Expression of Ca2+-permeable two-pore channels rescues NAADP signalling in TPC-deficient cells
The second messenger NAADP triggers Ca2+ release from endo-lysosomes. Although two-pore channels (TPCs) have been proposed to be regulated by NAADP, recent studies have challenged this. By generating the first mouse line with demonstrable absence of both Tpcn1 and Tpcn2 expression (Tpcn1/2–/–), we show that the loss of endogenous TPCs abolished NAADP-dependent Ca2+ responses as assessed by single-cell Ca2+ imaging or patch-clamp of single endo-lysosomes. In contrast, currents stimulated by PI(3,5)P2 were only partially dependent on TPCs. In Tpcn1/2–/– cells, NAADP sensitivity was restored by re-expr...
Source: EMBO Journal - June 30, 2015 Category: Molecular Biology Authors: Ruas, M., Davis, L. C., Chen, C.-C., Morgan, A. J., Chuang, K.-T., Walseth, T. F., Grimm, C., Garnham, C., Powell, T., Platt, N., Platt, F. M., Biel, M., Wahl-Schott, C., Parrington, J., Galione, A. Tags: Membrane & Intracellular Transport Articles Source Type: research

Simply the right time to turn on insulin
Recent research has made important progress in the directed differentiation of human pluripotent stem cells into insulin-producing beta-like cells in vitro. A new study published in this issue of The EMBO Journal reports that timely induction of NEUROG3 expression in pancreatic progenitors is a crucial checkpoint for generation of functional human beta cells. (Source: EMBO Journal)
Source: EMBO Journal - June 30, 2015 Category: Molecular Biology Authors: Spagnoli, F. M. Tags: Methods & Resources, Molecular Biology of Disease, Stem Cells Have you seen? Source Type: research

Departure gate of acidic Ca2+ confirmed
More potent, but less known than IP3 that liberates Ca2+ from the ER, NAADP releases Ca2+ from acidic stores. The notion that TPC channels mediate this Ca2+ release was questioned recently by studies suggesting that TPCs are rather PI(3,5)P2-activated Na+ channels. Ruas et al (2015) now partially reconcile these views by showing that TPCs significantly conduct both cations and confirm their activation by both NAADP and PI(3,5)P2. They attribute the failure of others to observe TPC-dependent NAADP-induced Ca2+ release in vivo to inadequate mouse models that retain partial TPC function. (Source: EMBO Journal)
Source: EMBO Journal - June 30, 2015 Category: Molecular Biology Authors: Jentsch, T. J., Hoegg-Beiler, M. B., Vogt, J. Tags: Membrane & Intracellular Transport Have you seen? Source Type: research

Alan Hall (1952-2015), an Englishman in New York
(Source: EMBO Journal)
Source: EMBO Journal - June 30, 2015 Category: Molecular Biology Authors: Self, A., Etienne-Manneville, S. Tags: Obituary Source Type: research

Short loop length and high thermal stability determine genomic instability induced by G-quadruplex-forming minisatellites
G-quadruplexes (G4) are polymorphic four-stranded structures formed by certain G-rich nucleic acids, with various biological roles. However, structural features dictating their formation and/or function in vivo are unknown. In S. cerevisiae, the pathological persistency of G4 within the CEB1 minisatellite induces its rearrangement during leading-strand replication. We now show that several other G4-forming sequences remain stable. Extensive mutagenesis of the CEB25 minisatellite motif reveals that only variants with very short (≤ 4 nt) G4 loops preferentially containing pyrimidine bases trigger genomic in...
Source: EMBO Journal - June 11, 2015 Category: Molecular Biology Authors: Piazza, A., Adrian, M., Samazan, F., Heddi, B., Hamon, F., Serero, A., Lopes, J., Teulade-Fichou, M.-P., Phan, A. T., Nicolas, A. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Dampening DNA damage checkpoint signalling via coordinated BRCT domain interactions
In response to DNA damage, checkpoint signalling protects genome integrity at the cost of repressing cell cycle progression and DNA replication. Mechanisms for checkpoint down-regulation are therefore necessary for proper cellular proliferation. We recently uncovered a phosphatase-independent mechanism for dampening checkpoint signalling, where the checkpoint adaptor Rad9 is counteracted by the repair scaffolds Slx4-Rtt107. Here, we establish the molecular requirements for this new mode of checkpoint regulation. We engineered a minimal multi-BRCT-domain (MBD) module that recapitulates the action of Slx4-Rtt107 in checkpoin...
Source: EMBO Journal - June 11, 2015 Category: Molecular Biology Authors: Cussiol, J. R., Jablonowski, C. M., Yimit, A., Brown, G. W., Smolka, M. B. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Noncanonical regulation of alkylation damage resistance by the OTUD4 deubiquitinase
Repair of DNA alkylation damage is critical for genomic stability and involves multiple conserved enzymatic pathways. Alkylation damage resistance, which is critical in cancer chemotherapy, depends on the overexpression of alkylation repair proteins. However, the mechanisms responsible for this upregulation are unknown. Here, we show that an OTU domain deubiquitinase, OTUD4, is a positive regulator of ALKBH2 and ALKBH3, two DNA demethylases critical for alkylation repair. Remarkably, we find that OTUD4 catalytic activity is completely dispensable for this function. Rather, OTUD4 is a scaffold for USP7 and USP9X, two deubiq...
Source: EMBO Journal - June 11, 2015 Category: Molecular Biology Authors: Zhao, Y., Majid, M. C., Soll, J. M., Brickner, J. R., Dango, S., Mosammaparast, N. Tags: DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

The stress response neuropeptide CRF increases amyloid-{beta} production by regulating {gamma}-secretase activity
The biological underpinnings linking stress to Alzheimer's disease (AD) risk are poorly understood. We investigated how corticotrophin releasing factor (CRF), a critical stress response mediator, influences amyloid-β (Aβ) production. In cells, CRF treatment increases Aβ production and triggers CRF receptor 1 (CRFR1) and -secretase internalization. Co-immunoprecipitation studies establish that -secretase associates with CRFR1; this is mediated by β-arrestin binding motifs. Additionally, CRFR1 and -secretase co-localize in lipid raft fractions, with increased -secretase accumulation upon CRF treatment. CR...
Source: EMBO Journal - June 11, 2015 Category: Molecular Biology Authors: Park, H.-J., Ran, Y., Jung, J. I., Holmes, O., Price, A. R., Smithson, L., Ceballos-Diaz, C., Han, C., Wolfe, M. S., Daaka, Y., Ryabinin, A. E., Kim, S.-H., Hauger, R. L., Golde, T. E., Felsenstein, K. M. Tags: Neuroscience Articles Source Type: research

Adaptation of avian influenza A (H6N1) virus from avian to human receptor-binding preference
The receptor-binding specificity of influenza A viruses is a major determinant for the host tropism of the virus, which enables interspecies transmission. In 2013, the first human case of infection with avian influenza A (H6N1) virus was reported in Taiwan. To gather evidence concerning the epidemic potential of H6 subtype viruses, we performed comprehensive analysis of receptor-binding properties of Taiwan-isolated H6 HAs from 1972 to 2013. We propose that the receptor-binding properties of Taiwan-isolated H6 HAs have undergone three major stages: initially avian receptor-binding preference, secondarily obtaining human re...
Source: EMBO Journal - June 11, 2015 Category: Molecular Biology Authors: Wang, F., Qi, J., Bi, Y., Zhang, W., Wang, M., Zhang, B., Wang, M., Liu, J., Yan, J., Shi, Y., Gao, G. F. Tags: Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Neuropeptide Y regulates the hematopoietic stem cell microenvironment and prevents nerve injury in the bone marrow
Many reports have revealed the importance of the sympathetic nervous system (SNS) in the control of the bone marrow environment. However, the specific role of neuropeptide Y (NPY) in this process has not been systematically studied. Here we show that NPY-deficient mice have significantly reduced hematopoietic stem cell (HSC) numbers and impaired regeneration in bone marrow due to apoptotic destruction of SNS fibers and/or endothelial cells. Furthermore, pharmacological elevation of NPY prevented bone marrow impairments in a mouse model of chemotherapy-induced SNS injury, while NPY injection into conditional knockout mice l...
Source: EMBO Journal - June 11, 2015 Category: Molecular Biology Authors: Park, M. H., Jin, H. K., Min, W.-K., Lee, W. W., Lee, J. E., Akiyama, H., Herzog, H., Enikolopov, G. N., Schuchman, E. H., Bae, J.-s. Tags: Neuroscience, Signal Transduction, Stem Cells Articles Source Type: research

Smg6/Est1 licenses embryonic stem cell differentiation via nonsense-mediated mRNA decay
Nonsense-mediated mRNA decay (NMD) is a post-transcriptional mechanism that targets aberrant transcripts and regulates the cellular RNA reservoir. Genetic modulation in vertebrates suggests that NMD is critical for cellular and tissue homeostasis, although the underlying mechanism remains elusive. Here, we generate knockout mice lacking Smg6/Est1, a key nuclease in NMD and a telomerase cofactor. While the complete loss of Smg6 causes mouse lethality at the blastocyst stage, inducible deletion of Smg6 is compatible with embryonic stem cell (ESC) proliferation despite the absence of telomere maintenance and functional NMD. D...
Source: EMBO Journal - June 11, 2015 Category: Molecular Biology Authors: Li, T., Shi, Y., Wang, P., Guachalla, L. M., Sun, B., Joerss, T., Chen, Y.-S., Groth, M., Krueger, A., Platzer, M., Yang, Y.-G., Rudolph, K. L., Wang, Z.-Q. Tags: RNA Biology, Stem Cells Articles Source Type: research

USP18 lack in microglia causes destructive interferonopathy of the mouse brain
Microglia are tissue macrophages of the central nervous system (CNS) that control tissue homeostasis. Microglia dysregulation is thought to be causal for a group of neuropsychiatric, neurodegenerative and neuroinflammatory diseases, called "microgliopathies". However, how the intracellular stimulation machinery in microglia is controlled is poorly understood. Here, we identified the ubiquitin-specific protease (Usp) 18 in white matter microglia that essentially contributes to microglial quiescence. We further found that microglial Usp18 negatively regulates the activation of Stat1 and concomitant induction of int...
Source: EMBO Journal - June 11, 2015 Category: Molecular Biology Authors: Goldmann, T., Zeller, N., Raasch, J., Kierdorf, K., Frenzel, K., Ketscher, L., Basters, A., Staszewski, O., Brendecke, S. M., Spiess, A., Tay, T. L., Kreutz, C., Timmer, J., Mancini, G. M., Blank, T., Fritz, G., Biber, K., Lang, R., Malo, D., Merkler, D., Tags: Immunology, Neuroscience Articles Source Type: research

REV7/MAD2L2: the multitasking maestro emerges as a barrier to recombination
REV7/MAD2L2 plays important roles in translesion DNA synthesis and mitotic control. Two new papers extend its gamut by revealing its unexpected participation in pathway choice during DNA double-strand break repair. By inhibiting 5' DNA end resection downstream of 53BP1 and RIF1, REV7/MAD2L2 promotes non-homologous end joining at the expense of homologous recombination. Importantly, loss of REV7/MAD2L2 renders PARP inhibitors ineffective in BRCA1-deficient tumours, suggesting another possible mechanism for the acquisition of resistance to this important new class of drug. (Source: EMBO Journal)
Source: EMBO Journal - June 11, 2015 Category: Molecular Biology Authors: Sale, J. E. Tags: DNA Replication, Repair & Recombination Have you seen? Source Type: research

RNA degradation drives stem cell differentiation
The mechanisms by which multi-potent stem cells switch their program to become functional differentiated cells have intrigued biologists for decades. Most focus has been on transcriptional pathways, but whether they have sufficient dynamic range to cause discrete shifts in cell state is not clear. Because the steady-state level of RNAs is also dictated by their decay rate, an attractive possibility is that specific RNA decay mechanisms also have a role in promoting differentiation mechanisms. In this issue of The EMBO Journal, Li et al (2015) obtained evidence that a highly conserved RNA degradation pathway called non...
Source: EMBO Journal - June 11, 2015 Category: Molecular Biology Authors: Lou, C.-H., Shum, E. Y., Wilkinson, M. F. Tags: RNA Biology, Stem Cells Have you seen? Source Type: research

Poised for action: USP18 restrains microglial activation in the white matter
This study furthers our knowledge of the roles and regulation of microglial populations, adds insight into the processes underlying neuro-inflammation, and broadens our consideration of immune regulation to include the concept of active restraint as a necessary component to avoid excessive inflammation. (Source: EMBO Journal)
Source: EMBO Journal - June 11, 2015 Category: Molecular Biology Authors: Takata, K., Ginhoux, F. Tags: Immunology, Neuroscience Have you seen? Source Type: research

Dora the Brave
The San Francisco Declaration on Research Assessment (DORA) points out that using the Journal Impact Factor as a proxy measure for the value or quality of specific research and individual scientists leads to biased research assessment. How can we resist misusing metrics? (Source: EMBO Journal)
Source: EMBO Journal - June 11, 2015 Category: Molecular Biology Authors: Pulverer, B. Tags: Editorial Source Type: research

Crystal structures reveal transient PERK luminal domain tetramerization in endoplasmic reticulum stress signaling
Stress caused by accumulation of misfolded proteins within the endoplasmic reticulum (ER) elicits a cellular unfolded protein response (UPR) aimed at maintaining protein-folding capacity. PERK, a key upstream component, recognizes ER stress via its luminal sensor/transducer domain, but the molecular events that lead to UPR activation remain unclear. Here, we describe the crystal structures of mammalian PERK luminal domains captured in dimeric state as well as in a novel tetrameric state. Small angle X-ray scattering analysis (SAXS) supports the existence of both crystal structures also in solution. The salient feature of t...
Source: EMBO Journal - June 2, 2015 Category: Molecular Biology Authors: Carrara, M., Prischi, F., Nowak, P. R., Ali, M. M. Tags: Protein Biosynthesis & Quality Control, Structural Biology Articles Source Type: research

Sox2, Tlx, Gli3, and Her9 converge on Rx2 to define retinal stem cells in vivo
Transcriptional networks defining stemness in adult neural stem cells (NSCs) are largely unknown. We used the proximal cis-regulatory element (pCRE) of the retina-specific homeobox gene 2 (rx2) to address such a network. Lineage analysis in the fish retina identified rx2 as marker for multipotent NSCs. rx2-positive cells located in the peripheral ciliary marginal zone behave as stem cells for the neuroretina, or the retinal pigmented epithelium. We identified upstream regulators of rx2 interrogating the rx2 pCRE in a trans-regulation screen and focused on four TFs (Sox2, Tlx, Gli3, and Her9) activating or repressing rx2 ex...
Source: EMBO Journal - June 2, 2015 Category: Molecular Biology Authors: Reinhardt, R., Centanin, L., Tavhelidse, T., Inoue, D., Wittbrodt, B., Concordet, J.-P., Martinez-Morales, J. R., Wittbrodt, J. Tags: Development & Differentiation, Stem Cells, Transcription Articles Source Type: research

Repression of SRF target genes is critical for Myc-dependent apoptosis of epithelial cells
Oncogenic levels of Myc expression sensitize cells to multiple apoptotic stimuli, and this protects long-lived organisms from cancer development. How cells discriminate physiological from supraphysiological levels of Myc is largely unknown. Here, we show that induction of apoptosis by Myc in breast epithelial cells requires association of Myc with Miz1. Gene expression and ChIP-Sequencing experiments show that high levels of Myc invade target sites that lack consensus E-boxes in a complex with Miz1 and repress transcription. Myc/Miz1-repressed genes encode proteins involved in cell adhesion and migration and include severa...
Source: EMBO Journal - June 2, 2015 Category: Molecular Biology Authors: Wiese, K. E., Haikala, H. M., von Eyss, B., Wolf, E., Esnault, C., Rosenwald, A., Treisman, R., Klefstrom, J., Eilers, M. Tags: Cancer, Autophagy & Cell Death, Transcription Articles Source Type: research

The transcription factor Cabut coordinates energy metabolism and the circadian clock in response to sugar sensing
Nutrient sensing pathways adjust metabolism and physiological functions in response to food intake. For example, sugar feeding promotes lipogenesis by activating glycolytic and lipogenic genes through the Mondo/ChREBP-Mlx transcription factor complex. Concomitantly, other metabolic routes are inhibited, but the mechanisms of transcriptional repression upon sugar sensing have remained elusive. Here, we characterize cabut (cbt), a transcription factor responsible for the repressive branch of the sugar sensing transcriptional network in Drosophila. We demonstrate that cbt is rapidly induced upon sugar feeding through direct r...
Source: EMBO Journal - June 2, 2015 Category: Molecular Biology Authors: Bartok, O., Teesalu, M., Ashwall-Fluss, R., Pandey, V., Hanan, M., Rovenko, B. M., Poukkula, M., Havula, E., Moussaieff, A., Vodala, S., Nahmias, Y., Kadener, S., Hietakangas, V. Tags: Metabolism, Transcription Articles Source Type: research

The first murine zygotic transcription is promiscuous and uncoupled from splicing and 3' processing
Initiation of zygotic transcription in mammals is poorly understood. In mice, zygotic transcription is first detected shortly after pronucleus formation in 1-cell embryos, but the identity of the transcribed loci and mechanisms regulating their expression are not known. Using total RNA-Seq, we have found that transcription in 1-cell embryos is highly promiscuous, such that intergenic regions are extensively expressed and thousands of genes are transcribed at comparably low levels. Striking is that transcription can occur in the absence of defined core-promoter elements. Furthermore, accumulation of translatable zygotic mRN...
Source: EMBO Journal - June 2, 2015 Category: Molecular Biology Authors: Abe, K.-i., Yamamoto, R., Franke, V., Cao, M., Suzuki, Y., Suzuki, M. G., Vlahovicek, K., Svoboda, P., Schultz, R. M., Aoki, F. Tags: Development & Differentiation, RNA Biology, Transcription Articles Source Type: research

Synthetic viability genomic screening defines Sae2 function in DNA repair
DNA double-strand break (DSB) repair by homologous recombination (HR) requires 3' single-stranded DNA (ssDNA) generation by 5' DNA-end resection. During meiosis, yeast Sae2 cooperates with the nuclease Mre11 to remove covalently bound Spo11 from DSB termini, allowing resection and HR to ensue. Mitotic roles of Sae2 and Mre11 nuclease have remained enigmatic, however, since cells lacking these display modest resection defects but marked DNA damage hypersensitivities. By combining classic genetic suppressor screening with high-throughput DNA sequencing, we identify Mre11 mutations that strongly suppress DNA damage sensitivit...
Source: EMBO Journal - June 2, 2015 Category: Molecular Biology Authors: Puddu, F., Oelschlaegel, T., Guerini, I., Geisler, N. J., Niu, H., Herzog, M., Salguero, I., Ochoa-Montano, B., Vire, E., Sung, P., Adams, D. J., Keane, T. M., Jackson, S. P. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Shp2 signaling suppresses senescence in PyMT-induced mammary gland cancer in mice
In this study, we have used techniques from cell biology, biochemistry, and genetics to investigate the role of the tyrosine phosphatase Shp2 in tumor cells of MMTV-PyMT mouse mammary glands. Genetic ablation or pharmacological inhibition of Shp2 induces senescence, as determined by the activation of senescence-associated β-gal (SA-β-gal), cyclin-dependent kinase inhibitor 1B (p27), p53, and histone 3 trimethylated lysine 9 (H3K9me3). Senescence induction leads to the inhibition of self-renewal of tumor cells and blockage of tumor formation and growth. A signaling cascade was identified that acts downstream of Sh...
Source: EMBO Journal - June 2, 2015 Category: Molecular Biology Authors: Lan, L., Holland, J. D., Qi, J., Grosskopf, S., Vogel, R., Gyorffy, B., Wulf-Goldenberg, A., Birchmeier, W. Tags: Molecular Biology of Disease Articles Source Type: research

Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA
There is an expanding list of examples by which one mRNA can posttranscriptionally influence the expression of others. This can involve RNA sponges that sequester regulatory RNAs of mRNAs in the same regulon, but the underlying molecular mechanism of such mRNA cross talk remains little understood. Here, we report sponge-mediated mRNA cross talk in the posttranscriptional network of GcvB, a conserved Hfq-dependent small RNA with one of the largest regulons known in bacteria. We show that mRNA decay from the gltIJKL locus encoding an amino acid ABC transporter generates a stable fragment (SroC) that base-pairs with GcvB. Thi...
Source: EMBO Journal - June 2, 2015 Category: Molecular Biology Authors: Miyakoshi, M., Chao, Y., Vogel, J. Tags: Microbiology, Virology & Host Pathogen Interaction, RNA Biology Articles Source Type: research

Probing disorders of the nervous system using reprogramming approaches
The groundbreaking technologies of induced pluripotency and lineage conversion have generated a genuine opportunity to address fundamental aspects of the diseases that affect the nervous system. These approaches have granted us unrestricted access to the brain and spinal cord of patients and have allowed for the study of disease in the context of human cells, expressing physiological levels of proteins and under each patient's unique genetic constellation. Along with this unprecedented opportunity have come significant challenges, particularly in relation to patient variability, experimental design and data interpretation....
Source: EMBO Journal - June 2, 2015 Category: Molecular Biology Authors: Ichida, J. K., Kiskinis, E. Tags: Neuroscience, Stem Cells Reviews Source Type: research

Forward engineering neuronal diversity using direct reprogramming
The nervous system is comprised of a vast diversity of distinct neural cell types. Differences between neuronal subtypes drive the assembly of neuronal circuits and underlie the subtype specificity of many neurological diseases. Yet, because neurons are irreversibly post-mitotic and not readily available from patients, it has not been feasible to study specific subtypes of human neurons in larger numbers. A powerful means to study neuronal diversity and neurological disease is to establish methods to produce desired neuronal subtypes in vitro. Traditionally this has been accomplished by treating pluripotent or neural ...
Source: EMBO Journal - June 2, 2015 Category: Molecular Biology Authors: Tsunemoto, R. K., Eade, K. T., Blanchard, J. W., Baldwin, K. K. Tags: Molecular Biology of Disease, Neuroscience, Stem Cells Reviews Source Type: research

A grab to move on: ER-endosome contacts in membrane protrusion formation and neurite outgrowth
A key feature of many eukaryotic cells, most prominently seen in developing neurons, is their ability to form and extend membrane protrusions. How protrusion formation is linked to exocytic membrane trafficking is largely unclear. In a recent paper published in Nature, Raiborg et al identify a crucial role in this process for dynamic membrane contact sites (MCSs) between the ER and endosomes. The MCSs are formed by endoplasmic reticulum (ER)-localized protein protrudin and the late endosomal kinesin adaptor FYCO1 and the small GTPase Rab7. (Source: EMBO Journal)
Source: EMBO Journal - June 2, 2015 Category: Molecular Biology Authors: Krauss, M., Haucke, V. Tags: Membrane & Intracellular Transport, Neuroscience Have you seen? Source Type: research

SHP2: a new target for pro-senescence cancer therapies
Cellular senescence is a response to stress that disables cell proliferation and orchestrates an inflammatory process that eliminates damaged cells. The first pro-senescence drugs for cancer treatment are now a clinical reality, but still few targets have been identified whose inactivation results in cancer cell senescence. Current work published in this issue of The EMBO Journal makes an important contribution to this area by discovering that pharmacological inhibition of the tyrosine phosphatase SHP2 blocks mouse mammary cancer through the induction of senescence (Lan et al, 2015). (Source: EMBO Journal)
Source: EMBO Journal - June 2, 2015 Category: Molecular Biology Authors: Serrano, M. Tags: Molecular Biology of Disease Have you seen? Source Type: research

Talk among yourselves: RNA sponges mediate cross talk between functionally related messenger RNAs
When Francis Crick first proposed the central dogma, he predicted that genetic information flows from DNA to RNA and finally to proteins. By this classical concept, the sole purpose of mRNA is to serve as a template for translation. Recent work has expanded our understanding of the function of mRNA well beyond this singular definition. A paper published in this issue sheds more light on the myriad roles mRNAs can play in genetic regulation. Miyakoshi et al (2015a) report an intriguing scenario in Salmonella where a small RNA molecule derived from a larger polycistronic mRNA promotes cross talk between physically unlin...
Source: EMBO Journal - June 2, 2015 Category: Molecular Biology Authors: Azam, M. S., Vanderpool, C. K. Tags: Microbiology, Virology & Host Pathogen Interaction, RNA Biology Have you seen? Source Type: research

Focus on induced pluripotency and cellular reprogramming
Reflecting on the opportunities that ‘induced pluripotency’ offers for basic research and clinical translation, the 2015 Focus of The EMBO Journal highlights some of the most challenging biological questions studied using advanced iPSC-based technologies. (Source: EMBO Journal)
Source: EMBO Journal - June 2, 2015 Category: Molecular Biology Authors: Schwarz-Romond, T., Kiskinis, E., Eggan, K. Tags: Editorial Source Type: research

Insm1 cooperates with Neurod1 and Foxa2 to maintain mature pancreatic {beta}-cell function
Key transcription factors control the gene expression program in mature pancreatic β-cells, but their integration into regulatory networks is little understood. Here, we show that Insm1, Neurod1 and Foxa2 directly interact and together bind regulatory sequences in the genome of mature pancreatic β-cells. We used Insm1 ablation in mature β-cells in mice and found pronounced deficits in insulin secretion and gene expression. Insm1-dependent genes identified previously in developing β-cells markedly differ from the ones identified in the adult. In particular, adult mutant β-cells resemble immature &be...
Source: EMBO Journal - May 11, 2015 Category: Molecular Biology Authors: Jia, S., Ivanov, A., Blasevic, D., Muller, T., Purfurst, B., Sun, W., Chen, W., Poy, M. N., Rajewsky, N., Birchmeier, C. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Development & Differentiation, Molecular Biology of Disease Articles Source Type: research

Cockayne syndrome group B protein regulates DNA double-strand break repair and checkpoint activation
Mutations of CSB account for the majority of Cockayne syndrome (CS), a devastating hereditary disorder characterized by physical impairment, neurological degeneration and segmental premature aging. Here we report the generation of a human CSB-knockout cell line. We find that CSB facilitates HR and represses NHEJ. Loss of CSB or a CS-associated CSB mutation abrogating its ATPase activity impairs the recruitment of BRCA1, RPA and Rad51 proteins to damaged chromatin but promotes the formation of 53BP1-Rif1 damage foci in S and G2 cells. Depletion of 53BP1 rescues the formation of BRCA1 damage foci in CSB-knockout cells. In ad...
Source: EMBO Journal - May 11, 2015 Category: Molecular Biology Authors: Batenburg, N. L., Thompson, E. L., Hendrickson, E. A., Zhu, X.-D. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Ubiquitin-like protein UBL5 promotes the functional integrity of the Fanconi anemia pathway
Ubiquitin and ubiquitin-like proteins (UBLs) function in a wide array of cellular processes. UBL5 is an atypical UBL that does not form covalent conjugates with cellular proteins and which has a known role in modulating pre-mRNA splicing. Here, we report an unexpected involvement of human UBL5 in promoting the function of the Fanconi anemia (FA) pathway for repair of DNA interstrand crosslinks (ICLs), mediated by a specific interaction with the central FA pathway component FANCI. UBL5-deficient cells display spliceosome-independent reduction of FANCI protein stability, defective FANCI function in response to DNA damage and...
Source: EMBO Journal - May 11, 2015 Category: Molecular Biology Authors: Oka, Y., Bekker-Jensen, S., Mailand, N. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Telomerase abrogates aneuploidy-induced telomere replication stress, senescence and cell depletion
The causal role of aneuploidy in cancer initiation remains under debate since mutations of euploidy-controlling genes reduce cell fitness but aneuploidy strongly associates with human cancers. Telomerase activation allows immortal growth by stabilizing telomere length, but its role in aneuploidy survival has not been characterized. Here, we analyze the response of primary human cells and murine hematopoietic stem cells (HSCs) to aneuploidy induction and the role of telomeres and the telomerase in this process. The study shows that aneuploidy induces replication stress at telomeres leading to telomeric DNA damage and p53 ac...
Source: EMBO Journal - May 11, 2015 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., d'Adda di Fagagna, F., Gunes, C., Rudolph, K. L. Tags: Cancer, Cell Cycle, DNA Replication, Repair & Recombination Articles Source Type: research

Aerobic glycolysis tunes YAP/TAZ transcriptional activity
Increased glucose metabolism and reprogramming toward aerobic glycolysis are a hallmark of cancer cells, meeting their metabolic needs for sustained cell proliferation. Metabolic reprogramming is usually considered as a downstream consequence of tumor development and oncogene activation; growing evidence indicates, however, that metabolism on its turn can support oncogenic signaling to foster tumor malignancy. Here, we explored how glucose metabolism regulates gene transcription and found an unexpected link with YAP/TAZ, key transcription factors regulating organ growth, tumor cell proliferation and aggressiveness. When ce...
Source: EMBO Journal - May 11, 2015 Category: Molecular Biology Authors: Enzo, E., Santinon, G., Pocaterra, A., Aragona, M., Bresolin, S., Forcato, M., Grifoni, D., Pession, A., Zanconato, F., Guzzo, G., Bicciato, S., Dupont, S. Tags: Cancer, Metabolism, Signal Transduction Articles Source Type: research

Thymus-derived regulatory T cells restrain pro-inflammatory Th1 responses by downregulating CD70 on dendritic cells
The severity and intensity of autoimmune disease in immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) patients and in scurfy mice emphasize the critical role played by thymus-derived regulatory T cells (tTregs) in maintaining peripheral immune tolerance. However, although tTregs are critical to prevent lethal autoimmunity and excessive inflammatory responses, their suppressive mechanism remains elusive. Here, we demonstrate that tTregs selectively inhibit CD27/CD70-dependent Th1 priming, while leaving the IL-12-dependent pathway unaffected. Immunized mice depleted of tTregs showed an increased response...
Source: EMBO Journal - May 11, 2015 Category: Molecular Biology Authors: Dhainaut, M., Coquerelle, C., Uzureau, S., Denoeud, J., Acolty, V., Oldenhove, G., Galuppo, A., Sparwasser, T., Thielemans, K., Pays, E., Yagita, H., Borst, J., Moser, M. Tags: Immunology Articles Source Type: research

Snai1 regulates cell lineage allocation and stem cell maintenance in the mouse intestinal epithelium
Snail family members regulate epithelial-to-mesenchymal transition (EMT) during invasion of intestinal tumours, but their role in normal intestinal homeostasis is unknown. Studies in breast and skin epithelia indicate that Snail proteins promote an undifferentiated state. Here, we demonstrate that conditional knockout of Snai1 in the intestinal epithelium results in apoptotic loss of crypt base columnar stem cells and bias towards differentiation of secretory lineages. In vitro organoid cultures derived from Snai1 conditional knockout mice also undergo apoptosis when Snai1 is deleted. Conversely, ectopic expression of Snai...
Source: EMBO Journal - May 11, 2015 Category: Molecular Biology Authors: Horvay, K., Jarde, T., Casagranda, F., Perreau, V. M., Haigh, K., Nefzger, C. M., Akhtar, R., Gridley, T., Berx, G., Haigh, J. J., Barker, N., Polo, J. M., Hime, G. R., Abud, H. E. Tags: Development & Differentiation, Stem Cells, Transcription Articles Source Type: research

Chemokine-guided cell migration and motility in zebrafish development
We present the current knowledge concerning the formation of the chemokine gradient, its interpretation within the cell, and the molecular mechanisms underlying the cellular response to chemokine signals during directed migration. (Source: EMBO Journal)
Source: EMBO Journal - May 11, 2015 Category: Molecular Biology Authors: Bussmann, J., Raz, E. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation Reviews Source Type: research

Reprogramming of cell fate: epigenetic memory and the erasure of memories past
Cell identity is a reflection of a cell type-specific gene expression profile, and consequently, cell type-specific transcription factor networks are considered to be at the heart of a given cellular phenotype. Although generally stable, cell identity can be reprogrammed in vitro by forced changes to the transcriptional network, the most dramatic example of which was shown by the induction of pluripotency in somatic cells by the ectopic expression of defined transcription factors alone. Although changes to cell fate can be achieved in this way, the efficiency of such conversion remains very low, in large part due to specif...
Source: EMBO Journal - May 11, 2015 Category: Molecular Biology Authors: Nashun, B., Hill, P. W., Hajkova, P. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Molecular Biology of Disease, Stem Cells Reviews Source Type: research

Blocking integrin inactivation as an anti-angiogenic therapy
During angiogenesis, endothelial cell migration is coordinated by integrin-mediated contact with the extra-cellular matrix (ECM), coupled with receptor tyrosine kinase signalling to regulate dynamic cytoskeletal and plasma membrane reorganization. A recent paper by Vitorino et al (2015) defined a new MAP4K4–moesin–talin–β1-integrin pathway that could be therapeutically exploited to suppress pathologic angiogenesis. (Source: EMBO Journal)
Source: EMBO Journal - May 11, 2015 Category: Molecular Biology Authors: Saharinen, P., Ivaska, J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Signal Transduction, Vascular Biology & Angiogenesis Have you seen? Source Type: research

Tregs strip dendritic cells of CD70 to regulate Th1 differentiation
When the immune system encounters an antigen, the response can result in the mobilization of effector cells or in tolerance. The outcome is largely dependent on immunosuppressive CD4 T cells that express the transcription factor Foxp3 (Tregs). Yet, how Tregs control different immune effector cells remains elusive. In this issue of The EMBO Journal, Dhainaut et al report on a novel mechanism used by Tregs to prevent differentiation of naïve CD4 T cells to proinflammatory Th1CD4 (Th1) effectors. (Source: EMBO Journal)
Source: EMBO Journal - May 11, 2015 Category: Molecular Biology Authors: Wojciech, L., Ignatowicz, L. Tags: Immunology Have you seen? Source Type: research

Gut stem cells, a story of snails, flies and mice
Intestinal stem cells (ISCs) replenish and regenerate several types of cells in the gut, both during normal homeostasis and in response to various insults such as infections. Although gut structure and complexity vary across phyla, two functional categories of differentiated cell types are always present: absorptive cells and those of the secretory lineage. A series of studies in Drosophila and mouse published in The EMBO Journal, including one in this issue, identifies conserved roles for the Snail family of zinc finger transcription factors in regulating self-renewal and differentiation of ISCs (Korzelius et al, 201...
Source: EMBO Journal - May 11, 2015 Category: Molecular Biology Authors: Amoyel, M. Tags: Development & Differentiation, Stem Cells, Transcription Have you seen? Source Type: research

X-ray and Cryo-EM structures reveal mutual conformational changes of Kinesin and GTP-state microtubules upon binding
The molecular motor kinesin moves along microtubules using energy from ATP hydrolysis in an initial step coupled with ADP release. In neurons, kinesin-1/KIF5C preferentially binds to the GTP-state microtubules over GDP-state microtubules to selectively enter an axon among many processes; however, because the atomic structure of nucleotide-free KIF5C is unavailable, its molecular mechanism remains unresolved. Here, the crystal structure of nucleotide-free KIF5C and the cryo-electron microscopic structure of nucleotide-free KIF5C complexed with the GTP-state microtubule are presented. The structures illustrate mutual conform...
Source: EMBO Journal - May 5, 2015 Category: Molecular Biology Authors: Morikawa, M., Yajima, H., Nitta, R., Inoue, S., Ogura, T., Sato, C., Hirokawa, N. Tags: Cell Adhesion, Polarity & Cytoskeleton, Membrane & Intracellular Transport Articles Source Type: research

Error-free and mutagenic processing of topoisomerase 1-provoked damage at genomic ribonucleotides
Genomic ribonucleotides incorporated during DNA replication are commonly repaired by RNase H2-dependent ribonucleotide excision repair (RER). When RNase H2 is compromised, such as in Aicardi-Goutières patients, genomic ribonucleotides either persist or are processed by DNA topoisomerase 1 (Top1) by either error-free or mutagenic repair. Here, we present a biochemical analysis of these pathways. Top1 cleavage at genomic ribonucleotides can produce ribonucleoside-2',3'-cyclic phosphate-terminated nicks. Remarkably, this nick is rapidly reverted by Top1, thereby providing another opportunity for repair by RER. However,...
Source: EMBO Journal - May 5, 2015 Category: Molecular Biology Authors: Sparks, J. L., Burgers, P. M. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

An LXR-NCOA5 gene regulatory complex directs inflammatory crosstalk-dependent repression of macrophage cholesterol efflux
LXR–cofactor complexes activate the gene expression program responsible for cholesterol efflux in macrophages. Inflammation antagonizes this program, resulting in foam cell formation and atherosclerosis; however, the molecular mechanisms underlying this antagonism remain to be fully elucidated. We use promoter enrichment-quantitative mass spectrometry (PE-QMS) to characterize the composition of gene regulatory complexes assembled at the promoter of the lipid transporter Abca1 following downregulation of its expression. We identify a subset of proteins that show LXR ligand- and binding-dependent association with the A...
Source: EMBO Journal - May 5, 2015 Category: Molecular Biology Authors: Gillespie, M. A., Gold, E. S., Ramsey, S. A., Podolsky, I., Aderem, A., Ranish, J. A. Tags: Immunology, Metabolism Articles Source Type: research

FGF22 signaling regulates synapse formation during post-injury remodeling of the spinal cord
The remodeling of axonal circuits after injury requires the formation of new synaptic contacts to enable functional recovery. Which molecular signals initiate such axonal and synaptic reorganisation in the adult central nervous system is currently unknown. Here, we identify FGF22 as a key regulator of circuit remodeling in the injured spinal cord. We show that FGF22 is produced by spinal relay neurons, while its main receptors FGFR1 and FGFR2 are expressed by cortical projection neurons. FGF22 deficiency or the targeted deletion of FGFR1 and FGFR2 in the hindlimb motor cortex limits the formation of new synapses between co...
Source: EMBO Journal - May 5, 2015 Category: Molecular Biology Authors: Jacobi, A., Loy, K., Schmalz, A. M., Hellsten, M., Umemori, H., Kerschensteiner, M., Bareyre, F. M. Tags: Neuroscience Articles Source Type: research

Che-1-induced inhibition of mTOR pathway enables stress-induced autophagy
In this study, we demonstrate that Che-1, a RNA polymerase II-binding protein activated by the DNA damage response, inhibits mTOR activity in response to stress conditions. We found that, under stress, Che-1 induces the expression of two important mTOR inhibitors, Redd1 and Deptor, and that this activity is required for sustaining stress-induced autophagy. Strikingly, Che-1 expression correlates with the progression of multiple myeloma and is required for cell growth and survival, a malignancy characterized by high autophagy response. (Source: EMBO Journal)
Source: EMBO Journal - May 5, 2015 Category: Molecular Biology Authors: Desantis, A., Bruno, T., Catena, V., De Nicola, F., Goeman, F., Iezzi, S., Sorino, C., Ponzoni, M., Bossi, G., Federico, V., La Rosa, F., Ricciardi, M. R., Lesma, E., De Meo, P. D., Castrignano, T., Petrucci, M. T., Pisani, F., Chesi, M., Bergsagel, P. L. Tags: Cancer, Autophagy & Cell Death, DNA Replication, Repair & Recombination Articles Source Type: research

Induced miR-99a expression represses Mtor cooperatively with miR-150 to promote regulatory T-cell differentiation
Peripheral induction of regulatory T (Treg) cells provides essential protection from inappropriate immune responses. CD4+ T cells that lack endogenous miRNAs are impaired to differentiate into Treg cells, but the relevant miRNAs are unknown. We performed an overexpression screen with T-cell-expressed miRNAs in naive mouse CD4+ T cells undergoing Treg differentiation. Among 130 candidates, the screen identified 29 miRNAs with a negative and 10 miRNAs with a positive effect. Testing reciprocal Th17 differentiation revealed specific functions for miR-100, miR-99a and miR-10b, since all of these promoted the Treg and inhibited...
Source: EMBO Journal - May 5, 2015 Category: Molecular Biology Authors: Warth, S. C., Hoefig, K. P., Hiekel, A., Schallenberg, S., Jovanovic, K., Klein, L., Kretschmer, K., Ansel, K. M., Heissmeyer, V. Tags: Immunology Articles Source Type: research

Let-7 and miR-125 cooperate to prime progenitors for astrogliogenesis
The molecular basis of astrocyte differentiation and maturation is poorly understood. As microRNAs have important roles in cell fate transitions, we set out to study their function during the glial progenitor cell (GPC) to astrocyte transition. Inducible deletion of all canonical microRNAs in GPCs in vitro led to a block in the differentiation to astrocytes. In an unbiased screen, the reintroduction of let-7 and miR-125 families of microRNAs rescued differentiation. Let-7 and miR-125 shared many targets and functioned in parallel to JAK-STAT signaling, a known regulator of astrogliogenesis. While individual knockdown of sh...
Source: EMBO Journal - May 5, 2015 Category: Molecular Biology Authors: Shenoy, A., Danial, M., Blelloch, R. H. Tags: Neuroscience, RNA Biology Articles Source Type: research

Switching roles: the functional plasticity of adult tissue stem cells
Adult organisms have to adapt to survive, and the same is true for their tissues. Rates and types of cell production must be rapidly and reversibly adjusted to meet tissue demands in response to both local and systemic challenges. Recent work reveals how stem cell (SC) populations meet these requirements by switching between functional states tuned to homoeostasis or regeneration. This plasticity extends to differentiating cells, which are capable of reverting to SCs after injury. The concept of the niche, the micro-environment that sustains and regulates stem cells, is broadening, with a new appreciation of the role of ph...
Source: EMBO Journal - May 5, 2015 Category: Molecular Biology Authors: Wabik, A., Jones, P. H. Tags: Development & Differentiation, Molecular Biology of Disease, Stem Cells Reviews Source Type: research