Methionine metabolism is essential for SIRT1-regulated mouse embryonic stem cell maintenance and embryonic development
Methionine metabolism is critical for epigenetic maintenance, redox homeostasis, and animal development. However, the regulation of methionine metabolism remains unclear. Here, we provide evidence that SIRT1, the most conserved mammalian NAD+-dependent protein deacetylase, is critically involved in modulating methionine metabolism, thereby impacting maintenance of mouse embryonic stem cells (mESCs) and subsequent embryogenesis. We demonstrate that SIRT1-deficient mESCs are hypersensitive to methionine restriction/depletion-induced differentiation and apoptosis, primarily due to a reduced conversion of methionine to S-adeno...
Source: EMBO Journal - November 2, 2017 Category: Molecular Biology Authors: Tang, S., Fang, Y., Huang, G., Xu, X., Padilla-Banks, E., Fan, W., Xu, Q., Sanderson, S. M., Foley, J. F., Dowdy, S., McBurney, M. W., Fargo, D. C., Williams, C. J., Locasale, J. W., Guan, Z., Li, X. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Metabolism, Stem Cells Articles Source Type: research

Sterol transfer, PI4P consumption, and control of membrane lipid order by endogenous OSBP
The network of proteins that orchestrate the distribution of cholesterol among cellular organelles is not fully characterized. We previously proposed that oxysterol-binding protein (OSBP) drives cholesterol/PI4P exchange at contact sites between the endoplasmic reticulum (ER) and the trans-Golgi network (TGN). Using the inhibitor OSW-1, we report here that the sole activity of endogenous OSBP makes a major contribution to cholesterol distribution, lipid order, and PI4P turnover in living cells. Blocking OSBP causes accumulation of sterols at ER/lipid droplets at the expense of TGN, thereby reducing the gradient of lipid or...
Source: EMBO Journal - November 2, 2017 Category: Molecular Biology Authors: Mesmin, B., Bigay, J., Polidori, J., Jamecna, D., Lacas-Gervais, S., Antonny, B. Tags: Membrane & Intracellular Transport Articles Source Type: research

Transcriptional memory of cells of origin overrides {beta}-catenin requirement of MLL cancer stem cells
While β-catenin has been demonstrated as an essential molecule and therapeutic target for various cancer stem cells (CSCs) including those driven by MLL fusions, here we show that transcriptional memory from cells of origin predicts AML patient survival and allows β-catenin-independent transformation in MLL-CSCs derived from hematopoietic stem cell (HSC)-enriched LSK population but not myeloid–granulocyte progenitors. Mechanistically, β-catenin regulates expression of downstream targets of a key transcriptional memory gene, Hoxa9 that is highly enriched in LSK-derived MLL-CSCs and helps sustain leukemi...
Source: EMBO Journal - November 2, 2017 Category: Molecular Biology Authors: Siriboonpiputtana, T., Zeisig, B. B., Zarowiecki, M., Fung, T. K., Mallardo, M., Tsai, C.-T., Lau, P. N. I., Hoang, Q. C., Veiga, P., Barnes, J., Lynn, C., Wilson, A., Lenhard, B., So, C. W. E. Tags: Cancer, Stem Cells, Transcription Articles Source Type: research

Somatodendritic accumulation of Tau in Alzheimer's disease is promoted by Fyn-mediated local protein translation
The cause of protein accumulation in neurodegenerative disease is incompletely understood. In Alzheimer's disease (AD), the axonally enriched protein Tau forms hyperphosphorylated aggregates in the somatodendritic domain. Consequently, a process of subcellular relocalization driven by Tau phosphorylation and detachment from microtubules has been proposed. Here, we reveal an alternative mechanism of de novo protein synthesis of Tau and its hyperphosphorylation in the somatodendritic domain, induced by oligomeric amyloid-β (Aβ) and mediated by the kinase Fyn that activates the ERK/S6 signaling pathway. Activation o...
Source: EMBO Journal - November 2, 2017 Category: Molecular Biology Authors: Li, C., Götz, J. Tags: Neuroscience, Protein Biosynthesis & Quality Control Articles Source Type: research

Bone morphogenetic protein and retinoic acid synergistically specify female germ-cell fate in mice
The mechanism for sex determination in mammalian germ cells remains unclear. Here, we reconstitute the female sex determination in mouse germ cells in vitro under a defined condition without the use of gonadal somatic cells. We show that retinoic acid (RA) and its key effector, STRA8, are not sufficient to induce the female germ-cell fate. In contrast, bone morphogenetic protein (BMP) and RA synergistically induce primordial germ cells (PGCs)/PGC-like cells (PGCLCs) derived from embryonic stem cells (ESCs) into fetal primary oocytes. The induction is characterized by entry into the meiotic prophase, occurs synchronous...
Source: EMBO Journal - November 2, 2017 Category: Molecular Biology Authors: Miyauchi, H., Ohta, H., Nagaoka, S., Nakaki, F., Sasaki, K., Hayashi, K., Yabuta, Y., Nakamura, T., Yamamoto, T., Saitou, M. Tags: Development & Differentiation, Signal Transduction, Stem Cells Articles Source Type: research

Initiating meiosis in a dish
Embryonic germ cells are formed from embryonic progenitors through a highly complex differentiation process, recapitulation of which in vitro has proved challenging. Two new studies in The EMBO Journal report culture conditions for embryonic stem cell-derived primordial germ cell-like cells (PGCLCs) that enable global DNA demethylation (Ohta et al, 2017), and subsequent initiation of meiosis (Miyauchi et al, 2017), allowing future manipulations to elucidate mechanisms driving germ line differentiation. (Source: EMBO Journal)
Source: EMBO Journal - November 2, 2017 Category: Molecular Biology Authors: Gill, M. E., Peters, A. H. Tags: Development & Differentiation, Signal Transduction, Stem Cells News [amp ] Views Source Type: research

Structure of a VirD4 coupling protein bound to a VirB type IV secretion machinery
Type IV secretion (T4S) systems are versatile bacterial secretion systems mediating transport of protein and/or DNA. T4S systems are generally composed of 11 VirB proteins and 1 VirD protein (VirD4). The VirB1-11 proteins assemble to form a secretion machinery and a pilus while the VirD4 protein is responsible for substrate recruitment. The structure of VirD4 in isolation is known; however, its structure bound to the VirB1-11 apparatus has not been determined. Here, we purify a T4S system with VirD4 bound, define the biochemical requirements for complex formation and describe the protein–protein interaction network i...
Source: EMBO Journal - October 16, 2017 Category: Molecular Biology Authors: Redzej, A., Ukleja, M., Connery, S., Trokter, M., Felisberto-Rodrigues, C., Cryar, A., Thalassinos, K., Hayward, R. D., Orlova, E. V., Waksman, G. Tags: Microbiology, Virology & Host Pathogen Interaction, Structural Biology Articles Source Type: research

Structural basis for antibacterial peptide self-immunity by the bacterial ABC transporter McjD
In this study, we have determined its structure in a novel conformation, apo inward-occluded and a new nucleotide-bound state, high-energy outward-occluded intermediate state, with a defined ligand binding cavity. Predictive cysteine cross-linking in E. coli membranes and PELDOR measurements along the transport cycle indicate that McjD does not undergo major conformational changes as previously proposed for multi-drug ABC exporters. Combined with transport assays and molecular dynamics simulations, we propose a novel mechanism for toxic peptide ABC exporters that only requires the transient opening of the cavity for r...
Source: EMBO Journal - October 16, 2017 Category: Molecular Biology Authors: Bountra, K., Hagelueken, G., Choudhury, H. G., Corradi, V., El Omari, K., Wagner, A., Mathavan, I., Zirah, S., Yuan Wahlgren, W., Tieleman, D. P., Schiemann, O., Rebuffat, S., Beis, K. Tags: Membrane & Intracellular Transport, Microbiology, Virology & Host Pathogen Interaction, Structural Biology Articles Source Type: research

Casein kinase 1-epsilon or 1-delta required for Wnt-mediated intestinal stem cell maintenance
The intestinal epithelium holds an immense regenerative capacity mobilized by intestinal stem cells (ISCs), much of it supported by Wnt pathway activation. Several unique regulatory mechanisms ensuring optimal levels of Wnt signaling have been recognized in ISCs. Here, we identify another Wnt signaling amplifier, CKI, which is specifically upregulated in ISCs and is essential for ISC maintenance, especially in the absence of its close isoform CKI. Co-ablation of CKI/ in the mouse gut epithelium results in rapid ISC elimination, with subsequent growth arrest, crypt–villous shrinking, and rapid mouse death. Unexpectedl...
Source: EMBO Journal - October 16, 2017 Category: Molecular Biology Authors: Morgenstern, Y., Das Adhikari, U., Ayyash, M., Elyada, E., Toth, B., Moor, A., Itzkovitz, S., Ben-Neriah, Y. Tags: Cell Cycle, Signal Transduction, Stem Cells Articles Source Type: research

Ret receptor tyrosine kinase sustains proliferation and tissue maturation in intestinal epithelia
We report a new and physiologically significant site of Ret expression in the intestine: the intestinal epithelium. Experiments in Drosophila indicate that Ret is expressed both by enteric neurons and adult intestinal epithelial progenitors, which require Ret to sustain their proliferation. Mechanistically, Ret is engaged in a positive feedback loop with Wnt/Wingless signalling, modulated by Src and Fak kinases. We find that Ret is also expressed by the developing intestinal epithelium of mice, where its expression is maintained into the adult stage in a subset of enteroendocrine/enterochromaffin cells. Mouse organoid expe...
Source: EMBO Journal - October 16, 2017 Category: Molecular Biology Authors: Perea, D., Guiu, J., Hudry, B., Konstantinidou, C., Milona, A., Hadjieconomou, D., Carroll, T., Hoyer, N., Natarajan, D., Kallijärvi, J., Walker, J. A., Soba, P., Thapar, N., Burns, A. J., Jensen, K. B., Miguel-Aliaga, I. Tags: Development & Differentiation, Signal Transduction, Stem Cells Articles Source Type: research

Qualitative differences in T-cell activation by dendritic cell-derived extracellular vesicle subtypes
Exosomes, nano-sized secreted extracellular vesicles (EVs), are actively studied for their diagnostic and therapeutic potential. In particular, exosomes secreted by dendritic cells (DCs) have been shown to carry MHC-peptide complexes allowing efficient activation of T lymphocytes, thus displaying potential as promoters of adaptive immune responses. DCs also secrete other types of EVs of different size, subcellular origin and protein composition, whose immune capacities have not been yet compared to those of exosomes. Here, we show that large EVs (lEVs) released by human DCs are as efficient as small EVs (sEVs), including e...
Source: EMBO Journal - October 16, 2017 Category: Molecular Biology Authors: Tkach, M., Kowal, J., Zucchetti, A. E., Enserink, L., Jouve, M., Lankar, D., Saitakis, M., Martin-Jaular, L., Thery, C. Tags: Immunology, Membrane & Intracellular Transport Articles Source Type: research

Snapin promotes HIV-1 transmission from dendritic cells by dampening TLR8 signaling
HIV-1 traffics through dendritic cells (DCs) en route to establishing a productive infection in T lymphocytes but fails to induce an innate immune response. Within DC endosomes, HIV-1 somehow evades detection by the pattern-recognition receptor (PRR) Toll-like receptor 8 (TLR8). Using a phosphoproteomic approach, we identified a robust and diverse signaling cascade triggered by HIV-1 upon entry into human DCs. A secondary siRNA screen of the identified signaling factors revealed several new mediators of HIV-1 trans-infection of CD4+ T cells in DCs, including the dynein motor protein Snapin. Inhibition of Snapin enhanced lo...
Source: EMBO Journal - October 16, 2017 Category: Molecular Biology Authors: Khatamzas, E., Hipp, M. M., Gaughan, D., Pichulik, T., Leslie, A., Fernandes, R. A., Muraro, D., Booth, S., Zausmer, K., Sun, M.-Y., Kessler, B., Rowland-Jones, S., Cerundolo, V., Simmons, A. Tags: Immunology, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Epigenetic regulation of left-right asymmetry by DNA methylation
DNA methylation is a major epigenetic modification; however, the precise role of DNA methylation in vertebrate development is still not fully understood. Here, we show that DNA methylation is essential for the establishment of the left–right (LR) asymmetric body plan during vertebrate embryogenesis. Perturbation of DNA methylation by depletion of DNA methyltransferase 1 (dnmt1) or dnmt3bb.1 in zebrafish embryos leads to defects in dorsal forerunner cell (DFC) specification or collective migration, laterality organ malformation, and disruption of LR patterning. Knockdown of dnmt1 in Xenopus embryos also causes similar...
Source: EMBO Journal - October 16, 2017 Category: Molecular Biology Authors: Wang, L., Liu, Z., Lin, H., Ma, D., Tao, Q., Liu, F. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Development & Differentiation, Signal Transduction Articles Source Type: research

Dual function of UPF3B in early and late translation termination
Nonsense-mediated mRNA decay (NMD) is a cellular surveillance pathway that recognizes and degrades mRNAs with premature termination codons (PTCs). The mechanisms underlying translation termination are key to the understanding of RNA surveillance mechanisms such as NMD and crucial for the development of therapeutic strategies for NMD-related diseases. Here, we have used a fully reconstituted in vitro translation system to probe the NMD proteins for interaction with the termination apparatus. We discovered that UPF3B (i) interacts with the release factors, (ii) delays translation termination and (iii) dissociates post-t...
Source: EMBO Journal - October 16, 2017 Category: Molecular Biology Authors: Neu-Yilik, G., Raimondeau, E., Eliseev, B., Yeramala, L., Amthor, B., Deniaud, A., Huard, K., Kerschgens, K., Hentze, M. W., Schaffitzel, C., Kulozik, A. E. Tags: Protein Biosynthesis & Quality Control, RNA Biology Articles Source Type: research

Phosphorylation of the FUS low-complexity domain disrupts phase separation, aggregation, and toxicity
Neuronal inclusions of aggregated RNA-binding protein fused in sarcoma (FUS) are hallmarks of ALS and frontotemporal dementia subtypes. Intriguingly, FUS's nearly uncharged, aggregation-prone, yeast prion-like, low sequence-complexity domain (LC) is known to be targeted for phosphorylation. Here we map in vitro and in-cell phosphorylation sites across FUS LC. We show that both phosphorylation and phosphomimetic variants reduce its aggregation-prone/prion-like character, disrupting FUS phase separation in the presence of RNA or salt and reducing FUS propensity to aggregate. Nuclear magnetic resonance spectroscopy demon...
Source: EMBO Journal - October 16, 2017 Category: Molecular Biology Authors: Monahan, Z., Ryan, V. H., Janke, A. M., Burke, K. A., Rhoads, S. N., Zerze, G. H., O'Meally, R., Dignon, G. L., Conicella, A. E., Zheng, W., Best, R. B., Cole, R. N., Mittal, J., Shewmaker, F., Fawzi, N. L. Tags: Neuroscience, Protein Biosynthesis & Quality Control Articles Source Type: research

Dysregulated molecular pathways in amyotrophic lateral sclerosis-frontotemporal dementia spectrum disorder
Frontotemporal dementia (FTD), the second most common form of dementia in people under 65 years of age, is characterized by progressive atrophy of the frontal and/or temporal lobes. FTD overlaps extensively with the motor neuron disease amyotrophic lateral sclerosis (ALS), especially at the genetic level. Both FTD and ALS can be caused by many mutations in the same set of genes; the most prevalent of these mutations is a GGGGCC repeat expansion in the first intron of C9ORF72. As shown by recent intensive studies, some key cellular pathways are dysregulated in the ALS-FTD spectrum disorder, including autophagy, nucleoc...
Source: EMBO Journal - October 16, 2017 Category: Molecular Biology Authors: Gao, F.-B., Almeida, S., Lopez-Gonzalez, R. Tags: Molecular Biology of Disease, Neuroscience Review Source Type: research

New functions in translation termination uncovered for NMD factor UPF3B
Despite a wealth of biochemical data, the mechanism by which targets of the nonsense-mediated mRNA decay (NMD) pathway are recognized during translation termination remains elusive. A new study by Neu-Yilik et al (2017) using a fully reconstituted in vitro translation termination system reveals new roles for the NMD factor UPF3B in translation termination and a direct interaction between UPF3B and ribosome release factors. (Source: EMBO Journal)
Source: EMBO Journal - October 16, 2017 Category: Molecular Biology Authors: Mühlemann, O., Karousis, E. D. Tags: Protein Biosynthesis & Quality Control, RNA Biology News [amp ] Views Source Type: research

Liquidizing FUS via prion-like domain phosphorylation
FUS is an RNA-binding protein (RBP) with a prion-like domain (PrLD) that condenses into functional liquids, which can aberrantly phase transition into solid aggregates comprised of pathological fibrils connected to neurodegenerative disease. How cells prevent aberrant phase transitions of FUS and other disease-linked RBPs with PrLDs is poorly understood. In this issue of The EMBO Journal, Monahan et al (2017) establish that phosphorylation of specific serine and threonine residues in the FUS PrLD inhibits aberrant phase separation and toxicity. (Source: EMBO Journal)
Source: EMBO Journal - October 16, 2017 Category: Molecular Biology Authors: Shorter, J. Tags: Neuroscience, Protein Biosynthesis & Quality Control News [amp ] Views Source Type: research

Telomerase abrogates aneuploidy-induced telomere replication stress, senescence and cell depletion
(Source: EMBO Journal)
Source: EMBO Journal - October 2, 2017 Category: Molecular Biology Authors: Meena, J. K., Cerutti, A., Beichler, C., Morita, Y., Bruhn, C., Kumar, M., Kraus, J. M., Speicher, M. R., Wang, Z.-Q., Kestler, H. A., Fagagna, F. d. d., Günes, C., Rudolph, K. L. Tags: Cancer, Cell Cycle, DNA Replication, Repair & Recombination Corrigenda Source Type: research

Wnt activity and basal niche position sensitize intestinal stem and progenitor cells to DNA damage
(Source: EMBO Journal)
Source: EMBO Journal - October 2, 2017 Category: Molecular Biology Authors: Tao, S., Tang, D., Morita, Y., Sperka, T., Omrani, O., Lechel, A., Sakk, V., Kraus, J., Kestler, H. A., Kühl, M., Rudolph, K. L. Tags: Corrigenda Source Type: research

BLM and SLX4 play opposing roles in recombination-dependent replication at human telomeres
Alternative lengthening of telomeres (ALT) is a telomere lengthening pathway that predominates in aggressive tumors of mesenchymal origin; however, the underlying mechanism of telomere synthesis is not fully understood. Here, we show that the BLM–TOP3A–RMI (BTR) dissolvase complex is required for ALT-mediated telomere synthesis. We propose that recombination intermediates formed during strand invasion are processed by the BTR complex, initiating rapid and extensive POLD3-dependent telomere synthesis followed by dissolution, with no overall exchange of telomeric DNA. This process is counteracted by the SLX4&ndas...
Source: EMBO Journal - October 2, 2017 Category: Molecular Biology Authors: Sobinoff, A. P., Allen, J. A., Neumann, A. A., Yang, S. F., Walsh, M. E., Henson, J. D., Reddel, R. R., Pickett, H. A. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

The Hox proteins Ubx and AbdA collaborate with the transcription pausing factor M1BP to regulate gene transcription
In metazoans, the pausing of RNA polymerase II at the promoter (paused Pol II) has emerged as a widespread and conserved mechanism in the regulation of gene transcription. While critical in recruiting Pol II to the promoter, the role transcription factors play in transitioning paused Pol II into productive Pol II is, however, little known. By studying how Drosophila Hox transcription factors control transcription, we uncovered a molecular mechanism that increases productive transcription. We found that the Hox proteins AbdA and Ubx target gene promoters previously bound by the transcription pausing factor M1BP, containing ...
Source: EMBO Journal - October 2, 2017 Category: Molecular Biology Authors: Zouaz, A., Auradkar, A., Delfini, M. C., Macchi, M., Barthez, M., Ela Akoa, S., Bastianelli, L., Xie, G., Deng, W.-M., Levine, S. S., Graba, Y., Saurin, A. J. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Development & Differentiation, Transcription Articles Source Type: research

Exosome cofactor hMTR4 competes with export adaptor ALYREF to ensure balanced nuclear RNA pools for degradation and export
The exosome is a key RNA machine that functions in the degradation of unwanted RNAs. Here, we found that significant fractions of precursors and mature forms of mRNAs and long noncoding RNAs are degraded by the nuclear exosome in normal human cells. Exosome-mediated degradation of these RNAs requires its cofactor hMTR4. Significantly, hMTR4 plays a key role in specifically recruiting the exosome to its targets. Furthermore, we provide several lines of evidence indicating that hMTR4 executes this role by directly competing with the mRNA export adaptor ALYREF for associating with ARS2, a component of the cap-binding complex ...
Source: EMBO Journal - October 2, 2017 Category: Molecular Biology Authors: Fan, J., Kuai, B., Wu, G., Wu, X., Chi, B., Wang, L., Wang, K., Shi, Z., Zhang, H., Chen, S., He, Z., Wang, S., Zhou, Z., Li, G., Cheng, H. Tags: RNA Biology Articles Source Type: research

Noise in a phosphorelay drives stochastic entry into sporulation in Bacillus subtilis
Entry into sporulation in Bacillus subtilis is governed by a phosphorelay in which phosphoryl groups from a histidine kinase are successively transferred via relay proteins to the response regulator Spo0A. Spo0A~P, in turn, sets in motion events that lead to asymmetric division and activation of the cell-specific transcription factor F, a hallmark for entry into sporulation. Here, we have used a microfluidics-based platform to investigate the activation of Spo0A and F in individual cells held under constant, sporulation-inducing conditions. The principal conclusions were that: (i) activation of F occurs with an approximate...
Source: EMBO Journal - October 2, 2017 Category: Molecular Biology Authors: Russell, J. R., Cabeen, M. T., Wiggins, P. A., Paulsson, J., Losick, R. Tags: Microbiology, Virology & Host Pathogen Interaction, Signal Transduction Articles Source Type: research

Redox regulation of plant stem cell fate
Despite the importance of stem cells in plant and animal development, the common mechanisms of stem cell maintenance in both systems have remained elusive. Recently, the importance of hydrogen peroxide (H2O2) signaling in priming stem cell differentiation has been extensively studied in animals. Here, we show that different forms of reactive oxygen species (ROS) have antagonistic roles in plant stem cell regulation, which were established by distinct spatiotemporal patterns of ROS-metabolizing enzymes. The superoxide anion (O2·–) is markedly enriched in stem cells to activate WUSCHEL and maintain stemness, whe...
Source: EMBO Journal - October 2, 2017 Category: Molecular Biology Authors: Zeng, J., Dong, Z., Wu, H., Tian, Z., Zhao, Z. Tags: Plant Biology, Stem Cells Articles Source Type: research

Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis
In this study, we present the first quantitative human genome-wide map of DNA lesions induced by ultraviolet (UV) radiation, the ubiquitous carcinogen in sunlight that causes skin cancer. Remarkably, the pattern of carcinogen susceptibility across the genome of primary cells significantly reflects mutation frequency in malignant melanoma. Surprisingly, DNase-accessible euchromatin is protected from UV, while lamina-associated heterochromatin at the nuclear periphery is vulnerable. Many cancer driver genes have an intrinsic increase in carcinogen susceptibility, including the BRAF oncogene that has the highest mutation freq...
Source: EMBO Journal - October 2, 2017 Category: Molecular Biology Authors: Garcia-Nieto, P. E., Schwartz, E. K., King, D. A., Paulsen, J., Collas, P., Herrera, R. E., Morrison, A. J. Tags: Cancer, Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination Articles Source Type: research

Formin 2 links neuropsychiatric phenotypes at young age to an increased risk for dementia
In conclusion, our data present a new approach to explore the connection between AD risk factors across life span and provide mechanistic insight to the processes by which neuropsychiatric diseases at a young age affect the risk for developing dementia. (Source: EMBO Journal)
Source: EMBO Journal - October 2, 2017 Category: Molecular Biology Authors: Agis-Balboa, R. C., Pinheiro, P. S., Rebola, N., Kerimoglu, C., Benito, E., Gertig, M., Bahari-Javan, S., Jain, G., Burkhardt, S., Delalle, I., Jatzko, A., Dettenhofer, M., Zunszain, P. A., Schmitt, A., Falkai, P., Pape, J. C., Binder, E. B., Mulle, C., F Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research

Molecular cartography of mutational landscapes in melanomas
Understanding the origins of mutations in genes and how these give rise to tumors is a central problem in biology. A new study in The EMBO Journal has produced a 3-dimensional map of DNA damage induced by sunlight, a pervasive carcinogen, and found that genes on the periphery, located near the nuclear lamin, are more prone to damage than those in the interior of the nucleus. In addition, high levels of damage showed a remarkable correlation with driver mutations in melanoma. (Source: EMBO Journal)
Source: EMBO Journal - October 2, 2017 Category: Molecular Biology Authors: Beckwitt, E. C., Van Houten, B. Tags: Cancer, Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination News [amp ] Views Source Type: research

FORMINg a link between PTSD and AD
Epidemiological evidence suggests that people suffering from post-traumatic stress disorder have a higher risk for developing Alzheimer's disease. The underlying mechanisms, however, remained thus far unexplored. In this issue of The EMBO Journal, Agís-Balboa et al (2017) show that the actin-associated protein Formin 2 is reduced in both conditions and that its downregulation in mice accelerates Alzheimer-related pathophysiology via aberrant epigenetic and transcriptional changes. Treating mice with a histone deacetylase inhibitor (HDACi) delayed Alzheimer-related pathologies, lending experimental support to on...
Source: EMBO Journal - October 2, 2017 Category: Molecular Biology Authors: Gräff, J. Tags: Molecular Biology of Disease, Neuroscience News [amp ] Views Source Type: research

Rab35 GTPase recruits NPD52 to autophagy targets
Autophagy targets intracellular molecules, damaged organelles, and invading pathogens for degradation in lysosomes. Recent studies have identified autophagy receptors that facilitate this process by binding to ubiquitinated targets, including NDP52. Here, we demonstrate that the small guanosine triphosphatase Rab35 directs NDP52 to the corresponding targets of multiple forms of autophagy. The active GTP-bound form of Rab35 accumulates on bacteria-containing endosomes, and Rab35 directly binds and recruits NDP52 to internalized bacteria. Additionally, Rab35 promotes interaction of NDP52 with ubiquitin. This process is inhib...
Source: EMBO Journal - September 15, 2017 Category: Molecular Biology Authors: Minowa-Nozawa, A., Nozawa, T., Okamoto-Furuta, K., Kohda, H., Nakagawa, I. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport Articles Source Type: research

Heteromeric channels formed by TRPC1, TRPC4 and TRPC5 define hippocampal synaptic transmission and working memory
Canonical transient receptor potential (TRPC) channels influence various neuronal functions. Using quantitative high-resolution mass spectrometry, we demonstrate that TRPC1, TRPC4, and TRPC5 assemble into heteromultimers with each other, but not with other TRP family members in the mouse brain and hippocampus. In hippocampal neurons from Trpc1/Trpc4/Trpc5-triple-knockout (Trpc1/4/5–/–) mice, lacking any TRPC1-, TRPC4-, or TRPC5-containing channels, action potential-triggered excitatory postsynaptic currents (EPSCs) were significantly reduced, whereas frequency, amplitude, and kinetics of quantal miniature EPSC ...
Source: EMBO Journal - September 15, 2017 Category: Molecular Biology Authors: Bröker-Lai, J., Kollewe, A., Schindeldecker, B., Pohle, J., Nguyen Chi, V., Mathar, I., Guzman, R., Schwarz, Y., Lai, A., Weissgerber, P., Schwegler, H., Dietrich, A., Both, M., Sprengel, R., Draguhn, A., Köhr, G., Fakler, B., Flockerzi, V Tags: Membrane & Intracellular Transport, Neuroscience Articles Source Type: research

A plant effector-triggered immunity signaling sector is inhibited by pattern-triggered immunity
Since signaling machineries for two modes of plant-induced immunity, pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), extensively overlap, PTI and ETI signaling likely interact. In an Arabidopsis quadruple mutant, in which four major sectors of the signaling network, jasmonate, ethylene, PAD4, and salicylate, are disabled, the hypersensitive response (HR) typical of ETI is abolished when the Pseudomonas syringae effector AvrRpt2 is bacterially delivered but is intact when AvrRpt2 is directly expressed in planta. These observations led us to discovery of a network-buffered signaling mechanism that med...
Source: EMBO Journal - September 15, 2017 Category: Molecular Biology Authors: Hatsugai, N., Igarashi, D., Mase, K., Lu, Y., Tsuda, Y., Chakravarthy, S., Wei, H.-L., Foley, J. W., Collmer, A., Glazebrook, J., Katagiri, F. Tags: Immunology, Plant Biology, Systems & Computational Biology Articles Source Type: research

The innate immune receptor MDA5 limits rotavirus infection but promotes cell death and pancreatic inflammation
Melanoma differentiation-associated protein 5 (MDA5) mediates the innate immune response to viral infection. Polymorphisms in IFIH1, the gene coding for MDA5, correlate with the risk of developing type 1 diabetes (T1D). Here, we demonstrate that MDA5 is crucial for the immune response to enteric rotavirus infection, a proposed etiological agent for T1D. MDA5 variants encoded by minor IFIH1 alleles associated with lower T1D risk exhibit reduced activity against rotavirus infection. We find that MDA5 activity limits rotavirus infection not only through the induction of antiviral interferons and pro-inflammatory cytokines, bu...
Source: EMBO Journal - September 15, 2017 Category: Molecular Biology Authors: Dou, Y., Yim, H. C., Kirkwood, C. D., Williams, B. R., Sadler, A. J. Tags: Immunology, Molecular Biology of Disease Articles Source Type: research

Histone H4K20 tri-methylation at late-firing origins ensures timely heterochromatin replication
Among other targets, the protein lysine methyltransferase PR-Set7 induces histone H4 lysine 20 monomethylation (H4K20me1), which is the substrate for further methylation by the Suv4-20h methyltransferase. Although these enzymes have been implicated in control of replication origins, the specific contribution of H4K20 methylation to DNA replication remains unclear. Here, we show that H4K20 mutation in mammalian cells, unlike in Drosophila, partially impairs S-phase progression and protects from DNA re-replication induced by stabilization of PR-Set7. Using Epstein–Barr virus-derived episomes, we further demonstrate tha...
Source: EMBO Journal - September 15, 2017 Category: Molecular Biology Authors: Brustel, J., Kirstein, N., Izard, F., Grimaud, C., Prorok, P., Cayrou, C., Schotta, G., Abdelsamie, A. F., Dejardin, J., Mechali, M., Baldacci, G., Sardet, C., Cadoret, J.-C., Schepers, A., Julien, E. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination Articles Source Type: research

Coactivators and general transcription factors have two distinct dynamic populations dependent on transcription
SAGA and ATAC are two distinct chromatin modifying co-activator complexes with distinct enzymatic activities involved in RNA polymerase II (Pol II) transcription regulation. To investigate the mobility of co-activator complexes and general transcription factors in live-cell nuclei, we performed imaging experiments based on photobleaching. SAGA and ATAC, but also two general transcription factors (TFIID and TFIIB), were highly dynamic, exhibiting mainly transient associations with chromatin, contrary to Pol II, which formed more stable chromatin interactions. Fluorescence correlation spectroscopy analyses revealed that the ...
Source: EMBO Journal - September 15, 2017 Category: Molecular Biology Authors: Vosnakis, N., Koch, M., Scheer, E., Kessler, P., Mely, Y., Didier, P., Tora, L. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription Articles Source Type: research

Structural insights into transcription initiation by yeast RNA polymerase I
In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre-rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of a multi-subunit pre-initiation complex (PIC) at the ribosomal RNA promoter. In yeast, the minimal PIC includes Pol I, the transcription factor Rrn3, and Core Factor (CF) composed of subunits Rrn6, Rrn7, and Rrn11. Here, we present the cryo-EM structure of the 18-subunit yeast Pol I PIC bound to a transcription scaffold. The cryo-EM map reveals an unexpected arrangement of the DNA and CF subunits relative to Pol I. The upstream...
Source: EMBO Journal - September 15, 2017 Category: Molecular Biology Authors: Sadian, Y., Tafur, L., Kosinski, J., Jakobi, A. J., Wetzel, R., Buczak, K., Hagen, W. J., Beck, M., Sachse, C., Müller, C. W. Tags: Structural Biology, Transcription Articles Source Type: research

Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle
Duplication and segregation of chromosomes involves dynamic reorganization of their internal structure by conserved architectural proteins, including the structural maintenance of chromosomes (SMC) complexes cohesin and condensin. Despite active investigation of the roles of these factors, a genome-wide view of dynamic chromosome architecture at both small and large scale during cell division is still missing. Here, we report the first comprehensive 4D analysis of the higher-order organization of the Saccharomyces cerevisiae genome throughout the cell cycle and investigate the roles of SMC complexes in controlling structur...
Source: EMBO Journal - September 15, 2017 Category: Molecular Biology Authors: Lazar-Stefanita, L., Scolari, V. F., Mercy, G., Muller, H., Guerin, T. M., Thierry, A., Mozziconacci, J., Koszul, R. Tags: Cell Cycle, Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination Articles Source Type: research

Modulating NAD+ metabolism, from bench to bedside
Discovered in the beginning of the 20th century, nicotinamide adenine dinucleotide (NAD+) has evolved from a simple oxidoreductase cofactor to being an essential cosubstrate for a wide range of regulatory proteins that include the sirtuin family of NAD+-dependent protein deacylases, widely recognized regulators of metabolic function and longevity. Altered NAD+ metabolism is associated with aging and many pathological conditions, such as metabolic diseases and disorders of the muscular and neuronal systems. Conversely, increased NAD+ levels have shown to be beneficial in a broad spectrum of diseases. Here, we review the fun...
Source: EMBO Journal - September 15, 2017 Category: Molecular Biology Authors: Katsyuba, E., Auwerx, J. Tags: Metabolism, Molecular Biology of Disease Reviews Source Type: research

Stem cells make leukemia grow again
Leukemic stem cells were hypothesized to play a critical role in acute myeloid leukemia relapse, but data to support this were lacking. In a recent study elegantly combining sequencing with functional xenograft assays, Shlush et al (2017) identified two distinct origins of leukemic relapse. They provided direct experimental evidence linking relapse to cancer stem cell clones already present before therapeutic intervention. (Source: EMBO Journal)
Source: EMBO Journal - September 15, 2017 Category: Molecular Biology Authors: Bahr, C., Correia, N. C., Trumpp, A. Tags: Cancer, Molecular Biology of Disease, Stem Cells News [amp ] Views Source Type: research

RNA polymerase I, bending the rules?
Transcription initiation is one of the key regulatory steps in expressing the genetic information encoded in the DNA. Mechanisms of RNA Pol II transcription have been extensively studied, whereas the structural basis of RNA Pol I and III transcription is still poorly defined. Three recent studies discussed here give a first glimpse into the molecular mechanisms underlying the process of RNA Pol I transcriptional initiation and reveal unexpected structural differences compared to the previously described homologous Pol II structures. (Source: EMBO Journal)
Source: EMBO Journal - September 15, 2017 Category: Molecular Biology Authors: Jochem, L., Ramsay, E. P., Vannini, A. Tags: Structural Biology, Transcription News [amp ] Views Source Type: research

Chromosome structure dynamics during the cell cycle: a structure to fit every phase
Chromosomes undergo dramatic morphological changes as cells advance through the cell cycle. Using powerful molecular and computational methods, several recent studies revealed an outstanding complexity of continuous structural changes accompanying cell cycle progression. In agreement with cell division being a fundamental cellular process, characteristic features of cell cycle stage-specific genome structure are conserved from yeast to mouse. These studies further shine light on the critical roles that SMC complexes, already well known as fundamental regulators of chromosome topology, have in orchestrating structural dynam...
Source: EMBO Journal - September 15, 2017 Category: Molecular Biology Authors: Barrington, C., Pezic, D., Hadjur, S. Tags: Cell Cycle, Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination News [amp ] Views Source Type: research

Mitochondrial genome inheritance and replacement in the human germline
(Source: EMBO Journal)
Source: EMBO Journal - September 1, 2017 Category: Molecular Biology Authors: Wolf, D. P., Hayama, T., Mitalipov, S. Tags: Corrigendum Source Type: research

Epigenome profiling and editing of neocortical progenitor cells during development
The generation of neocortical neurons from neural progenitor cells (NPCs) is primarily controlled by transcription factors binding to DNA in the context of chromatin. To understand the complex layer of regulation that orchestrates different NPC types from the same DNA sequence, epigenome maps with cell type resolution are required. Here, we present genomewide histone methylation maps for distinct neural cell populations in the developing mouse neocortex. Using different chromatin features, we identify potential novel regulators of cortical NPCs. Moreover, we identify extensive H3K27me3 changes between NPC subtypes coincidi...
Source: EMBO Journal - September 1, 2017 Category: Molecular Biology Authors: Albert, M., Kalebic, N., Florio, M., Lakshmanaperumal, N., Haffner, C., Brandl, H., Henry, I., Huttner, W. B. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Methods & Resources, Neuroscience Source Type: research

Selective termination of lncRNA transcription promotes heterochromatin silencing and cell differentiation
Long non-coding RNAs (lncRNAs) regulating gene expression at the chromatin level are widespread among eukaryotes. However, their functions and the mechanisms by which they act are not fully understood. Here, we identify new fission yeast regulatory lncRNAs that are targeted, at their site of transcription, by the YTH domain of the RNA-binding protein Mmi1 and degraded by the nuclear exosome. We uncover that one of them, nam1, regulates entry into sexual differentiation. Importantly, we demonstrate that Mmi1 binding to this lncRNA not only triggers its degradation but also mediates its transcription termination, thus preven...
Source: EMBO Journal - September 1, 2017 Category: Molecular Biology Authors: Touat-Todeschini, L., Shichino, Y., Dangin, M., Thierry-Mieg, N., Gilquin, B., Hiriart, E., Sachidanandam, R., Lambert, E., Brettschneider, J., Reuter, M., Kadlec, J., Pillai, R., Yamashita, A., Yamamoto, M., Verdel, A. Tags: Development & Differentiation, RNA Biology, Transcription Articles Source Type: research

Recombination at subtelomeres is regulated by physical distance, double-strand break resection and chromatin status
Homologous recombination (HR) is a conserved mechanism that repairs broken chromosomes via intact homologous sequences. How different genomic, chromatin and subnuclear contexts influence HR efficiency and outcome is poorly understood. We developed an assay to assess HR outcome by gene conversion (GC) and break-induced replication (BIR), and discovered that subtelomeric double-stranded breaks (DSBs) are preferentially repaired by BIR despite the presence of flanking homologous sequences. Overexpression of a silencing-deficient SIR3 mutant led to active grouping of telomeres and specifically increased the GC efficiency betwe...
Source: EMBO Journal - September 1, 2017 Category: Molecular Biology Authors: Batte, A., Brocas, C., Bordelet, H., Hocher, A., Ruault, M., Adjiri, A., Taddei, A., Dubrana, K. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination Articles Source Type: research

Chromatin stiffening underlies enhanced locus mobility after DNA damage in budding yeast
DNA double-strand breaks (DSBs) induce a cellular response that involves histone modifications and chromatin remodeling at the damaged site and increases chromosome dynamics both locally at the damaged site and globally in the nucleus. In parallel, it has become clear that the spatial organization and dynamics of chromosomes can be largely explained by the statistical properties of tethered, but randomly moving, polymer chains, characterized mainly by their rigidity and compaction. How these properties of chromatin are affected during DNA damage remains, however, unclear. Here, we use live cell microscopy to track chromati...
Source: EMBO Journal - September 1, 2017 Category: Molecular Biology Authors: Herbert, S., Brion, A., Arbona, J.-M., Lelek, M., Veillet, A., Lelandais, B., Parmar, J., Fernandez, F. G., Almayrac, E., Khalil, Y., Birgy, E., Fabre, E., Zimmer, C. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination, Systems & Computational Biology Articles Source Type: research

GT-rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes
Genome-wide transcription studies are revealing an increasing number of "dispersed promoters" that, unlike "focused promoters", lack well-conserved sequence motifs and tight regulation. Dispersed promoters are nevertheless marked by well-defined chromatin structures, suggesting that specific sequence elements must exist in these unregulated promoters. Here, we have analyzed regions of transcription initiation in the eukaryotic parasite Trypanosoma brucei, in which RNA polymerase II transcription initiation occurs over broad regions without distinct promoter motifs and lacks regulation. Using a combinati...
Source: EMBO Journal - September 1, 2017 Category: Molecular Biology Authors: Wedel, C., Förstner, K. U., Derr, R., Siegel, T. N. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Microbiology, Virology & Host Pathogen Interaction, Transcription Articles Source Type: research

The Shigella type III effector IpgD recodes Ca2+ signals during invasion of epithelial cells
The role of second messengers in the diversion of cellular processes by pathogens remains poorly studied despite their importance. Among these, Ca2+ virtually regulates all known cell processes, including cytoskeletal reorganization, inflammation, or cell death pathways. Under physiological conditions, cytosolic Ca2+ increases are transient and oscillatory, defining the so-called Ca2+ code that links cell responses to specific Ca2+ oscillatory patterns. During cell invasion, Shigella induces atypical local and global Ca2+ signals. Here, we show that by hydrolyzing phosphatidylinositol-(4,5)bisphosphate, the Shigella type I...
Source: EMBO Journal - September 1, 2017 Category: Molecular Biology Authors: Sun, C. H., Wacquier, B., Aguilar, D. I., Carayol, N., Denis, K., Boucherie, S., Valencia-Gallardo, C., Simsek, C., Erneux, C., Lehman, A., Enninga, J., Arbibe, L., Sansonetti, P., Dupont, G., Combettes, L., Tran Van Nhieu, G. Tags: Microbiology, Virology & Host Pathogen Interaction, Signal Transduction Articles Source Type: research

Centriole translocation and degeneration during ciliogenesis in Caenorhabditis elegans neurons
Neuronal cilia that are formed at the dendritic endings of sensory neurons are essential for sensory perception. However, it remains unclear how the centriole-derived basal body is positioned to form a template for cilium formation. Using fluorescence time-lapse microscopy, we show that the centriole translocates from the cell body to the dendrite tip in the Caenorhabditis elegans sensory neurons. The centriolar protein SAS-5 interacts with the dynein light-chain LC8 and conditional mutations of cytoplasmic dynein-1 block centriole translocation and ciliogenesis. The components of the central tube are essential for the bio...
Source: EMBO Journal - September 1, 2017 Category: Molecular Biology Authors: Li, W., Yi, P., Zhu, Z., Zhang, X., Li, W., Ou, G. Tags: Cell Adhesion, Polarity & Cytoskeleton, Membrane & Intracellular Transport Articles Source Type: research

STUB1 regulates TFEB-induced autophagy-lysosome pathway
TFEB is a master regulator for transcription of genes involved in autophagy and lysosome biogenesis. Activity of TFEB is inhibited upon its serine phosphorylation by mTOR. The overall mechanisms by which TFEB activity in the cell is regulated are not well elucidated. Specifically, the mechanisms of TFEB turnover and how they might influence its activity remain unknown. Here, we show that STUB1, a chaperone-dependent E3 ubiquitin ligase, modulates TFEB activity by preferentially targeting inactive phosphorylated TFEB for degradation by the ubiquitin–proteasome pathway. Phosphorylated TFEB accumulated in STUB1-deficien...
Source: EMBO Journal - September 1, 2017 Category: Molecular Biology Authors: Sha, Y., Rao, L., Settembre, C., Ballabio, A., Eissa, N. T. Tags: Autophagy & Cell Death, Metabolism, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research