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

Sensing of viral and endogenous RNA by ZBP1/DAI induces necroptosis
Nucleic acids are potent triggers for innate immunity. Double-stranded DNA and RNA adopt different helical conformations, including the unusual Z-conformation. Z-DNA/RNA is recognised by Z-binding domains (ZBDs), which are present in proteins implicated in antiviral immunity. These include ZBP1 (also known as DAI or DLM-1), which induces necroptosis, an inflammatory form of cell death. Using reconstitution and knock-in models, we report that mutation of key amino acids involved in Z-DNA/RNA binding in ZBP1's ZBDs prevented necroptosis upon infection with mouse cytomegalovirus. Induction of cell death was cell autonomous an...
Source: EMBO Journal - September 1, 2017 Category: Molecular Biology Authors: Maelfait, J., Liverpool, L., Bridgeman, A., Ragan, K. B., Upton, J. W., Rehwinkel, J. Tags: Immunology, RNA Biology Articles Source Type: research

Mechanical cue-induced YAP instructs Skp2-dependent cell cycle exit and oncogenic signaling
Mechanical tensions are usually generated during development at spatially defined regions within tissues. Such physical cues dictate the cellular decisions of proliferation or cell cycle arrest. Yet, the mechanisms by which mechanical stress controls the cell cycle are not yet fully understood. Here, we report that mechanical cues function upstream of Skp2 transcription in human breast cancer cells. We found that YAP, the mechano-responsive oncogenic Hippo signaling effector, directly promotes Skp2 transcription. YAP inactivation induces cell cycle exit (G0) by down-regulating Skp2, causing p21/p27 to accumulate. Both Skp2...
Source: EMBO Journal - September 1, 2017 Category: Molecular Biology Authors: Jang, W., Kim, T., Koo, J. S., Kim, S.-k., Lim, D.-S. Tags: Cancer, Cell Cycle, Signal Transduction Articles Source Type: research

Fundamental cell cycle kinases collaborate to ensure timely destruction of the synaptonemal complex during meiosis
The synaptonemal complex (SC) is a proteinaceous macromolecular assembly that forms during meiotic prophase I and mediates adhesion of paired homologous chromosomes along their entire lengths. Although prompt disassembly of the SC during exit from prophase I is a landmark event of meiosis, the underlying mechanism regulating SC destruction has remained elusive. Here, we show that DDK (Dbf4-dependent Cdc7 kinase) is central to SC destruction. Upon exit from prophase I, Dbf4, the regulatory subunit of DDK, directly associates with and is phosphorylated by the Polo-like kinase Cdc5. In parallel, upregulated CDK1 activity also...
Source: EMBO Journal - September 1, 2017 Category: Molecular Biology Authors: Argunhan, B., Leung, W.-K., Afshar, N., Terentyev, Y., Subramanian, V. V., Murayama, Y., Hochwagen, A., Iwasaki, H., Tsubouchi, T., Tsubouchi, H. Tags: Cell Cycle, DNA Replication, Repair & Recombination Articles Source Type: research

APP mouse models for Alzheimer's disease preclinical studies
Animal models of human diseases that accurately recapitulate clinical pathology are indispensable for understanding molecular mechanisms and advancing preclinical studies. The Alzheimer's disease (AD) research community has historically used first-generation transgenic (Tg) mouse models that overexpress proteins linked to familial AD (FAD), mutant amyloid precursor protein (APP), or APP and presenilin (PS). These mice exhibit AD pathology, but the overexpression paradigm may cause additional phenotypes unrelated to AD. Second-generation mouse models contain humanized sequences and clinical mutations in the endogenous mouse...
Source: EMBO Journal - September 1, 2017 Category: Molecular Biology Authors: Sasaguri, H., Nilsson, P., Hashimoto, S., Nagata, K., Saito, T., De Strooper, B., Hardy, J., Vassar, R., Winblad, B., Saido, T. C. Tags: Molecular Biology of Disease, Neuroscience Review Source Type: research

Live and let die: ZBP1 senses viral and cellular RNAs to trigger necroptosis
Necroptosis is a programmed form of inflammatory cell death involved in various pathologies, such as viral infections. In two new papers published in The EMBO Journal and EMBO Reports, Z-DNA binding protein 1 (ZBP1) is now shown to sense RNAs during viral infection or after caspase inhibition and activate necroptosis. This may suggest that Z-RNAs are molecular patterns for activation of necroptosis. (Source: EMBO Journal)
Source: EMBO Journal - September 1, 2017 Category: Molecular Biology Authors: Assil, S., Paludan, S. R. Tags: Autophagy & Cell Death, Immunology News [amp ] Views Source Type: research

A forceful connection: mechanoregulation of oncogenic YAP
The Yes-associated protein (YAP) is an important transcriptional co-activator that mediates the cellular response to mechanical and cytoskeletal cues. In two recent papers published in The EMBO Journal, Dae-Sik Lim and colleagues show how YAP activity affects cancer formation and metastasis via a crosstalk with myocardin-related transcription factors (MRTFs; Kim et al, 2017) and SKP2-dependent cell cycle progression (Jang et al, 2017). (Source: EMBO Journal)
Source: EMBO Journal - September 1, 2017 Category: Molecular Biology Authors: Böttcher, R. T., Sun, Z., Fässler, R. Tags: Cancer, Signal Transduction, Transcription News [amp ] Views Source Type: research

Protease cleavage site fingerprinting by label-free in-gel degradomics reveals pH-dependent specificity switch of legumain
Determination of protease specificity is of crucial importance for understanding protease function. We have developed the first gel-based label-free proteomic approach (DIPPS—direct in-gel profiling of protease specificity) that enables quick and reliable determination of protease cleavage specificities under large variety of experimental conditions. The methodology is based on in-gel digestion of the gel-separated proteome with the studied protease, enrichment of cleaved peptides by gel extraction, and subsequent mass spectrometry analysis combined with a length-limited unspecific database search. We applied the met...
Source: EMBO Journal - August 15, 2017 Category: Molecular Biology Authors: Vidmar, R., Vizovisek, M., Turk, D., Turk, B., Fonovic, M. Tags: Chemical Biology, Methods & Resources, Post-translational Modifications, Proteolysis & Proteomics Source Type: research

PPR polyadenylation factor defines mitochondrial mRNA identity and stability in trypanosomes
In Trypanosoma brucei, most mitochondrial mRNAs undergo internal changes by RNA editing and 3' end modifications. The temporally separated and functionally distinct modifications are manifested by adenylation prior to editing, and by post-editing extension of a short A-tail into a long A/U-heteropolymer. The A-tail stabilizes partially and fully edited mRNAs, while the A/U-tail enables mRNA binding to the ribosome. Here, we identify an essential pentatricopeptide repeat-containing RNA binding protein, kinetoplast polyadenylation factor 3 (KPAF3), and demonstrate its role in protecting pre-mRNA against degradation by the pr...
Source: EMBO Journal - August 15, 2017 Category: Molecular Biology Authors: Zhang, L., Sement, F. M., Suematsu, T., Yu, T., Monti, S., Huang, L., Aphasizhev, R., Aphasizheva, I. Tags: Microbiology, Virology & Host Pathogen Interaction, RNA Biology Articles Source Type: research

The AAA+ ATPase TRIP13 remodels HORMA domains through N-terminal engagement and unfolding
Proteins of the conserved HORMA domain family, including the spindle assembly checkpoint protein MAD2 and the meiotic HORMADs, assemble into signaling complexes by binding short peptides termed "closure motifs". The AAA+ ATPase TRIP13 regulates both MAD2 and meiotic HORMADs by disassembling these HORMA domain–closure motif complexes, but its mechanisms of substrate recognition and remodeling are unknown. Here, we combine X-ray crystallography and crosslinking mass spectrometry to outline how TRIP13 recognizes MAD2 with the help of the adapter protein p31comet. We show that p31comet binding to the TRIP13 N-t...
Source: EMBO Journal - August 15, 2017 Category: Molecular Biology Authors: Ye, Q., Kim, D. H., Dereli, I., Rosenberg, S. C., Hagemann, G., Herzog, F., Toth, A., Cleveland, D. W., Corbett, K. D. Tags: Cell Cycle, Structural Biology Articles Source Type: research

Type I interferon is required for T helper (Th) 2 induction by dendritic cells
Type 2 inflammation is a defining feature of infection with parasitic worms (helminths), as well as being responsible for widespread suffering in allergies. However, the precise mechanisms involved in T helper (Th) 2 polarization by dendritic cells (DCs) are currently unclear. We have identified a previously unrecognized role for type I IFN (IFN-I) in enabling this process. An IFN-I signature was evident in DCs responding to the helminth Schistosoma mansoni or the allergen house dust mite (HDM). Further, IFN-I signaling was required for optimal DC phenotypic activation in response to helminth antigen (Ag), and efficient mi...
Source: EMBO Journal - August 15, 2017 Category: Molecular Biology Authors: Webb, L. M., Lundie, R. J., Borger, J. G., Brown, S. L., Connor, L. M., Cartwright, A. N., Dougall, A. M., Wilbers, R. H., Cook, P. C., Jackson-Jones, L. H., Phythian-Adams, A. T., Johansson, C., Davis, D. M., Dewals, B. G., Ronchese, F., MacDonald, A. S. Tags: Immunology, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Integrin {alpha}v{beta}3 enhances the suppressive effect of interferon-{gamma} on hematopoietic stem cells
Hematopoietic homeostasis depends on the maintenance of hematopoietic stem cells (HSCs), which are regulated within a specialized bone marrow (BM) niche. When HSC sense external stimuli, their adhesion status may be critical for determining HSC cell fate. The cell surface molecule, integrin αvβ3, is activated through HSC adhesion to extracellular matrix and niche cells. Integrin β3 signaling maintains HSCs within the niche. Here, we showed the synergistic negative regulation of the pro-inflammatory cytokine interferon- (IFN) and β3 integrin signaling in murine HSC function by a novel definitive phenoty...
Source: EMBO Journal - August 15, 2017 Category: Molecular Biology Authors: Umemoto, T., Matsuzaki, Y., Shiratsuchi, Y., Hashimoto, M., Yoshimoto, T., Nakamura-Ishizu, A., Petrich, B., Yamato, M., Suda, T. Tags: Immunology, Signal Transduction, Stem Cells Articles Source Type: research

Tumor matrix stiffness promotes metastatic cancer cell interaction with the endothelium
Tumor progression alters the composition and physical properties of the extracellular matrix. Particularly, increased matrix stiffness has profound effects on tumor growth and metastasis. While endothelial cells are key players in cancer progression, the influence of tumor stiffness on the endothelium and the impact on metastasis is unknown. Through quantitative mass spectrometry, we find that the matricellular protein CCN1/CYR61 is highly regulated by stiffness in endothelial cells. We show that stiffness-induced CCN1 activates β-catenin nuclear translocation and signaling and that this contributes to upregulate N-ca...
Source: EMBO Journal - August 15, 2017 Category: Molecular Biology Authors: Reid, S. E., Kay, E. J., Neilson, L. J., Henze, A.-T., Serneels, J., McGhee, E. J., Dhayade, S., Nixon, C., Mackey, J. B., Santi, A., Swaminathan, K., Athineos, D., Papalazarou, V., Patella, F., Roman-Fernandez, A., ElMaghloob, Y., Hernandez-Fernaud, J. R Tags: Cancer, Cell Adhesion, Polarity & Cytoskeleton Articles Source Type: research

SIRT1 regulates macrophage self-renewal
Mature differentiated macrophages can self-maintain by local proliferation in tissues and can be extensively expanded in culture under specific conditions, but the mechanisms of this phenomenon remain only partially defined. Here, we show that SIRT1, an evolutionary conserved regulator of life span, positively affects macrophage self-renewal ability in vitro and in vivo. Overexpression of SIRT1 during bone marrow-derived macrophage differentiation increased their proliferative capacity. Conversely, decrease of SIRT1 expression by shRNA inactivation, CRISPR/Cas9 mediated deletion and pharmacological inhibition res...
Source: EMBO Journal - August 15, 2017 Category: Molecular Biology Authors: Imperatore, F., Maurizio, J., Vargas Aguilar, S., Busch, C. J., Favret, J., Kowenz-Leutz, E., Cathou, W., Gentek, R., Perrin, P., Leutz, A., Berruyer, C., Sieweke, M. H. Tags: Development & Differentiation, Immunology Articles Source Type: research

Role of glutamine and interlinked asparagine metabolism in vessel formation
Endothelial cell (EC) metabolism is emerging as a regulator of angiogenesis, but the precise role of glutamine metabolism in ECs is unknown. Here, we show that depriving ECs of glutamine or inhibiting glutaminase 1 (GLS1) caused vessel sprouting defects due to impaired proliferation and migration, and reduced pathological ocular angiogenesis. Inhibition of glutamine metabolism in ECs did not cause energy distress, but impaired tricarboxylic acid (TCA) cycle anaplerosis, macromolecule production, and redox homeostasis. Only the combination of TCA cycle replenishment plus asparagine supplementation restored the metabolic abe...
Source: EMBO Journal - August 15, 2017 Category: Molecular Biology Authors: Huang, H., Vandekeere, S., Kalucka, J., Bierhansl, L., Zecchin, A., Brüning, U., Visnagri, A., Yuldasheva, N., Goveia, J., Cruys, B., Brepoels, K., Wyns, S., Rayport, S., Ghesquiere, B., Vinckier, S., Schoonjans, L., Cubbon, R., Dewerchin, M., Eel Tags: Metabolism, Vascular Biology & Angiogenesis Articles Source Type: research

Glutamine fuels proliferation but not migration of endothelial cells
Endothelial metabolism is a key regulator of angiogenesis. Glutamine metabolism in endothelial cells (ECs) has been poorly studied. We used genetic modifications and 13C tracing approaches to define glutamine metabolism in these cells. Glutamine supplies the majority of carbons in the tricyclic acid (TCA) cycle of ECs and contributes to lipid biosynthesis via reductive carboxylation. EC-specific deletion in mice of glutaminase, the initial enzyme in glutamine catabolism, markedly blunts angiogenesis. In cell culture, glutamine deprivation or inhibition of glutaminase prevents EC proliferation, but does not prevent cell mig...
Source: EMBO Journal - August 15, 2017 Category: Molecular Biology Authors: Kim, B., Li, J., Jang, C., Arany, Z. Tags: Metabolism, Vascular Biology & Angiogenesis Articles Source Type: research

A chief source of cancer and repair in stomachs
Differentiated cells had long been thought to be non-dividing, though we now know many can proliferate after injury. A new study by Leushacke et al (2017) shows how injury recruits mature, Lgr5-expressing gastric chief cells to become stem cells that can either regenerate damaged tissue or fuel precancerous lesions. (Source: EMBO Journal)
Source: EMBO Journal - August 15, 2017 Category: Molecular Biology Authors: Radyk, M. D., Mills, J. C. Tags: Cancer, Development & Differentiation, Stem Cells News [amp ] Views Source Type: research

New Q(ues) to keep blood vessels growing
How endothelial cells adapt their metabolism to the rising energy and biomass demands of sprouting vessels is an exciting field of research in vascular biology with numerous open questions. Two new studies published in this issue of The EMBO Journal now show the importance of glutamine in endothelial metabolism, required to sustain endothelial cell proliferation and vascular expansion. These results provide insight into how endothelial cells selectively use nutrients for energy and biomass production and illuminate new levels of regulation of the angiogenic process. (Source: EMBO Journal)
Source: EMBO Journal - August 15, 2017 Category: Molecular Biology Authors: Andrade, J., Potente, M. Tags: Metabolism, Vascular Biology & Angiogenesis News [amp ] Views Source Type: research

Expanding our scientific horizons: utilization of unique model organisms in biological research
During the past century, research studies using animal models have contributed to numerous scientific discoveries and have been vital for the understanding of numerous biological processes, including disease. Over the past decades, the scientific community has defined a small number of model organisms that includes a few mammals, fish (mainly zebrafish), birds (mainly chicken), frogs, flies, and nematodes. Rodents are by far the most commonly employed laboratory animals in biomedical research. Mice share many biological similarities to humans and can be genetically manipulated to express mutations linked to human diseases....
Source: EMBO Journal - August 15, 2017 Category: Molecular Biology Authors: Peter, A. K., Crocini, C., Leinwand, L. A. Tags: Molecular Biology of Disease Commentary Source Type: research

The endoplasmic reticulum HSP40 co-chaperone ERdj3/DNAJB11 assembles and functions as a tetramer
ERdj3/DNAJB11 is an endoplasmic reticulum (ER)-targeted HSP40 co-chaperone that performs multifaceted functions involved in coordinating ER and extracellular proteostasis. Here, we show that ERdj3 assembles into a native tetramer that is distinct from the dimeric structure observed for other HSP40 co-chaperones. An electron microscopy structural model of full-length ERdj3 shows that these tetramers are arranged as a dimer of dimers formed by distinct inter-subunit interactions involving ERdj3 domain II and domain III. Targeted deletion of residues 175-190 within domain II renders ERdj3 a stable dimer that is folded and eff...
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Chen, K.-C., Qu, S., Chowdhury, S., Noxon, I. C., Schonhoft, J. D., Plate, L., Powers, E. T., Kelly, J. W., Lander, G. C., Wiseman, R. L. Tags: Membrane & Intracellular Transport, Protein Biosynthesis & Quality Control, Structural Biology Articles Source Type: research

p21 maintains senescent cell viability under persistent DNA damage response by restraining JNK and caspase signaling
Cellular senescence is a permanent state of cell cycle arrest that protects the organism from tumorigenesis and regulates tissue integrity upon damage and during tissue remodeling. However, accumulation of senescent cells in tissues during aging contributes to age-related pathologies. A deeper understanding of the mechanisms regulating the viability of senescent cells is therefore required. Here, we show that the CDK inhibitor p21 (CDKN1A) maintains the viability of DNA damage-induced senescent cells. Upon p21 knockdown, senescent cells acquired multiple DNA lesions that activated ataxia telangiectasia mutated (ATM) and nu...
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Yosef, R., Pilpel, N., Papismadov, N., Gal, H., Ovadya, Y., Vadai, E., Miller, S., Porat, Z., Ben-Dor, S., Krizhanovsky, V. Tags: Cell Cycle, DNA Replication, Repair & Recombination, Molecular Biology of Disease Articles Source Type: research

Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation
Replacement of canonical histones with specialized histone variants promotes altering of chromatin structure and function. The essential histone variant H2A.Z affects various DNA-based processes via poorly understood mechanisms. Here, we determine the comprehensive interactome of H2A.Z and identify PWWP2A as a novel H2A.Z-nucleosome binder. PWWP2A is a functionally uncharacterized, vertebrate-specific protein that binds very tightly to chromatin through a concerted multivalent binding mode. Two internal protein regions mediate H2A.Z-specificity and nucleosome interaction, whereas the PWWP domain exhibits direct DNA binding...
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Pünzeler, S., Link, S., Wagner, G., Keilhauer, E. C., Kronbeck, N., Spitzer, R. M., Leidescher, S., Markaki, Y., Mentele, E., Regnard, C., Schneider, K., Takahashi, D., Kusakabe, M., Vardabasso, C., Zink, L. M., Straub, T., Bernstein, E., Harata, Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Structural basis of divergent cyclin-dependent kinase activation by Spy1/RINGO proteins
Cyclin-dependent kinases (Cdks) are principal drivers of cell division and are an important therapeutic target to inhibit aberrant proliferation. Cdk enzymatic activity is tightly controlled through cyclin interactions, posttranslational modifications, and binding of inhibitors such as the p27 tumor suppressor protein. Spy1/RINGO (Spy1) proteins bind and activate Cdk but are resistant to canonical regulatory mechanisms that establish cell-cycle checkpoints. Cancer cells exploit Spy1 to stimulate proliferation through inappropriate activation of Cdks, yet the mechanism is unknown. We have determined crystal structures of th...
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: McGrath, D. A., Fifield, B.-A., Marceau, A. H., Tripathi, S., Porter, L. A., Rubin, S. M. Tags: Cell Cycle, Structural Biology Articles Source Type: research

Glycosylation of KEAP1 links nutrient sensing to redox stress signaling
O-GlcNAcylation is an essential, nutrient-sensitive post-translational modification, but its biochemical and phenotypic effects remain incompletely understood. To address this question, we investigated the global transcriptional response to perturbations in O-GlcNAcylation. Unexpectedly, many transcriptional effects of O-GlcNAc transferase (OGT) inhibition were due to the activation of NRF2, the master regulator of redox stress tolerance. Moreover, we found that a signature of low OGT activity strongly correlates with NRF2 activation in multiple tumor expression datasets. Guided by this information, we identified KEAP1 (al...
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Chen, P.-H., Smith, T. J., Wu, J., Siesser, P. F., Bisnett, B. J., Khan, F., Hogue, M., Soderblom, E., Tang, F., Marks, J. R., Major, M. B., Swarts, B. M., Boyce, M., Chi, J.-T. Tags: Metabolism, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Fam60a defines a variant Sin3a-Hdac complex in embryonic stem cells required for self-renewal
Sin3a is the central scaffold protein of the prototypical Hdac1/2 chromatin repressor complex, crucially required during early embryonic development for the growth of pluripotent cells of the inner cell mass. Here, we compare the composition of the Sin3a-Hdac complex between pluripotent embryonic stem (ES) and differentiated cells by establishing a method that couples two independent endogenous immunoprecipitations with quantitative mass spectrometry. We define the precise composition of the Sin3a complex in multiple cell types and identify the Fam60a subunit as a key defining feature of a variant Sin3a complex present in ...
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Streubel, G., Fitzpatrick, D. J., Oliviero, G., Scelfo, A., Moran, B., Das, S., Munawar, N., Watson, A., Wynne, K., Negri, G. L., Dillon, E. T., Jammula, S., Hokamp, K., O'Connor, D. P., Pasini, D., Cagney, G., Bracken, A. P. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Stem Cells, Transcription Articles Source Type: research

Structural and functional dissection of the interplay between lipid and Notch binding by human Notch ligands
We present novel structures of human ligands Jagged2 and Delta-like4 and human Notch2, together with functional assays, which suggest that ligand-mediated coupling of membrane recognition and Notch binding is likely to be critical in establishing the optimal context for Notch signalling. Comparisons between the Jagged and Delta family show a huge diversity in the structures of the loops at the apex of the C2 domain implicated in membrane recognition and Jagged1 missense mutations, which affect these loops and are associated with extrahepatic biliary atresia, lead to a loss of membrane recognition, but do not alter Notch bi...
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Suckling, R. J., Korona, B., Whiteman, P., Chillakuri, C., Holt, L., Handford, P. A., Lea, S. M. Tags: Signal Transduction, Structural Biology Articles Source Type: research

Endothelial cell metabolism in health and disease: impact of hypoxia
In contrast to the general belief, endothelial cell (EC) metabolism has recently been identified as a driver rather than a bystander effect of angiogenesis in health and disease. Indeed, different EC subtypes present with distinct metabolic properties, which determine their function in angiogenesis upon growth factor stimulation. One of the main stimulators of angiogenesis is hypoxia, frequently observed in disease settings such as cancer and atherosclerosis. It has long been established that hypoxic signalling and metabolism changes are highly interlinked. In this review, we will provide an overview of the literature and ...
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Wong, B. W., Marsch, E., Treps, L., Baes, M., Carmeliet, P. Tags: Metabolism, Molecular Biology of Disease, Vascular Biology & Angiogenesis Review Source Type: research

A new twist to Sin3 complexes in pluripotent cells
Sin3a is a central component of a class of histone deacetylase-containing transcriptional co-regulatory complexes. In this issue of The EMBO Journal, Streubel et al (2017) purify Sin3a and identify a variant Sin3a complex containing Fam60a in undifferentiated embryonic stem cells (ESCs). Fam60a is a critical component of the ESC Sin3a complex since Fam60a knockdown leads to an extended G1 cell cycle phase and reduced ESC self-renewal. These exciting results open up new questions about how biochemical differences between variant Sin3a complexes may facilitate alterations in cell-specific function. (Source: EMBO Journal)
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Pantier, R., Mullin, N. P., Chambers, I. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Stem Cells, Transcription News [amp ] Views Source Type: research

The lipid-binding side of Notch ligands
Notch signaling is adjusted to different physiological contexts by expression patterns of Notch ligands and receptors, as well as by posttranslational modifications that modulate the ligand/receptor affinity. In this issue of The EMBO Journal, Suckling et al (2017) show that an interaction of Notch ligands with membrane lipids promotes Notch binding and activation, thus proposing a new mode of Notch activity regulation. (Source: EMBO Journal)
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Shilo, B.-Z., Sprinzak, D. Tags: Signal Transduction, Structural Biology News [amp ] Views Source Type: research

Mitochondrial genome inheritance and replacement in the human germline
Mitochondria, the ubiquitous power packs in nearly every eukaryotic cell, contain their own DNA, known as mtDNA, which is inherited exclusively from the mother. The number of mitochondrial genomes varies depending on the cell's energy needs. The mature oocyte contains the highest number of mitochondria of any cell type, although there is little if any mtDNA replication after fertilization until the embryo implants. This has potential repercussions for mitochondrial replacement therapy (MRT; see description of currently employed methods below) used to prevent the transmission of mtDNA-based disorders. If only a few mitochon...
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Wolf, D. P., Hayama, T., Mitalipov, S. Tags: Genetics, Gene Therapy & Genetic Disease, Metabolism, Molecular Biology of Disease Commentary Source Type: research

ATM/Wip1 activities at chromatin control Plk1 re-activation to determine G2 checkpoint duration
After DNA damage, the cell cycle is arrested to avoid propagation of mutations. Arrest in G2 phase is initiated by ATM-/ATR-dependent signaling that inhibits mitosis-promoting kinases such as Plk1. At the same time, Plk1 can counteract ATR-dependent signaling and is required for eventual resumption of the cell cycle. However, what determines when Plk1 activity can resume remains unclear. Here, we use FRET-based reporters to show that a global spread of ATM activity on chromatin and phosphorylation of ATM targets including KAP1 control Plk1 re-activation. These phosphorylations are rapidly counteracted by the chromatin-boun...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Jaiswal, H., Benada, J., Müllers, E., Akopyan, K., Burdova, K., Koolmeister, T., Helleday, T., Medema, R. H., Macurek, L., Lindqvist, A. Tags: Cell Cycle, DNA Replication, Repair & Recombination Articles Source Type: research

Autotaxin-lysophosphatidic acid-LPA3 signaling at the embryo-epithelial boundary controls decidualization pathways
During pregnancy, up-regulation of heparin-binding (HB-) EGF and cyclooxygenase-2 (COX-2) in the uterine epithelium contributes to decidualization, a series of uterine morphological changes required for placental formation and fetal development. Here, we report a key role for the lipid mediator lysophosphatidic acid (LPA) in decidualization, acting through its G-protein-coupled receptor LPA3 in the uterine epithelium. Knockout of Lpar3 or inhibition of the LPA-producing enzyme autotaxin (ATX) in pregnant mice leads to HB-EGF and COX-2 down-regulation near embryos and attenuates decidual reactions. Conversely, selective pha...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Aikawa, S., Kano, K., Inoue, A., Wang, J., Saigusa, D., Nagamatsu, T., Hirota, Y., Fujii, T., Tsuchiya, S., Taketomi, Y., Sugimoto, Y., Murakami, M., Arita, M., Kurano, M., Ikeda, H., Yatomi, Y., Chun, J., Aoki, J. Tags: Development & Differentiation, Signal Transduction Articles Source Type: research

OPA1 deficiency promotes secretion of FGF21 from muscle that prevents obesity and insulin resistance
Mitochondrial dynamics is a conserved process by which mitochondria undergo repeated cycles of fusion and fission, leading to exchange of mitochondrial genetic content, ions, metabolites, and proteins. Here, we examine the role of the mitochondrial fusion protein optic atrophy 1 (OPA1) in differentiated skeletal muscle by reducing OPA1 gene expression in an inducible manner. OPA1 deficiency in young mice results in non-lethal progressive mitochondrial dysfunction and loss of muscle mass. Mutant mice are resistant to age- and diet-induced weight gain and insulin resistance, by mechanisms that involve activation of ER stress...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Pereira, R. O., Tadinada, S. M., Zasadny, F. M., Oliveira, K. J., Pires, K. M. P., Olvera, A., Jeffers, J., Souvenir, R., Mcglauflin, R., Seei, A., Funari, T., Sesaki, H., Potthoff, M. J., Adams, C. M., Anderson, E. J., Abel, E. D. Tags: Ageing, Metabolism, Molecular Biology of Disease Articles Source Type: research

A TRPV1-to-secretagogin regulatory axis controls pancreatic {beta}-cell survival by modulating protein turnover
Ca2+-sensor proteins are generally implicated in insulin release through SNARE interactions. Here, secretagogin, whose expression in human pancreatic islets correlates with their insulin content and the incidence of type 2 diabetes, is shown to orchestrate an unexpectedly distinct mechanism. Single-cell RNA-seq reveals retained expression of the TRP family members in β-cells from diabetic donors. Amongst these, pharmacological probing identifies Ca2+-permeable transient receptor potential vanilloid type 1 channels (TRPV1) as potent inducers of secretagogin expression through recruitment of Sp1 transcription factors. A...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Malenczyk, K., Girach, F., Szodorai, E., Storm, P., Segerstolpe, A., Tortoriello, G., Schnell, R., Mulder, J., Romanov, R. A., Borok, E., Piscitelli, F., Di Marzo, V., Szabo, G., Sandberg, R., Kubicek, S., Lubec, G., Hökfelt, T., Wagner, L., Groop Tags: Molecular Biology of Disease, Signal Transduction Articles Source Type: research