repress downstream translation
Upstream open reading frames (uORFs) are known to regulate a few specific transcripts, and recent computational and experimental studies have suggested candidate uORF regulation across the genome. In this issue, Johnstone et al (2016) use ribosome profiling to identify translated uORFs and measure their effects on downstream translation. Furthermore, they show that regulatory uORFs are conserved across species and subject to selective constraint. Recognizing the potential of uORFs in regulating translation expands our understanding of the dynamic regulation of gene expression. (Source: EMBO Journal)
Source: EMBO Journal - March 31, 2016 Category: Molecular Biology Authors: McGeachy, A. M., Ingolia, N. T. Tags: Protein Biosynthesis & Quality Control, RNA Biology, Systems & Computational Biology News [amp ] Views Source Type: research

Neutralization of pro-inflammatory monocytes by targeting TLR2 dimerization ameliorates colitis
We report that TLR2-p directly interacts with TLR2 within the membrane, leading to inhibition of TLR2–TLR6/1 assembly induced by natural ligands. This was associated with decreased levels of extracellular signal-regulated kinases (ERK) signaling and reduced secretion of pro-inflammatory cytokines, such as interleukin (IL)-6, IL-23, IL-12, and IL-1β. Altogether, our study provides insights into the essential role of TLR2 dimerization in the activation of pathogenic pro-inflammatory Ly6Chi monocytes and suggests that inhibition of this aggregation by TLR2-p might have therapeutic potential in the treatment of acut...
Source: EMBO Journal - March 16, 2016 Category: Molecular Biology Authors: Shmuel-Galia, L., Aychek, T., Fink, A., Porat, Z., Zarmi, B., Bernshtein, B., Brenner, O., Jung, S., Shai, Y. Tags: Immunology Articles Source Type: research

Wnt-induced deubiquitination FoxM1 ensures nucleus {beta}-catenin transactivation
A key step of Wnt signaling activation is the recruitment of β-catenin to the Wnt target-gene promoter in the nucleus, but its mechanisms are largely unknown. Here, we identified FoxM1 as a novel target of Wnt signaling, which is essential for β-catenin/TCF4 transactivation. GSK3 phosphorylates FoxM1 on serine 474 which induces FoxM1 ubiquitination mediated by FBXW7. Wnt signaling activation inhibits FoxM1 phosphorylation by GSK3–Axin complex and leads to interaction between FoxM1 and deubiquitinating enzyme USP5, thereby deubiquitination and stabilization of FoxM1. FoxM1 accumulation in the nucleus promote...
Source: EMBO Journal - March 16, 2016 Category: Molecular Biology Authors: Chen, Y., Li, Y., Xue, J., Gong, A., Yu, G., Zhou, A., Lin, K., Zhang, S., Zhang, N., Gottardi, C. J., Huang, S. Tags: Development & Differentiation, Signal Transduction Articles Source Type: research

Pseudouridines in U2 snRNA stimulate the ATPase activity of Prp5 during spliceosome assembly
Pseudouridine () is the most abundant internal modification identified in RNA, and yet little is understood of its effects on downstream reactions. Yeast U2 snRNA contains three conserved s (35, 42, and 44) in the branch site recognition region (BSRR), which base pairs with the pre-mRNA branch site during splicing. Here, we show that blocks to pseudouridylation at these positions reduce the efficiency of pre-mRNA splicing, leading to growth-deficient phenotypes. Restoration of pseudouridylation at these positions using designer snoRNAs results in near complete rescue of splicing and cell growth. These s interact geneticall...
Source: EMBO Journal - March 16, 2016 Category: Molecular Biology Authors: Wu, G., Adachi, H., Ge, J., Stephenson, D., Query, C. C., Yu, Y.-T. Tags: RNA Biology Articles Source Type: research

Sororin actively maintains sister chromatid cohesion
Cohesion between sister chromatids is established during DNA replication but needs to be maintained to enable proper chromosome–spindle attachments in mitosis or meiosis. Cohesion is mediated by cohesin, but also depends on cohesin acetylation and sororin. Sororin contributes to cohesion by stabilizing cohesin on DNA. Sororin achieves this by inhibiting WAPL, which otherwise releases cohesin from DNA and destroys cohesion. Here we describe mouse models which enable the controlled depletion of sororin by gene deletion or auxin-induced degradation. We show that sororin is essential for embryonic development, cohesion m...
Source: EMBO Journal - March 16, 2016 Category: Molecular Biology Authors: Ladurner, R., Kreidl, E., Ivanov, M. P., Ekker, H., Idarraga-Amado, M. H., Busslinger, G. A., Wutz, G., Cisneros, D. A., Peters, J.-M. Tags: Cell Cycle, DNA Replication, Repair & Recombination Articles Source Type: research

Stat3 promotes mitochondrial transcription and oxidative respiration during maintenance and induction of naive pluripotency
Transcription factor Stat3 directs self-renewal of pluripotent mouse embryonic stem (ES) cells downstream of the cytokine leukemia inhibitory factor (LIF). Stat3 upregulates pivotal transcription factors in the ES cell gene regulatory network to sustain naïve identity. Stat3 also contributes to the rapid proliferation of ES cells. Here, we show that Stat3 increases the expression of mitochondrial-encoded transcripts and enhances oxidative metabolism. Chromatin immunoprecipitation reveals that Stat3 binds to the mitochondrial genome, consistent with direct transcriptional regulation. An engineered form of Stat3 that local...
Source: EMBO Journal - March 16, 2016 Category: Molecular Biology Authors: Carbognin, E., Betto, R. M., Soriano, M. E., Smith, A. G., Martello, G. Tags: Metabolism, Stem Cells Articles Source Type: research

Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer
The histological grade of carcinomas describes the ability of tumor cells to organize in differentiated epithelial structures and has prognostic and therapeutic impact. Here, we show that differential usage of the genomic repertoire of transcriptional enhancers leads to grade-specific gene expression programs in human pancreatic ductal adenocarcinoma (PDAC). By integrating gene expression profiling, epigenomic footprinting, and loss-of-function experiments in PDAC cell lines of different grade, we identified the repertoires of enhancers specific to high- and low-grade PDACs and the cognate set of transcription factors acti...
Source: EMBO Journal - March 16, 2016 Category: Molecular Biology Authors: Diaferia, G. R., Balestrieri, C., Prosperini, E., Nicoli, P., Spaggiari, P., Zerbi, A., Natoli, G. Tags: Cancer, Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription Articles Source Type: research

Cytokine-induced megakaryocytic differentiation is regulated by genome-wide loss of a uSTAT transcriptional program
Metazoan development is regulated by transcriptional networks, which must respond to extracellular cues including cytokines. The JAK/STAT pathway is a highly conserved regulatory module, activated by many cytokines, in which tyrosine-phosphorylated STATs (pSTATs) function as transcription factors. However, the mechanisms by which STAT activation modulates lineage-affiliated transcriptional programs are unclear. We demonstrate that in the absence of thrombopoietin (TPO), tyrosine-unphosphorylated STAT5 (uSTAT5) is present in the nucleus where it colocalizes with CTCF and represses a megakaryocytic transcriptional program. T...
Source: EMBO Journal - March 16, 2016 Category: Molecular Biology Authors: Park, H. J., Li, J., Hannah, R., Biddie, S., Leal-Cervantes, A. I., Kirschner, K., Flores Santa Cruz, D., Sexl, V., Göttgens, B., Green, A. R. Tags: Immunology, Signal Transduction, Transcription Articles Source Type: research

Phosphatidylinositol 3-phosphates--at the interface between cell signalling and membrane traffic
Phosphoinositides (PIs) form a minor class of phospholipids with crucial functions in cell physiology, ranging from cell signalling and motility to a role as signposts of compartmental membrane identity. Phosphatidylinositol 3-phosphates are present at the plasma membrane and within the endolysosomal system, where they serve as key regulators of both cell signalling and of intracellular membrane traffic. Here, we provide an overview of the metabolic pathways that regulate cellular synthesis of PI 3-phosphates at distinct intracellular sites and discuss the mechanisms by which these lipids regulate cell signalling and membr...
Source: EMBO Journal - March 16, 2016 Category: Molecular Biology Authors: Marat, A. L., Haucke, V. Tags: Membrane & Intracellular Transport, Metabolism, Signal Transduction Review Source Type: research

The cis-regulatory switchboard of pancreatic ductal cancer
Pancreatic ductal adenocarcinoma (PDAC) remains one of the most devastating human diseases. There is consequently a pressing need to understand its molecular underpinnings, which should enable new preventive and therapeutic strategies. A new study in The EMBO Journal (Diaferia et al, 2016) maps the transcriptome and epigenetic landscape associated with distinct PDAC grades and identifies cis- and trans-regulatory elements in tumour progression. (Source: EMBO Journal)
Source: EMBO Journal - March 16, 2016 Category: Molecular Biology Authors: Ferrer, J., Real, F. X. Tags: Cancer, Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription News [amp ] Views Source Type: research

Emancipation from transcriptional latency: unphosphorylated STAT5 as guardian of hematopoietic differentiation
The canonical paradigm of Jak-STAT signaling is that members of the signal transducers and activators of transcription (STATs) family of transcription factors are activated by Janus kinase (Jak)-mediated tyrosine phosphorylation. While the relationship between activation and tyrosine phosphorylation still appears axiomatic, several lines of evidence suggest that unactivated, unphosphorylated isoforms, uSTATs, are nonetheless also engaged in transcriptional regulation. In this issue of The EMBO Journal, Park et al (2015) make a convincing case that nuclear uSTAT5 controls hematopoietic differentiation. (Source: EMBO Journal)
Source: EMBO Journal - March 16, 2016 Category: Molecular Biology Authors: Decker, T. Tags: Immunology, Signal Transduction, Transcription News [amp ] Views Source Type: research

Two isoforms of Serpent containing either one or two GATA zinc fingers have different roles in Drosophila haematopoiesis
(Source: EMBO Journal)
Source: EMBO Journal - February 29, 2016 Category: Molecular Biology Authors: Waltzer, L., Bataille, L., Peyrefitte, S., Haenlin, M. Tags: Corrigendum Source Type: research

p38{gamma} and p38{delta} reprogram liver metabolism by modulating neutrophil infiltration
Non-alcoholic fatty liver disease (NAFLD) is a major health problem and the main cause of liver disease in Western countries. Although NAFLD is strongly associated with obesity and insulin resistance, its pathogenesis remains poorly understood. The disease begins with an excessive accumulation of triglycerides in the liver, which stimulates an inflammatory response. Alternative p38 mitogen-activated kinases (p38 and p38) have been shown to contribute to inflammation in different diseases. Here we demonstrate that p38 is elevated in livers of obese patients with NAFLD and that mice lacking p38/ in myeloid cells ar...
Source: EMBO Journal - February 29, 2016 Category: Molecular Biology Authors: Gonzalez-Teran, B., Matesanz, N., Nikolic, I., Verdugo, M. A., Sreeramkumar, V., Hernandez-Cosido, L., Mora, A., Crainiciuc, G., Saiz, M. L., Bernardo, E., Leiva-Vega, L., Rodriguez, E., Bondia, V., Torres, J. L., Perez-Sieira, S., Ortega, L., Cuenda, A., Tags: Immunology, Metabolism, Molecular Biology of Disease Articles Source Type: research

Inducible chromatin priming is associated with the establishment of immunological memory in T cells
Immunological memory is a defining feature of vertebrate physiology, allowing rapid responses to repeat infections. However, the molecular mechanisms required for its establishment and maintenance remain poorly understood. Here, we demonstrated that the first steps in the acquisition of T-cell memory occurred during the initial activation phase of naïve T cells by an antigenic stimulus. This event initiated extensive chromatin remodeling that reprogrammed immune response genes toward a stably maintained primed state, prior to terminal differentiation. Activation induced the transcription factors NFAT and AP-1 which creat...
Source: EMBO Journal - February 29, 2016 Category: Molecular Biology Authors: Bevington, S. L., Cauchy, P., Piper, J., Bertrand, E., Lalli, N., Jarvis, R. C., Gilding, L. N., Ott, S., Bonifer, C., Cockerill, P. N. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Immunology Articles Source Type: research

PAQR3 controls autophagy by integrating AMPK signaling to enhance ATG14L-associated PI3K activity
The Beclin1–VPS34 complex is recognized as a central node in regulating autophagy via interacting with diverse molecules such as ATG14L for autophagy initiation and UVRAG for autophagosome maturation. However, the underlying molecular mechanism that coordinates the timely activation of VPS34 complex is poorly understood. Here, we identify that PAQR3 governs the preferential formation and activation of ATG14L-linked VPS34 complex for autophagy initiation via two levels of regulation. Firstly, PAQR3 functions as a scaffold protein that facilitates the formation of ATG14L- but not UVRAG-linked VPS34 complex, leading to ...
Source: EMBO Journal - February 29, 2016 Category: Molecular Biology Authors: Xu, D.-Q., Wang, Z., Wang, C.-Y., Zhang, D.-Y., Wan, H.-D., Zhao, Z.-L., Gu, J., Zhang, Y.-X., Li, Z.-G., Man, K.-Y., Pan, Y., Wang, Z.-F., Ke, Z.-J., Liu, Z.-X., Liao, L.-J., Chen, Y. Tags: Autophagy & Cell Death, Metabolism, Signal Transduction Articles Source Type: research

TFEB and TFE3 are novel components of the integrated stress response
To reestablish homeostasis and mitigate stress, cells must activate a series of adaptive intracellular signaling pathways. The participation of the transcription factors TFEB and TFE3 in cellular adaptation to starvation is well established. Here, we show that TFEB and TFE3 also play an important role in the cellular response to ER stress. Treatment with ER stressors causes translocation of TFEB and TFE3 to the nucleus in a process that is dependent on PERK and calcineurin but not on mTORC1. Activated TFEB and TFE3 enhance cellular response to stress by inducing direct transcriptional upregulation of ATF4 and other UPR gen...
Source: EMBO Journal - February 29, 2016 Category: Molecular Biology Authors: Martina, J. A., Diab, H. I., Brady, O. A., Puertollano, R. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Transcription Articles Source Type: research

Actin remodeling confers BRAF inhibitor resistance to melanoma cells through YAP/TAZ activation
The activation of transcriptional coactivators YAP and its paralog TAZ has been shown to promote resistance to anti-cancer therapies. YAP/TAZ activity is tightly coupled to actin cytoskeleton architecture. However, the influence of actin remodeling on cancer drug resistance remains largely unexplored. Here, we report a pivotal role of actin remodeling in YAP/TAZ-dependent BRAF inhibitor resistance in BRAF V600E mutant melanoma cells. Melanoma cells resistant to the BRAF inhibitor PLX4032 exhibit an increase in actin stress fiber formation, which appears to promote the nuclear accumulation of YAP/TAZ. Knockdown of YAP/TAZ r...
Source: EMBO Journal - February 29, 2016 Category: Molecular Biology Authors: Kim, M. H., Kim, J., Hong, H., Lee, S.-H., Lee, J.-K., Jung, E., Kim, J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Molecular Biology of Disease Articles Source Type: research

Eradicating tumor drug resistance at its YAP-biomechanical roots
Treatment with BRAF kinase inhibitors leads to rapid resistance and tumor regression in BRAF V600E mutant melanoma patients. However, the underlying mechanism of the developed tumor resistance is not fully clear. In this issue of The EMBO Journal, Kim and colleagues show that melanoma cells acquire resistance to BRAF inhibitors by changing cell shape, modifying their cytoskeleton and, in turn, activating the YAP/TAZ mechanotransduction pathway (Kim et al, 2016). (Source: EMBO Journal)
Source: EMBO Journal - February 29, 2016 Category: Molecular Biology Authors: Zanconato, F., Piccolo, S. Tags: Cell Adhesion, Polarity & Cytoskeleton, Molecular Biology of Disease News [amp ] Views Source Type: research

Identification and function of conformational dynamics in the multidomain GTPase dynamin
Vesicle release upon endocytosis requires membrane fission, catalyzed by the large GTPase dynamin. Dynamin contains five domains that together orchestrate its mechanochemical activity. Hydrogen–deuterium exchange coupled with mass spectrometry revealed global nucleotide- and membrane-binding-dependent conformational changes, as well as the existence of an allosteric relay element in the α2S helix of the dynamin stalk domain. As predicted from structural studies, FRET analyses detect large movements of the pleckstrin homology domain (PHD) from a ‘closed’ conformation docked near the stalk to an &lsqu...
Source: EMBO Journal - February 14, 2016 Category: Molecular Biology Authors: Srinivasan, S., Dharmarajan, V., Reed, D. K., Griffin, P. R., Schmid, S. L. Tags: Membrane & Intracellular Transport, Structural Biology Articles Source Type: research

HDAC6 regulates cellular viral RNA sensing by deacetylation of RIG-I
RIG-I is a key cytosolic sensor that detects RNA viruses through its C-terminal region and activates the production of antiviral interferons (IFNs) and proinflammatory cytokines. While posttranslational modification has been demonstrated to regulate RIG-I signaling activity, its significance for the sensing of viral RNAs remains unclear. Here, we first show that the RIG-I C-terminal region undergoes deacetylation to regulate its viral RNA-sensing activity and that the HDAC6-mediated deacetylation of RIG-I is critical for viral RNA detection. HDAC6 transiently bound to RIG-I and removed the lysine 909 acetylation in the pre...
Source: EMBO Journal - February 14, 2016 Category: Molecular Biology Authors: Choi, S. J., Lee, H.-C., Kim, J.-H., Park, S. Y., Kim, T.-H., Lee, W.-K., Jang, D.-J., Yoon, J.-E., Choi, Y.-I., Kim, S., Ma, J., Kim, C.-J., Yao, T.-P., Jung, J. U., Lee, J.-Y., Lee, J.-S. Tags: Immunology, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Non-acidic activation of pain-related Acid-Sensing Ion Channel 3 by lipids
Extracellular pH variations are seen as the principal endogenous signal that triggers activation of Acid-Sensing Ion Channels (ASICs), which are basically considered as proton sensors, and are involved in various processes associated with tissue acidification. Here, we show that human painful inflammatory exudates, displaying non-acidic pH, induce a slow constitutive activation of human ASIC3 channels. This effect is largely driven by lipids, and we identify lysophosphatidylcholine (LPC) and arachidonic acid (AA) as endogenous activators of ASIC3 in the absence of any extracellular acidification. The combination of LPC and...
Source: EMBO Journal - February 14, 2016 Category: Molecular Biology Authors: Marra, S., Ferru-Clement, R., Breuil, V., Delaunay, A., Christin, M., Friend, V., Sebille, S., Cognard, C., Ferreira, T., Roux, C., Euller-Ziegler, L., Noel, J., Lingueglia, E., Deval, E. Tags: Membrane & Intracellular Transport, Neuroscience Articles Source Type: research