Generating human intestinal tissues from pluripotent stem cells to study development and disease
As one of the largest and most functionally complex organs of the human body, the intestines are primarily responsible for the breakdown and uptake of macromolecules from the lumen and the subsequent excretion of waste from the body. However, the intestine is also an endocrine organ, regulating digestion, metabolism, and feeding behavior. Intricate neuronal, lymphatic, immune, and vascular systems are integrated into the intestine and are required for its digestive and endocrine functions. In addition, the gut houses an extensive population of microbes that play roles in digestion, global metabolism, barrier function, and ...
Source: EMBO Journal - May 5, 2015 Category: Molecular Biology Authors: Sinagoga, K. L., Wells, J. M. Tags: Development & Differentiation, Methods & Resources, Stem Cells Reviews Source Type: research

Plasmolipin--a new player in endocytosis and epithelial development
Polarized vesicle sorting is essential not only for epithelial cell function but also for cell polarization and tissue morphogenesis. Endocytosis is a key determinant of the surface abundance of plasma membrane proteins and is highly regulated. In an important recent paper, Rodríguez-Fraticelli et al (2015) identify a new player in apical endocytosis—a previously uncharacterized protein called Plasmolipin. They report not only its mechanism of action through binding to an epsin, but also highlight an essential role in regulating Notch signaling, which controls epithelial differentiation. (Source: EMBO Journal)
Source: EMBO Journal - May 5, 2015 Category: Molecular Biology Authors: Le Guelte, A., Macara, I. G. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation, Membrane & Intracellular Transport Have you seen? Source Type: research

Regulatory T cell differentiation: cooperation saves the day
MicroRNA are important regulators of CD4 T cell differentiation, altering the balance between the immunogenic and tolerogenic pathways. Studies in mice with microRNA-deficient T cells have revealed defects in differentiation into the regulatory T cell lineage; however, the individual microRNA responsible have remained elusive. A recent paper in The EMBO Journal uses a systematic screen to find a novel cooperative action between an inducible and a constitutive microRNA in aiding regulatory T cell induction. (Source: EMBO Journal)
Source: EMBO Journal - May 5, 2015 Category: Molecular Biology Authors: Liston, A., Schlenner, S. M. Tags: Immunology Have you seen? Source Type: research

Astro-logics with microRNAs
Astrocytes are a subtype of glial cells in the central nervous system that are critical for normal brain activity. In this issue of The EMBO Journal, Shenoy et al provide evidence for the involvement of miRNAs in the molecular mechanism underlying the in vitro differentiation of astrocytes from glial progenitor cells. Let-7 and miR-125 jointly silence multiple mRNA targets that would have potentially disrupted differentiation if expressed, and function in concert with JAK-STAT signaling to promote astrocyte differentiation. (Source: EMBO Journal)
Source: EMBO Journal - May 5, 2015 Category: Molecular Biology Authors: Eitan, C., Hornstein, E. Tags: Neuroscience, RNA Biology Have you seen? Source Type: research

Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair
Eukaryotic DNA polymerase mu of the PolX family can promote the association of the two 3'-protruding ends of a DNA double-strand break (DSB) being repaired (DNA synapsis) even in the absence of the core non-homologous end-joining (NHEJ) machinery. Here, we show that terminal deoxynucleotidyltransferase (TdT), a closely related PolX involved in V(D)J recombination, has the same property. We solved its crystal structure with an annealed DNA synapsis containing one micro-homology (MH) base pair and one nascent base pair. This structure reveals how the N-terminal domain and Loop 1 of Tdt cooperate for bridging the two DNA ends...
Source: EMBO Journal - April 15, 2015 Category: Molecular Biology Authors: Gouge, J., Rosario, S., Romain, F., Poitevin, F., Beguin, P., Delarue, M. Tags: DNA Replication, Repair & Recombination, Structural Biology Articles Source Type: research

SIRT3-dependent GOT2 acetylation status affects the malate-aspartate NADH shuttle activity and pancreatic tumor growth
The malate–aspartate shuttle is indispensable for the net transfer of cytosolic NADH into mitochondria to maintain a high rate of glycolysis and to support rapid tumor cell growth. The malate–aspartate shuttle is operated by two pairs of enzymes that localize to the mitochondria and cytoplasm, glutamate oxaloacetate transaminases (GOT), and malate dehydrogenases (MDH). Here, we show that mitochondrial GOT2 is acetylated and that deacetylation depends on mitochondrial SIRT3. We have identified that acetylation occurs at three lysine residues, K159, K185, and K404 (3K), and enhances the association between GOT2 a...
Source: EMBO Journal - April 15, 2015 Category: Molecular Biology Authors: Yang, H., Zhou, L., Shi, Q., Zhao, Y., Lin, H., Zhang, M., Zhao, S., Yang, Y., Ling, Z.-Q., Guan, K.-L., Xiong, Y., Ye, D. Tags: Cancer, Metabolism, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Lysyl oxidase-like 2 represses Notch1 expression in the skin to promote squamous cell carcinoma progression
Lysyl oxidase-like 2 (LOXL2) is involved in a wide range of physiological and pathological processes, including fibrosis and tumor progression, implicating intracellular and extracellular functions. To explore the specific in vivo role of LOXL2 in physiological and tumor contexts, we generated conditional gain- and loss-of-function mouse models. Germ-line deletion of Loxl2 promotes lethality in half of newborn mice mainly associated to congenital heart defects, while Loxl2 overexpression triggers male sterility due to epididymal dysfunction caused by epithelial disorganization, fibrosis and acute inflammation. Remarka...
Source: EMBO Journal - April 15, 2015 Category: Molecular Biology Authors: Martin, A., Salvador, F., Moreno-Bueno, G., Floristan, A., Ruiz-Herguido, C., Cuevas, E. P., Morales, S., Santos, V., Csiszar, K., Dubus, P., Haigh, J. J., Bigas, A., Portillo, F., Cano, A. Tags: Cancer, Development & Differentiation Articles Source Type: research

Cyclin O (Ccno) functions during deuterosome-mediated centriole amplification of multiciliated cells
Mucociliary clearance and fluid transport along epithelial surfaces are carried out by multiciliated cells (MCCs). Recently, human mutations in Cyclin O (CCNO) were linked to severe airway disease. Here, we show that Ccno expression is restricted to MCCs and the genetic deletion of Ccno in mouse leads to reduced numbers of multiple motile cilia and characteristic phenotypes of MCC dysfunction including severe hydrocephalus and mucociliary clearance deficits. Reduced cilia numbers are caused by compromised generation of centrioles at deuterosomes, which serve as major amplification platform for centrioles in MCCs. Ccno-defi...
Source: EMBO Journal - April 15, 2015 Category: Molecular Biology Authors: Funk, M. C., Bera, A. N., Menchen, T., Kuales, G., Thriene, K., Lienkamp, S. S., Dengjel, J., Omran, H., Frank, M., Arnold, S. J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation, Molecular Biology of Disease Articles Source Type: research

Synaptic activity controls localization and function of CtBP1 via binding to Bassoon and Piccolo
Persistent experience-driven adaptation of brain function is associated with alterations in gene expression patterns, resulting in structural and functional neuronal remodeling. How synaptic activity—in particular presynaptic performance—is coupled to gene expression in nucleus remains incompletely understood. Here, we report on a role of CtBP1, a transcriptional co-repressor enriched in presynapses and nuclei, in the activity-driven reconfiguration of gene expression in neurons. We demonstrate that presynaptic and nuclear pools of CtBP1 are interconnected and that both synaptic retention and shuttling of CtBP1...
Source: EMBO Journal - April 15, 2015 Category: Molecular Biology Authors: Ivanova, D., Dirks, A., Montenegro-Venegas, C., Schone, C., Altrock, W. D., Marini, C., Frischknecht, R., Schanze, D., Zenker, M., Gundelfinger, E. D., Fejtova, A. Tags: Neuroscience Articles Source Type: research

The E3 ligase synoviolin controls body weight and mitochondrial biogenesis through negative regulation of PGC-1{beta}
In this study, a gene knockout strategy was used in post-neonatal mice to delete synoviolin (Syvn)1/Hrd1/Der3, an ER-resident E3 ubiquitin ligase with known roles in homeostasis maintenance. Syvn1 deficiency resulted in weight loss and lower accumulation of white adipose tissue in otherwise wild-type animals as well as in genetically obese (ob/ob and db/db) and adipose tissue-specific knockout mice as compared to control animals. SYVN1 interacted with and ubiquitinated the thermogenic coactivator peroxisome proliferator-activated receptor coactivator (PGC)-1β, and Syvn1 mutants showed upregulation of PGC-1β targe...
Source: EMBO Journal - April 15, 2015 Category: Molecular Biology Authors: Fujita, H., Yagishita, N., Aratani, S., Saito-Fujita, T., Morota, S., Yamano, Y., Hansson, M. J., Inazu, M., Kokuba, H., Sudo, K., Sato, E., Kawahara, K.-i., Nakajima, F., Hasegawa, D., Higuchi, I., Sato, T., Araya, N., Usui, C., Nishioka, K., Nakatani, Y Tags: Metabolism, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Unsaturated fatty acids induce non-canonical autophagy
To obtain mechanistic insights into the cross talk between lipolysis and autophagy, two key metabolic responses to starvation, we screened the autophagy-inducing potential of a panel of fatty acids in human cancer cells. Both saturated and unsaturated fatty acids such as palmitate and oleate, respectively, triggered autophagy, but the underlying molecular mechanisms differed. Oleate, but not palmitate, stimulated an autophagic response that required an intact Golgi apparatus. Conversely, autophagy triggered by palmitate, but not oleate, required AMPK, PKR and JNK1 and involved the activation of the BECN1/PIK3C3 lipid kinas...
Source: EMBO Journal - April 15, 2015 Category: Molecular Biology Authors: Niso-Santano, M., Malik, S. A., Pietrocola, F., Bravo-San Pedro, J. M., Marino, G., Cianfanelli, V., Ben-Younes, A., Troncoso, R., Markaki, M., Sica, V., Izzo, V., Chaba, K., Bauvy, C., Dupont, N., Kepp, O., Rockenfeller, P., Wolinski, H., Madeo, F., Lava Tags: Autophagy & Cell Death Articles Source Type: research

Human primordial germ cell commitment in vitro associates with a unique PRDM14 expression profile
This study demonstrates that PGC commitment in humans shares key features with that of the mouse, but also highlights key differences, including transcriptional regulation during the early stage of human PGC development (3–6 weeks). A more comprehensive understanding of human germ cell development may lead to methodology for successfully generating PSC-derived gametes for reproductive medicine. (Source: EMBO Journal)
Source: EMBO Journal - April 15, 2015 Category: Molecular Biology Authors: Sugawa, F., Arauzo-Bravo, M. J., Yoon, J., Kim, K.-P., Aramaki, S., Wu, G., Stehling, M., Psathaki, O. E., Hubner, K., Scholer, H. R. Tags: Development & Differentiation, Methods & Resources, Stem Cells Articles Source Type: research

Application of biomaterials to advance induced pluripotent stem cell research and therapy
Derived from any somatic cell type and possessing unlimited self-renewal and differentiation potential, induced pluripotent stem cells (iPSCs) are poised to revolutionize stem cell biology and regenerative medicine research, bringing unprecedented opportunities for treating debilitating human diseases. To overcome the limitations associated with safety, efficiency, and scalability of traditional iPSC derivation, expansion, and differentiation protocols, biomaterials have recently been considered. Beyond addressing these limitations, the integration of biomaterials with existing iPSC culture platforms could offer additional...
Source: EMBO Journal - April 15, 2015 Category: Molecular Biology Authors: Tong, Z., Solanki, A., Hamilos, A., Levy, O., Wen, K., Yin, X., Karp, J. M. Tags: Methods & Resources, Molecular Biology of Disease, Stem Cells Review Source Type: research

Presynapses go nuclear!
Decades of research has shown that long-term changes in synaptic function ultimately require changes in gene expression. Recent work has focused on nuclear signaling by calcium and protein messengers initiated at postsynaptic sites. In this issue of The EMBO Journal, Ivanova and colleagues show that shuttling of CtBP-1 between presynaptic areas and nuclei regulates gene expression, which reminds us that presynaptic zones should not be ignored when considering synapse-to-nucleus signaling. (Source: EMBO Journal)
Source: EMBO Journal - April 15, 2015 Category: Molecular Biology Authors: Kravchick, D. O., Jordan, B. A. Tags: Neuroscience Have you seen? Source Type: research

Interrupting synoviolin play at the ER: a plausible action to elevate mitochondrial energetics and silence obesity
Obesity is a global concern, which has been linked to increased risk for cardiovascular disease, type 2 diabetes, atherosclerosis, non-alcoholic fatty liver, and cancer. In this issue of The EMBO Journal, Fujita et al (2015) describe the role of an endoplasmic reticulum (ER)-resident E3 ubiquitin ligase, synoviolin, and its ability to control body weight and energy expenditure by targeting PGC-1β, a transcriptional modulator of mitochondrial oxidative metabolism. (Source: EMBO Journal)
Source: EMBO Journal - April 15, 2015 Category: Molecular Biology Authors: Soustek, M. S., Puigserver, P. Tags: Metabolism, Post-translational Modifications, Proteolysis & Proteomics Have you seen? Source Type: research

Unsaturated fatty acid-induced non-canonical autophagy: unusual? or unappreciated?
The breakdown of cellular components via autophagy is crucial for cellular homeostasis. In this issue of The EMBO Journal, Niso-Santano et al (2015) report the important observation that feeding cells with saturated or unsaturated fatty acids triggers mechanistically distinct autophagic responses. Feeding cells saturated fatty acid induced the canonical, BECN1/PI3K-dependent autophagy pathway. Conversely, the unsaturated fatty acid oleate triggered autophagic responses that were independent of the BECN1/PI3K complex, but that required a functional Golgi system. (Source: EMBO Journal)
Source: EMBO Journal - April 15, 2015 Category: Molecular Biology Authors: Bankaitis, V. A. Tags: Autophagy & Cell Death Have you seen? Source Type: research

Human germline differentiation charts a new course
Understanding the molecular events of reproduction requires a system to differentiate human pluripotent stem cells to germline cells (gametes) in vitro. Such a system is not only critical to unlock the secrets of germline development; it may also allow screening for environmental agents that affect gametogenesis. Two recent papers, one in this issue of The EMBO Journal, have developed complementary approaches for generating human germline cells with unprecedented efficiency from pluripotent stem cells (Sugawa et al, 2015; Irie et al, 2015). This work illustrates the power and limitations of extrapolating mol...
Source: EMBO Journal - April 15, 2015 Category: Molecular Biology Authors: Chen, D., Clark, A. T. Tags: Development & Differentiation, Methods & Resources, Stem Cells Have you seen? Source Type: research

PI3P binding by Atg21 organises Atg8 lipidation
Autophagosome biogenesis requires two ubiquitin-like conjugation systems. One couples ubiquitin-like Atg8 to phosphatidylethanolamine, and the other couples ubiquitin-like Atg12 to Atg5. Atg12~Atg5 then forms a heterodimer with Atg16. Membrane recruitment of the Atg12~Atg5/Atg16 complex defines the Atg8 lipidation site. Lipidation requires a PI3P-containing precursor. How PI3P is sensed and used to coordinate the conjugation systems remained unclear. Here, we show that Atg21, a WD40 β-propeller, binds via PI3P to the preautophagosomal structure (PAS). Atg21 directly interacts with the coiled-coil domain of Atg16 and w...
Source: EMBO Journal - March 31, 2015 Category: Molecular Biology Authors: Juris, L., Montino, M., Rube, P., Schlotterhose, P., Thumm, M., Krick, R. Tags: Autophagy & Cell Death Articles Source Type: research

The Spectrin cytoskeleton regulates the Hippo signalling pathway
The Spectrin cytoskeleton is known to be polarised in epithelial cells, yet its role remains poorly understood. Here, we show that the Spectrin cytoskeleton controls Hippo signalling. In the developing Drosophila wing and eye, loss of apical Spectrins (alpha/beta-heavy dimers) produces tissue overgrowth and mis-regulation of Hippo target genes, similar to loss of Crumbs (Crb) or the FERM-domain protein Expanded (Ex). Apical beta-heavy Spectrin binds to Ex and co-localises with it at the apical membrane to antagonise Yki activity. Interestingly, in both the ovarian follicular epithelium and intestinal epithelium of Drosophi...
Source: EMBO Journal - March 31, 2015 Category: Molecular Biology Authors: Fletcher, G. C., Elbediwy, A., Khanal, I., Ribeiro, P. S., Tapon, N., Thompson, B. J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation Articles Source Type: research

CD19 and BAFF-R can signal to promote B-cell survival in the absence of Syk
The development and function of B lymphocytes is regulated by numerous signaling pathways, some emanating from the B-cell antigen receptor (BCR). The spleen tyrosine kinase (Syk) plays a central role in the activation of the BCR, but less is known about its contribution to the survival and maintenance of mature B cells. We generated mice with an inducible and B-cell-specific deletion of the Syk gene and found that a considerable fraction of mature Syk-negative B cells can survive in the periphery for an extended time. Syk-negative B cells are defective in BCR, RP105 and CD38 signaling but still respond to an IL-4, anti-CD4...
Source: EMBO Journal - March 31, 2015 Category: Molecular Biology Authors: Hobeika, E., Levit-Zerdoun, E., Anastasopoulou, V., Pohlmeyer, R., Altmeier, S., Alsadeq, A., Dobenecker, M.-W., Pelanda, R., Reth, M. Tags: Immunology, Signal Transduction Articles Source Type: research

Regulation of mitochondrial pyruvate uptake by alternative pyruvate carrier complexes
At the pyruvate branch point, the fermentative and oxidative metabolic routes diverge. Pyruvate can be transformed either into lactate in mammalian cells or into ethanol in yeast, or transported into mitochondria to fuel ATP production by oxidative phosphorylation. The recently discovered mitochondrial pyruvate carrier (MPC), encoded by MPC1, MPC2, and MPC3 in yeast, is required for uptake of pyruvate into the organelle. Here, we show that while expression of Mpc1 is not dependent on the carbon source, expression of Mpc2 and Mpc3 is specific to fermentative or respiratory conditions, respectively. This gives rise to two al...
Source: EMBO Journal - March 31, 2015 Category: Molecular Biology Authors: Bender, T., Pena, G., Martinou, J.-C. Tags: Membrane & Intracellular Transport, Metabolism Articles Source Type: research

Tox: a multifunctional transcription factor and novel regulator of mammalian corticogenesis
Major efforts are invested to characterize the factors controlling the proliferation of neural stem cells. During mammalian corticogenesis, our group has identified a small pool of genes that are transiently downregulated in the switch of neural stem cells to neurogenic division and reinduced in newborn neurons. Among these switch genes, we found Tox, a transcription factor with hitherto uncharacterized roles in the nervous system. Here, we investigated the role of Tox in corticogenesis by characterizing its expression at the tissue, cellular and temporal level. We found that Tox is regulated by calcineurin/Nfat signalling...
Source: EMBO Journal - March 31, 2015 Category: Molecular Biology Authors: Artegiani, B., de Jesus Domingues, A. M., Bragado Alonso, S., Brandl, E., Massalini, S., Dahl, A., Calegari, F. Tags: Neuroscience Articles Source Type: research

SIGNR3-dependent immune regulation by Lactobacillus acidophilus surface layer protein A in colitis
Intestinal immune regulatory signals govern gut homeostasis. Breakdown of such regulatory mechanisms may result in inflammatory bowel disease (IBD). Lactobacillus acidophilus contains unique surface layer proteins (Slps), including SlpA, SlpB, SlpX, and lipoteichoic acid (LTA), which interact with pattern recognition receptors to mobilize immune responses. Here, to elucidate the role of SlpA in protective immune regulation, the NCK2187 strain, which solely expresses SlpA, was generated. NCK2187 and its purified SlpA bind to the C-type lectin SIGNR3 to exert regulatory signals that result in mitigation of colitis, maintenan...
Source: EMBO Journal - March 31, 2015 Category: Molecular Biology Authors: Lightfoot, Y. L., Selle, K., Yang, T., Goh, Y. J., Sahay, B., Zadeh, M., Owen, J. L., Colliou, N., Li, E., Johannssen, T., Lepenies, B., Klaenhammer, T. R., Mohamadzadeh, M. Tags: Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Autophagy in malignant transformation and cancer progression
Autophagy plays a key role in the maintenance of cellular homeostasis. In healthy cells, such a homeostatic activity constitutes a robust barrier against malignant transformation. Accordingly, many oncoproteins inhibit, and several oncosuppressor proteins promote, autophagy. Moreover, autophagy is required for optimal anticancer immunosurveillance. In neoplastic cells, however, autophagic responses constitute a means to cope with intracellular and environmental stress, thus favoring tumor progression. This implies that at least in some cases, oncogenesis proceeds along with a temporary inhibition of autophagy or a gain of ...
Source: EMBO Journal - March 31, 2015 Category: Molecular Biology Authors: Galluzzi, L., Pietrocola, F., Bravo-San Pedro, J. M., Amaravadi, R. K., Baehrecke, E. H., Cecconi, F., Codogno, P., Debnath, J., Gewirtz, D. A., Karantza, V., Kimmelman, A., Kumar, S., Levine, B., Maiuri, M. C., Martin, S. J., Penninger, J., Piacentini, M Tags: Cancer, Autophagy & Cell Death Reviews Source Type: research

Toward beta cell replacement for diabetes
The discovery of insulin more than 90 years ago introduced a life-saving treatment for patients with type 1 diabetes, and since then, significant progress has been made in clinical care for all forms of diabetes. However, no method of insulin delivery matches the ability of the human pancreas to reliably and automatically maintain glucose levels within a tight range. Transplantation of human islets or of an intact pancreas can in principle cure diabetes, but this approach is generally reserved for cases with simultaneous transplantation of a kidney, where immunosuppression is already a requirement. Recent advances in ...
Source: EMBO Journal - March 31, 2015 Category: Molecular Biology Authors: Johannesson, B., Sui, L., Freytes, D. O., Creusot, R. J., Egli, D. Tags: Metabolism, Molecular Biology of Disease, Stem Cells Reviews Source Type: research

The BAFFling function of Syk in B-cell homeostasis
The TNF receptor family member BAFFR is essential for providing mature B cells with pro-survival signals and has recently been claimed to transduce these, though not exclusively, via a Syk-dependent signaling hub that feeds into ERK/AKT activation. In this issue of The EMBO Journal, Hobeika et al (2015) describe a synergistic pro-survival scenario involving BAFFR and CD19, which remains functional under Syk null conditions and is able to maintain mature B-cell survival. The authors hence propose a BAFFR-/CD19-driven mechanism to act in parallel with homeostatic NF-B/AKT activation in non-stimulated B cells. (Source: EMBO Journal)
Source: EMBO Journal - March 31, 2015 Category: Molecular Biology Authors: Konigsberger, S., Kiefer, F. Tags: Immunology, Signal Transduction Have you seen? Source Type: research

Metabolic remodeling: a pyruvate transport affair
Metabolic remodeling is a major determinant for many cell fate decisions, and a switch from respiration to aerobic glycolysis is generally considered as a hallmark of cancer cell transformation. Pyruvate is a key metabolite at the major junction of carbohydrate metabolism between cytosolic glycolysis and the mitochondrial Krebs cycle. In this issue of The EMBO Journal, Bender et al show that yeast cells regulate pyruvate uptake into mitochondria, and thus its metabolic fate, by expressing alternative pyruvate carrier complexes with different activities. (Source: EMBO Journal)
Source: EMBO Journal - March 31, 2015 Category: Molecular Biology Authors: Rampelt, H., van der Laan, M. Tags: Membrane & Intracellular Transport, Metabolism Have you seen? Source Type: research

In-TOX-icating neurogenesis
Early development of the mammalian cerebral cortex proceeds via a sequence of proliferative and differentiative steps from neural stem cells toward neurons and glia. However, how these steps are molecularly orchestrated is still only partially understood. In this issue of The EMBO Journal, Artegiani and colleagues implicate Tox, a HMG-box transcription factor previously known only for its role in lymphocyte development, in early cortical development. (Source: EMBO Journal)
Source: EMBO Journal - March 31, 2015 Category: Molecular Biology Authors: Karow, M., Berninger, B. Tags: Immunology, Signal Transduction Have you seen? Source Type: research

SIGNing a symbiotic treaty with gut microbiota
Beneficial microbes hold great promise for the treatment of a wide range of immune and inflammatory disorders. In this issue of The EMBO Journal, Lightfoot and colleagues report how the food-grade bacterium Lactobacillus acidophilus helps the immune system to limit experimental colitis in mice through interaction between SIGNR3 and surface layer protein A (SlpA) in L. acidophilus. These results pave the way for future development of novel therapies for inflammatory diseases, including inflammatory bowel disease. (Source: EMBO Journal)
Source: EMBO Journal - March 31, 2015 Category: Molecular Biology Authors: Lugo-Villarino, G., Neyrolles, O. Tags: Microbiology, Virology & Host Pathogen Interaction Have you seen? Source Type: research

BRCA1 and CtIP promote alternative non-homologous end-joining at uncapped telomeres
(Source: EMBO Journal)
Source: EMBO Journal - March 11, 2015 Category: Molecular Biology Authors: Badie, S., Carlos, A. R., Folio, C., Okamoto, K., Bouwman, P., Jonkers, J., Tarsounas, M. Tags: Erratum Source Type: research

TFG clusters COPII-coated transport carriers and promotes early secretory pathway organization
We report here that COPII-coated transport carriers traverse a submicron, TFG (Trk-fused gene)-enriched zone at the ER/ERGIC interface. The architecture of TFG complexes as determined by three-dimensional electron microscopy reveals the formation of flexible, octameric cup-like structures, which are able to self-associate to generate larger polymers in vitro. In cells, loss of TFG function dramatically slows protein export from the ER and results in the accumulation of COPII-coated carriers throughout the cytoplasm. Additionally, the tight association between ER and ERGIC membranes is lost in the absence of TFG. We propose...
Source: EMBO Journal - March 11, 2015 Category: Molecular Biology Authors: Johnson, A., Bhattacharya, N., Hanna, M., Pennington, J. G., Schuh, A. L., Wang, L., Otegui, M. S., Stagg, S. M., Audhya, A. Tags: Membrane & Intracellular Transport Articles Source Type: research

Space exploration by dendritic cells requires maintenance of myosin II activity by IP3 receptor 1
Dendritic cells (DCs) patrol the interstitial space of peripheral tissues. The mechanisms that regulate their migration in such constrained environment remain unknown. We here investigated the role of calcium in immature DCs migrating in confinement. We found that they displayed calcium oscillations that were independent of extracellular calcium and more frequently observed in DCs undergoing strong speed fluctuations. In these cells, calcium spikes were associated with fast motility phases. IP3 receptors (IP3Rs) channels, which allow calcium release from the endoplasmic reticulum, were identified as required for immature D...
Source: EMBO Journal - March 11, 2015 Category: Molecular Biology Authors: Solanes, P., Heuze, M. L., Maurin, M., Bretou, M., Lautenschlaeger, F., Maiuri, P., Terriac, E., Thoulouze, M.-I., Launay, P., Piel, M., Vargas, P., Lennon-Dumenil, A.-M. Tags: Cell Adhesion, Polarity & Cytoskeleton, Immunology Articles Source Type: research

Compartment-specific aggregases direct distinct nuclear and cytoplasmic aggregate deposition
Disruption of the functional protein balance in living cells activates protective quality control systems to repair damaged proteins or sequester potentially cytotoxic misfolded proteins into aggregates. The established model based on Saccharomyces cerevisiae indicates that aggregating proteins in the cytosol of eukaryotic cells partition between cytosolic juxtanuclear (JUNQ) and peripheral deposits. Substrate ubiquitination acts as the sorting principle determining JUNQ deposition and subsequent degradation. Here, we show that JUNQ unexpectedly resides inside the nucleus, defining a new intranuclear quality control compar...
Source: EMBO Journal - March 11, 2015 Category: Molecular Biology Authors: Miller, S. B., Ho, C.-T., Winkler, J., Khokhrina, M., Neuner, A., Mohamed, M. Y., Guilbride, D. L., Richter, K., Lisby, M., Schiebel, E., Mogk, A., Bukau, B. Tags: Membrane & Intracellular Transport, Post-translational Modifications, Proteolysis & Proteomics, Protein Biosynthesis & Quality Control Articles Source Type: research

Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence
Scl/Tal1 confers hemogenic competence and prevents ectopic cardiomyogenesis in embryonic endothelium by unknown mechanisms. We discovered that Scl binds to hematopoietic and cardiac enhancers that become epigenetically primed in multipotent cardiovascular mesoderm, to regulate the divergence of hematopoietic and cardiac lineages. Scl does not act as a pioneer factor but rather exploits a pre-established epigenetic landscape. As the blood lineage emerges, Scl binding and active epigenetic modifications are sustained in hematopoietic enhancers, whereas cardiac enhancers are decommissioned by removal of active epigenetic...
Source: EMBO Journal - March 11, 2015 Category: Molecular Biology Authors: Org, T., Duan, D., Ferrari, R., Montel-Hagen, A., Van Handel, B., Kerenyi, M. A., Sasidharan, R., Rubbi, L., Fujiwara, Y., Pellegrini, M., Orkin, S. H., Kurdistani, S. K., Mikkola, H. K. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Development & Differentiation, Stem Cells Articles Source Type: research

The Sm protein methyltransferase PRMT5 is not required for primordial germ cell specification in mice
PRMT5 is a type II protein arginine methyltransferase with roles in stem cell biology, reprograming, cancer and neurogenesis. During embryogenesis in the mouse, it was hypothesized that PRMT5 functions with the master germline determinant BLIMP1 to promote primordial germ cell (PGC) specification. Using a Blimp1-Cre germline conditional knockout, we discovered that Prmt5 has no major role in murine germline specification, or the first global epigenetic reprograming event involving depletion of cytosine methylation from DNA and histone H3 lysine 9 dimethylation from chromatin. Instead, we discovered that PRMT5 functions at ...
Source: EMBO Journal - March 11, 2015 Category: Molecular Biology Authors: Li, Z., Yu, J., Hosohama, L., Nee, K., Gkountela, S., Chaudhari, S., Cass, A. A., Xiao, X., Clark, A. T. Tags: Cell Cycle, Development & Differentiation, Stem Cells Articles Source Type: research

Reprogramming of human cancer cells to pluripotency for models of cancer progression
The ability to study live cells as they progress through the stages of cancer provides the opportunity to discover dynamic networks underlying pathology, markers of early stages, and ways to assess therapeutics. Genetically engineered animal models of cancer, where it is possible to study the consequences of temporal-specific induction of oncogenes or deletion of tumor suppressors, have yielded major insights into cancer progression. Yet differences exist between animal and human cancers, such as in markers of progression and response to therapeutics. Thus, there is a need for human cell models of cancer progression. Most ...
Source: EMBO Journal - March 11, 2015 Category: Molecular Biology Authors: Kim, J., Zaret, K. S. Tags: Cancer, Chromatin, Epigenetics, Genomics & Functional Genomics, Stem Cells Reviews Source Type: research

Programming and reprogramming a human heart cell
The latest discoveries and advanced knowledge in the fields of stem cell biology and developmental cardiology hold great promise for cardiac regenerative medicine, enabling researchers to design novel therapeutic tools and approaches to regenerate cardiac muscle for diseased hearts. However, progress in this arena has been hampered by a lack of reproducible and convincing evidence, which at best has yielded modest outcomes and is still far from clinical practice. To address current controversies and move cardiac regenerative therapeutics forward, it is crucial to gain a deeper understanding of the key cellular and molecula...
Source: EMBO Journal - March 11, 2015 Category: Molecular Biology Authors: Sahara, M., Santoro, F., Chien, K. R. Tags: Development & Differentiation, Molecular Biology of Disease, Stem Cells Reviews Source Type: research

Transcription factor-mediated reprogramming toward hematopoietic stem cells
De novo generation of human hematopoietic stem cells (HSCs) from renewable cell types has been a long sought-after but elusive goal in regenerative medicine. Paralleling efforts to guide pluripotent stem cell differentiation by manipulating developmental cues, substantial progress has been made recently toward HSC generation via combinatorial transcription factor (TF)-mediated fate conversion, a paradigm established by Yamanaka's induction of pluripotency in somatic cells by mere four TFs. This review will integrate the recently reported strategies to directly convert a variety of starting cell types toward HSCs in the con...
Source: EMBO Journal - March 11, 2015 Category: Molecular Biology Authors: Ebina, W., Rossi, D. J. Tags: Development & Differentiation, Molecular Biology of Disease, Stem Cells Reviews Source Type: research

Creating cellular diversity through transcription factor competition
The development of blood cells has long served as a model system to study the generation of diverse mature cells from multipotent progenitors. The article by Org et al (2015) reveals how transcription factor competition on primed DNA templates may contribute to embryonic blood cell specification during the early stages of mesoderm development. The study not only provides new insights into the functionality of the key haematopoietic transcription factor Scl/Tal1, but also provides a potentially widely applicable framework for transcription factor-mediated cell fate specification. (Source: EMBO Journal)
Source: EMBO Journal - March 11, 2015 Category: Molecular Biology Authors: Gottgens, B. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Development & Differentiation, Stem Cells Have you seen? Source Type: research

Prmt5: a guardian of the germline protects future generations
Primordial germ cells (PGCs) are the embryonic precursors of the germ cell lineage that form sperm and egg cells. It is of great importance to preserve the germline from DNA damage and potentially from epimutations in order to ensure the survival of future generations. Recent research highlights the role of the protein arginine methyltransferase 5 (PRMT5) as an important player in DNA protection during germline development in the mouse (Kim et al, 2014 & Li et al, 2015). (Source: EMBO Journal)
Source: EMBO Journal - March 11, 2015 Category: Molecular Biology Authors: Berrens, R. V., Reik, W. Tags: Development & Differentiation, Stem Cells Have you seen? Source Type: research

Transport through recycling endosomes requires EHD1 recruitment by a phosphatidylserine translocase
P4-ATPases translocate aminophospholipids, such as phosphatidylserine (PS), to the cytosolic leaflet of membranes. PS is highly enriched in recycling endosomes (REs) and is essential for endosomal membrane traffic. Here, we show that PS flipping by an RE-localized P4-ATPase is required for the recruitment of the membrane fission protein EHD1. Depletion of ATP8A1 impaired the asymmetric transbilayer distribution of PS in REs, dissociated EHD1 from REs, and generated aberrant endosomal tubules that appear resistant to fission. EHD1 did not show membrane localization in cells defective in PS synthesis. ATP8A2, a tissue-specif...
Source: EMBO Journal - March 3, 2015 Category: Molecular Biology Authors: Lee, S., Uchida, Y., Wang, J., Matsudaira, T., Nakagawa, T., Kishimoto, T., Mukai, K., Inaba, T., Kobayashi, T., Molday, R. S., Taguchi, T., Arai, H. Tags: Membrane & Intracellular Transport, Neuroscience Articles Source Type: research

Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB
Matrin3 is an RNA- and DNA-binding nuclear matrix protein found to be associated with neural and muscular degenerative diseases. A number of possible functions of Matrin3 have been suggested, but no widespread role in RNA metabolism has yet been clearly demonstrated. We identified Matrin3 by its interaction with the second RRM domain of the splicing regulator PTB. Using a combination of RNAi knockdown, transcriptome profiling and iCLIP, we find that Matrin3 is a regulator of hundreds of alternative splicing events, principally acting as a splicing repressor with only a small proportion of targeted events being co-regulated...
Source: EMBO Journal - March 3, 2015 Category: Molecular Biology Authors: Coelho, M. B., Attig, J., Bellora, N., Konig, J., Hallegger, M., Kayikci, M., Eyras, E., Ule, J., Smith, C. W. Tags: RNA Biology Articles Source Type: research

Progesterone and Wnt4 control mammary stem cells via myoepithelial crosstalk
Ovarian hormones increase breast cancer risk by poorly understood mechanisms. We assess the role of progesterone on global stem cell function by serially transplanting mouse mammary epithelia. Progesterone receptor (PR) deletion severely reduces the regeneration capacity of the mammary epithelium. The PR target, receptor activator of Nf-B ligand (RANKL), is not required for this function, and the deletion of Wnt4 reduces the mammary regeneration capacity even more than PR ablation. A fluorescent reporter reveals so far undetected perinatal Wnt4 expression that is independent of hormone signaling. Pubertal and adult Wnt4 ex...
Source: EMBO Journal - March 3, 2015 Category: Molecular Biology Authors: Rajaram, R. D., Buric, D., Caikovski, M., Ayyanan, A., Rougemont, J., Shan, J., Vainio, S. J., Yalcin-Ozuysal, O., Brisken, C. Tags: Development & Differentiation, Signal Transduction, Stem Cells Articles Source Type: research

Wnt activity and basal niche position sensitize intestinal stem and progenitor cells to DNA damage
Aging and carcinogenesis coincide with the accumulation of DNA damage and mutations in stem and progenitor cells. Molecular mechanisms that influence responses of stem and progenitor cells to DNA damage remain to be delineated. Here, we show that niche positioning and Wnt signaling activity modulate the sensitivity of intestinal stem and progenitor cells (ISPCs) to DNA damage. ISPCs at the crypt bottom with high Wnt/β-catenin activity are more sensitive to DNA damage compared to ISPCs in position 4 with low Wnt activity. These differences are not induced by differences in cell cycle activity but relate to DNA damage-d...
Source: EMBO Journal - March 3, 2015 Category: Molecular Biology Authors: Tao, S., Tang, D., Morita, Y., Sperka, T., Omrani, O., Lechel, A., Sakk, V., Kraus, J., Kestler, H. A., Kuhl, M., Rudolph, K. L. Tags: Development & Differentiation, Signal Transduction, Stem Cells Articles Source Type: research

miR-290/371-Mbd2-Myc circuit regulates glycolytic metabolism to promote pluripotency
Enhanced glycolysis is a main feature of pluripotent stem cells (PSCs) and is proposed to be important for the maintenance and induction of pluripotency. The molecular mechanism underlying enhanced glycolysis in PSCs is not clear. Using Dgcr8–/– mouse embryonic stem cells (ESCs) that lack mature miRNAs, we found that miR-290 cluster of miRNAs stimulates glycolysis by upregulating glycolytic enzymes Pkm2 and Ldha, which are also essential for the induction of pluripotency during reprogramming. Mechanistically, we identified Mbd2, a reader for methylated CpGs, as the target of miR-290 cluster that represses glyco...
Source: EMBO Journal - March 3, 2015 Category: Molecular Biology Authors: Cao, Y., Guo, W.-T., Tian, S., He, X., Wang, X.-W., Liu, X., Gu, K.-L., Ma, X., Huang, D., Hu, L., Cai, Y., Zhang, H., Wang, Y., Gao, P. Tags: Metabolism, RNA Biology, Stem Cells Articles Source Type: research

The mRNA decay factor PAT1 functions in a pathway including MAP kinase 4 and immune receptor SUMM2
We report here that MPK4 is found in complexes in vivo with PAT1, a component of the mRNA decapping machinery. PAT1 is also phosphorylated by MPK4 and, upon flagellin PAMP treatment, PAT1 accumulates and localizes to cytoplasmic processing (P) bodies which are sites for mRNA decay. Pat1 mutants exhibit dwarfism and de-repressed immunity dependent on the immune receptor SUMM2. Since mRNA decapping is a critical step in mRNA turnover, linking MPK4 to mRNA decay via PAT1 provides another mechanism by which MPK4 may rapidly instigate immune responses. (Source: EMBO Journal)
Source: EMBO Journal - March 3, 2015 Category: Molecular Biology Authors: Roux, M. E., Rasmussen, M. W., Palma, K., Lolle, S., Regue, A. M., Bethke, G., Glazebrook, J., Zhang, W., Sieburth, L., Larsen, M. R., Mundy, J., Petersen, M. Tags: Microbiology, Virology & Host Pathogen Interaction, Plant Biology, RNA Biology Articles Source Type: research

Specific but interdependent functions for Arabidopsis AGO4 and AGO6 in RNA-directed DNA methylation
In this report, our comprehensive, genomewide analyses of AGO4- and AGO6-dependent DNA methylation revealed that redundancy is unexpectedly negligible in the genetic interactions between AGO4 and AGO6. Immunofluorescence revealed that AGO4 and AGO6 differ in their subnuclear co-localization with RNA polymerases required for RdDM. Pol II and AGO6 are absent from perinucleolar foci, where Pol V and AGO4 are co-localized. In the nucleoplasm, AGO4 displays a strong co-localization with Pol II, whereas AGO6 co-localizes with Pol V. These patterns suggest that RdDM is mediated by distinct, spatially regulated combinations o...
Source: EMBO Journal - March 3, 2015 Category: Molecular Biology Authors: Duan, C.-G., Zhang, H., Tang, K., Zhu, X., Qian, W., Hou, Y.-J., Wang, B., Lang, Z., Zhao, Y., Wang, X., Wang, P., Zhou, J., Liang, G., Liu, N., Wang, C., Zhu, J.-K. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Plant Biology, RNA Biology Articles Source Type: research

Argonautes team up to silence transposable elements in Arabidopsis
The de novo silencing of transposable elements in plants and animals is mediated in part by RNA-directed chromatin modification. In flowering plants, AGO4 has been seen as the key argonaute protein in the RNA-directed DNA methylation pathway that links the plant-specific RNA polymerase V with the de novo DNA methyltransferase DRM2 (Zhong et al, 2014). Two recent papers in The EMBO Journal strongly implicate a role for the AGO6 protein in the process of de novo silencing. (Source: EMBO Journal)
Source: EMBO Journal - March 3, 2015 Category: Molecular Biology Authors: Underwood, C. J., Martienssen, R. A. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Plant Biology, RNA Biology Have you seen? Source Type: research

A Tetrahymena Hsp90 co-chaperone promotes siRNA loading by ATP-dependent and ATP-independent mechanisms
The loading of small interfering RNAs (siRNAs) and microRNAs into Argonaute proteins is enhanced by Hsp90 and ATP in diverse eukaryotes. However, whether this loading also occurs independently of Hsp90 and ATP remains unclear. We show that the Tetrahymena Hsp90 co-chaperone Coi12p promotes siRNA loading into the Argonaute protein Twi1p in both ATP-dependent and ATP-independent manners in vitro. The ATP-dependent activity requires Hsp90 and the tetratricopeptide repeat (TPR) domain of Coi12p, whereas these factors are dispensable for the ATP-independent activity. Both activities facilitate siRNA loading by counteracting the...
Source: EMBO Journal - February 11, 2015 Category: Molecular Biology Authors: Woehrer, S. L., Aronica, L., Suhren, J. H., Busch, C. J.-L., Noto, T., Mochizuki, K. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, RNA Biology Articles Source Type: research

NTR1 is required for transcription elongation checkpoints at alternative exons in Arabidopsis
We report that Arabidopsis homologue of spliceosome disassembly factor NTR1 is required for correct expression and splicing of DOG1, a regulator of seed dormancy. Global splicing analysis in atntr1 mutants revealed a bias for downstream 5' and 3' splice site selection and an enhanced rate of exon skipping. A local reduction in PolII occupancy at misspliced exons and introns in atntr1 mutants suggests that directionality in splice site selection is a manifestation of fast PolII elongation kinetics. In agreement with this model, we found AtNTR1 to bind target genes and co-localise with PolII. A minigene analysis further...
Source: EMBO Journal - February 11, 2015 Category: Molecular Biology Authors: Dolata, J., Guo, Y., Kołowerzo, A., Smolinski, D., Brzyzek, G., Jarmołowski, A., Swiezewski, S. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Plant Biology, Transcription Articles Source Type: research