Don't judge a cell by its cover: heterogeneity within early lymphoid progenitors
B-cell differentiation is one of the most recognized examples of the progressive lineage commitment that is distinctive for stem cell systems. However, the characteristics of the stage just before a cell becomes restricted to the B-cell lineage are less understood. Using single-cell RNA sequencing technology, Rolink and colleagues are able to define the cellular heterogeneity at this step and challenge our understanding of developmental trajectories in early B-lymphoid development (Alberti-Servera et al, 2017). (Source: EMBO Journal)
Source: EMBO Journal - December 15, 2017 Category: Molecular Biology Authors: Karlsson, G., Sigvardsson, M., Böiers, C. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Development & Differentiation, Immunology News [amp ] Views Source Type: research

Cohesin: building loops, but not compartments
DNA is subjected to major cellular events, such as transcription, replication and DNA repair. To control these processes, the architecture of the DNA is tightly regulated. Recent work, including two studies in this issue of The EMBO Journal, provides compelling evidence that cohesin structures chromosomes through the processive enlargement of loops. While cohesin promotes chromosomal looping, it rather counteracts nuclear compartmentalization. (Source: EMBO Journal)
Source: EMBO Journal - December 15, 2017 Category: Molecular Biology Authors: Haarhuis, J. H., Rowland, B. D. Tags: Cell Cycle, Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination News [amp ] Views Source Type: research

Human THO-Sin3A interaction reveals new mechanisms to prevent R-loops that cause genome instability
R-loops, formed by co-transcriptional DNA–RNA hybrids and a displaced DNA single strand (ssDNA), fulfill certain positive regulatory roles but are also a source of genomic instability. One key cellular mechanism to prevent R-loop accumulation centers on the conserved THO/TREX complex, an RNA-binding factor involved in transcription elongation and RNA export that contributes to messenger ribonucleoprotein (mRNP) assembly, but whose precise function is still unclear. To understand how THO restrains harmful R-loops, we searched for new THO-interacting factors. We found that human THO interacts with the Sin3A histone dea...
Source: EMBO Journal - December 1, 2017 Category: Molecular Biology Authors: Salas-Armenteros, I., Perez-Calero, C., Bayona-Feliu, A., Tumini, E., Luna, R., Aguilera, A. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination, RNA Biology Articles Source Type: research

Hierarchical protein targeting and secretion is controlled by an affinity switch in the type III secretion system of enteropathogenic Escherichia coli
Type III secretion (T3S), a protein export pathway common to Gram-negative pathogens, comprises a trans-envelope syringe, the injectisome, with a cytoplasm-facing translocase channel. Exported substrates are chaperone-delivered to the translocase, EscV in enteropathogenic Escherichia coli, and cross it in strict hierarchical manner, for example, first "translocators", then "effectors". We dissected T3S substrate targeting and hierarchical switching by reconstituting them in vitro using inverted inner membrane vesicles. EscV recruits and conformationally activates the tightly membrane-associated pse...
Source: EMBO Journal - December 1, 2017 Category: Molecular Biology Authors: Portaliou, A. G., Tsolis, K. C., Loos, M. S., Balabanidou, V., Rayo, J., Tsirigotaki, A., Crepin, V. F., Frankel, G., Kalodimos, C. G., Karamanou, S., Economou, A. Tags: Membrane & Intracellular Transport, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

A TNF-p100 pathway subverts noncanonical NF-{kappa}B signaling in inflamed secondary lymphoid organs
Lymphotoxin-beta receptor (LTβR) present on stromal cells engages the noncanonical NF-B pathway to mediate RelB-dependent expressions of homeostatic chemokines, which direct steady-state ingress of naìˆve lymphocytes to secondary lymphoid organs (SLOs). In this pathway, NIK promotes partial proteolysis of p100 into p52 that induces nuclear translocation of the RelB NF-B heterodimers. Microbial infections often deplete homeostatic chemokines; it is thought that infection-inflicted destruction of stromal cells results in the downregulation of these chemokines. Whether inflammation per se also regulates these processes ...
Source: EMBO Journal - December 1, 2017 Category: Molecular Biology Authors: Mukherjee, T., Chatterjee, B., Dhar, A., Bais, S. S., Chawla, M., Roy, P., George, A., Bal, V., Rath, S., Basak, S. Tags: Immunology, Signal Transduction Articles Source Type: research

The p53-inducible long noncoding RNA TRINGS protects cancer cells from necrosis under glucose starvation
The tumor suppressor p53 is activated in response to cellular stress to prevent malignant transformation. However, several recent studies have shown that p53 can play protective roles in tumor cell survival under adversity. Whether p53-regulated long noncoding RNAs are involved in this process remains to be fully understood. Here, we show that under glucose starvation condition, p53 directly upregulates a novel lncRNA named TRINGS (Tp53-regulated inhibitor of necrosis under glucose starvation) in human tumor cells. TRINGS binds to STRAP and inhibits STRAP–GSK3β–NF-B necrotic signaling to protect tumor cell...
Source: EMBO Journal - December 1, 2017 Category: Molecular Biology Authors: Khan, M. R., Xiang, S., Song, Z., Wu, M. Tags: Cancer, Autophagy & Cell Death, Signal Transduction Articles Source Type: research

Molecular basis for inner kinetochore configuration through RWD domain-peptide interactions
Kinetochores are dynamic cellular structures that connect chromosomes to microtubules. They form from multi-protein assemblies that are evolutionarily conserved between yeasts and humans. One of these assemblies—COMA—consists of subunits Ame1CENP-U, Ctf19CENP-P, Mcm21CENP-O and Okp1CENP-Q. A description of COMA molecular organization has so far been missing. We defined the subunit topology of COMA, bound with inner kinetochore proteins Nkp1 and Nkp2, from the yeast Kluyveromyces lactis, with nanoflow electrospray ionization mass spectrometry, and mapped intermolecular contacts with hydrogen-deuterium exchange c...
Source: EMBO Journal - December 1, 2017 Category: Molecular Biology Authors: Schmitzberger, F., Richter, M. M., Gordiyenko, Y., Robinson, C. V., Dadlez, M., Westermann, S. Tags: Cell Cycle, Structural Biology Articles Source Type: research

Real-time detection of condensin-driven DNA compaction reveals a multistep binding mechanism
Condensin, a conserved member of the SMC protein family of ring-shaped multi-subunit protein complexes, is essential for structuring and compacting chromosomes. Despite its key role, its molecular mechanism has remained largely unknown. Here, we employ single-molecule magnetic tweezers to measure, in real time, the compaction of individual DNA molecules by the budding yeast condensin complex. We show that compaction can proceed in large steps, driving DNA molecules into a fully condensed state against forces of up to 2 pN. Compaction can be reversed by applying high forces or adding buffer of high ionic strength. Whil...
Source: EMBO Journal - December 1, 2017 Category: Molecular Biology Authors: Eeftens, J. M., Bisht, S., Kerssemakers, J., Kschonsak, M., Haering, C. H., Dekker, C. Tags: Cell Cycle, Chromatin, Epigenetics, Genomics & Functional Genomics, Structural Biology Articles Source Type: research

KTN80 confers precision to microtubule severing by specific targeting of katanin complexes in plant cells
The microtubule (MT)-severing enzyme katanin triggers dynamic reorientation of cortical MT arrays that play crucial functions during plant cell morphogenesis, such as cell elongation, cell wall biosynthesis, and hormonal signaling. MT severing specifically occurs at crossover or branching nucleation sites in living Arabidopsis cells. This differs from the random severing observed along the entire length of single MTs in vitro and strongly suggests that a precise control mechanism must exist in vivo. However, how katanin senses and cleaves at MT crossover and branching nucleation sites in vivo has remained un...
Source: EMBO Journal - December 1, 2017 Category: Molecular Biology Authors: Wang, C., Liu, W., Wang, G., Li, J., Dong, L., Han, L., Wang, Q., Tian, J., Yu, Y., Gao, C., Kong, Z. Tags: Cell Adhesion, Polarity & Cytoskeleton, Plant Biology Articles Source Type: research

Isoform-specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands
DNA methylation is a prevalent epigenetic modification involved in transcriptional regulation and essential for mammalian development. While the genome-wide distribution of this mark has been studied to great detail, the mechanisms responsible for its correct deposition, as well as the cause for its aberrant localization in cancers, have not been fully elucidated. Here, we have compared the activity of individual DNMT3A isoforms in mouse embryonic stem and neuronal progenitor cells and report that these isoforms differ in their genomic binding and DNA methylation activity at regulatory sites. We identify that the longer is...
Source: EMBO Journal - December 1, 2017 Category: Molecular Biology Authors: Manzo, M., Wirz, J., Ambrosi, C., Villasenor, R., Roschitzki, B., Baubec, T. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription Articles Source Type: research

MYC and tumor metabolism: chicken and egg
Transcription factors of the MYC family are deregulated in the majority of all human cancers. Oncogenic levels of MYC reprogram cellular metabolism, a hallmark of cancer development, to sustain the high rate of proliferation of cancer cells. Conversely, cells need to modulate MYC function according to the availability of nutrients, in order to avoid a metabolic collapse. Here, we review recent evidence that the multiple interactions of MYC with cell metabolism are mutual and review mechanisms that control MYC levels and function in response to metabolic stress situations. The main hypothesis we put forward is that regulati...
Source: EMBO Journal - December 1, 2017 Category: Molecular Biology Authors: Dejure, F. R., Eilers, M. Tags: Cancer, Metabolism Review Source Type: research

Shoring up DNA methylation and H3K27me3 domain demarcation at developmental genes
Mutual antagonism between DNA methylation and H3K27me3 histone methylation suggests a dynamic crosstalk between these epigenetic marks that could help ensure correct gene expression programmes. Work from Manzo et al (2017) now shows that an isoform of de novo DNA methyltransferase DNMT3A provides specificity in the system by depositing DNA methylation at adjacent "shores" of hypomethylated bivalent CpG islands (CGI) in mouse embryonic stem cells (mESCs). DNMT3A1-directed methylation appears to be instructive in maintaining the H3K27me3 profile at the hypomethylated bivalent CGI promoters of developmenta...
Source: EMBO Journal - December 1, 2017 Category: Molecular Biology Authors: Meehan, R. R., Pennings, S. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription News [amp ] Views Source Type: research

Rab35 GTPase recruits NDP52 to autophagy targets
(Source: EMBO Journal)
Source: EMBO Journal - November 15, 2017 Category: Molecular Biology Authors: Minowa-Nozawa, A., Nozawa, T., Okamoto-Furuta, K., Kohda, H., Nakagawa, I. Tags: Erratum Source Type: research

Combinatorial regulation of the balance between dynein microtubule end accumulation and initiation of directed motility
Cytoplasmic dynein is involved in a multitude of essential cellular functions. Dynein's activity is controlled by the combinatorial action of several regulatory proteins. The molecular mechanism of this regulation is still poorly understood. Using purified proteins, we reconstitute the regulation of the human dynein complex by three prominent regulators on dynamic microtubules in the presence of end binding proteins (EBs). We find that dynein can be in biochemically and functionally distinct pools: either tracking dynamic microtubule plus-ends in an EB-dependent manner or moving processively towards minus ends in an adapto...
Source: EMBO Journal - November 15, 2017 Category: Molecular Biology Authors: Jha, R., Roostalu, J., Cade, N. I., Trokter, M., Surrey, T. Tags: Cell Adhesion, Polarity & Cytoskeleton, Membrane & Intracellular Transport Articles Source Type: research

Chromatin remodeler CHD1 promotes XPC-to-TFIIH handover of nucleosomal UV lesions in nucleotide excision repair
Ultraviolet (UV) light induces mutagenic cyclobutane pyrimidine dimers (CPDs) in nucleosomal DNA that is tightly wrapped around histone octamers. How global-genome nucleotide excision repair (GG-NER) processes CPDs despite that this chromatin arrangement is poorly understood. An increased chromatin association of CHD1 (chromodomain helicase DNA-binding 1) upon UV irradiation indicated possible roles of this chromatin remodeler in the UV damage response. Immunoprecipitation of chromatin fragments revealed that CHD1 co-localizes in part with GG-NER factors. Chromatin fractionation showed that the UV-dependent recruitment of ...
Source: EMBO Journal - November 15, 2017 Category: Molecular Biology Authors: Rüthemann, P., Balbo Pogliano, C., Codilupi, T., Garajova, Z., Naegeli, H. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination Articles Source Type: research

Increased localization of APP-C99 in mitochondria-associated ER membranes causes mitochondrial dysfunction in Alzheimer disease
In the amyloidogenic pathway associated with Alzheimer disease (AD), the amyloid precursor protein (APP) is cleaved by β-secretase to generate a 99-aa C-terminal fragment (C99) that is then cleaved by -secretase to generate the β-amyloid (Aβ) found in senile plaques. In previous reports, we and others have shown that -secretase activity is enriched in mitochondria-associated endoplasmic reticulum (ER) membranes (MAM) and that ER–mitochondrial connectivity and MAM function are upregulated in AD. We now show that C99, in addition to its localization in endosomes, can also be found in MAM, where it is nor...
Source: EMBO Journal - November 15, 2017 Category: Molecular Biology Authors: Pera, M., Larrea, D., Guardia-Laguarta, C., Montesinos, J., Velasco, K. R., Agrawal, R. R., Xu, Y., Chan, R. B., Di Paolo, G., Mehler, M. F., Perumal, G. S., Macaluso, F. P., Freyberg, Z. Z., Acin-Perez, R., Enriquez, J. A., Schon, E. A., Area-Gomez, E. Tags: Membrane & Intracellular Transport, Metabolism, Neuroscience Articles Source Type: research

Tumor-associated macrophages (TAMs) depend on ZEB1 for their cancer-promoting roles
Accumulation of tumor-associated macrophages (TAMs) associates with malignant progression in cancer. However, the mechanisms that drive the pro-tumor functions of TAMs are not fully understood. ZEB1 is best known for driving an epithelial-to-mesenchymal transition (EMT) in cancer cells to promote tumor progression. However, a role for ZEB1 in macrophages and TAMs has not been studied. Here we describe that TAMs require ZEB1 for their tumor-promoting and chemotherapy resistance functions in a mouse model of ovarian cancer. Only TAMs that expressed full levels of Zeb1 accelerated tumor growth. Mechanistically, ZEB1 expressio...
Source: EMBO Journal - November 15, 2017 Category: Molecular Biology Authors: Cortes, M., Sanchez-Moral, L., de Barrios, O., Fernandez-Acenero, M. J., Martinez-Campanario, M., Esteve-Codina, A., Darling, D. S., Gyorffy, B., Lawrence, T., Dean, D. C., Postigo, A. Tags: Cancer, Molecular Biology of Disease, Signal Transduction Articles Source Type: research

LncRNA wires up Hippo and Hedgehog signaling to reprogramme glucose metabolism
In this study, we report that lncRNA breast cancer anti-estrogen resistance 4 (BCAR4) is required for YAP-dependent glycolysis. Mechanistically, YAP promotes the expression of BCAR4, which subsequently coordinates the Hedgehog signaling to enhance the transcription of glycolysis activators HK2 and PFKFB3. Therapeutic delivery of locked nucleic acids (LNAs) targeting BCAR4 attenuated YAP-dependent glycolysis and tumor growth. The expression levels of BCAR4 and YAP are positively correlated in tissue samples from breast cancer patients, where high expression of both BCAR4 and YAP is associated with poor patient survival outc...
Source: EMBO Journal - November 15, 2017 Category: Molecular Biology Authors: Zheng, X., Han, H., Liu, G.-P., Ma, Y.-X., Pan, R.-L., Sang, L.-J., Li, R.-H., Yang, L.-J., Marks, J. R., Wang, W., Lin, A. Tags: Cancer, Metabolism, Signal Transduction Articles Source Type: research

The organic anion transporter SLCO2A1 constitutes the core component of the Maxi-Cl channel
The maxi-anion channels (MACs) are expressed in cells from mammals to amphibians with ~60% exhibiting a phenotype called Maxi-Cl. Maxi-Cl serves as the most efficient pathway for regulated fluxes of inorganic and organic anions including ATP. However, its molecular entity has long been elusive. By subjecting proteins isolated from bleb membranes rich in Maxi-Cl activity to LC-MS/MS combined with targeted siRNA screening, CRISPR/Cas9-mediated knockout, and heterologous overexpression, we identified the organic anion transporter SLCO2A1, known as a prostaglandin transporter (PGT), as a key component of Maxi-Cl. Recombinant S...
Source: EMBO Journal - November 15, 2017 Category: Molecular Biology Authors: Sabirov, R. Z., Merzlyak, P. G., Okada, T., Islam, M. R., Uramoto, H., Mori, T., Makino, Y., Matsuura, H., Xie, Y., Okada, Y. Tags: Membrane & Intracellular Transport Articles Source Type: research

A novel microglial subset plays a key role in myelinogenesis in developing brain
Microglia are resident macrophages of the central nervous system that contribute to homeostasis and neuroinflammation. Although known to play an important role in brain development, their exact function has not been fully described. Here, we show that in contrast to healthy adult and inflammation-activated cells, neonatal microglia show a unique myelinogenic and neurogenic phenotype. A CD11c+ microglial subset that predominates in primary myelinating areas of the developing brain expresses genes for neuronal and glial survival, migration, and differentiation. These cells are the major source of insulin-like growth factor 1...
Source: EMBO Journal - November 15, 2017 Category: Molecular Biology Authors: Wlodarczyk, A., Holtman, I. R., Krueger, M., Yogev, N., Bruttger, J., Khorooshi, R., Benmamar-Badel, A., de Boer-Bergsma, J. J., Martin, N. A., Karram, K., Kramer, I., Boddeke, E. W., Waisman, A., Eggen, B. J., Owens, T. Tags: Immunology, Neuroscience Articles Source Type: research

Membrane scission driven by the PROPPIN Atg18
Sorting, transport, and autophagic degradation of proteins in endosomes and lysosomes, as well as the division of these organelles, depend on scission of membrane-bound tubulo-vesicular carriers. How scission occurs is poorly understood, but family proteins bind these membranes. Here, we show that the yeast PROPPIN Atg18 carries membrane scission activity. Purified Atg18 drives tubulation and scission of giant unilamellar vesicles. Upon membrane contact, Atg18 folds its unstructured CD loop into an amphipathic α-helix that inserts into the bilayer. This allows the protein to engage its two lipid binding sites for PI3...
Source: EMBO Journal - November 15, 2017 Category: Molecular Biology Authors: Gopaldass, N., Fauvet, B., Lashuel, H., Roux, A., Mayer, A. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport Articles Source Type: research

Channel surfing uncovers a dual-use transporter
Beyond their roles in generating nerve impulses, ion channels are important for many facets of cell biology, including swelling and osmotic stress responses. Sabirov and colleagues now report that the prostaglandin transporter SLCO2A1 is a central component of the ubiquitous Maxi-Cl anion channel. These findings add to a growing number of transporters displaying ion channel activity and not only provide a molecular handle for future Maxi-Cl physiological and biophysical studies, but also underscore general questions about the principles that underlie such transporter/channel dual-use behavior. (Source: EMBO Journal)
Source: EMBO Journal - November 15, 2017 Category: Molecular Biology Authors: Minor, D. L. Tags: Membrane & Intracellular Transport News [amp ] Views Source Type: research

A genetically distinct microglial subset promotes myelination
Microglia are brain-resident macrophages with important, but insufficiently understood functions in development, health, and disease. In a new exciting study, Wlodarczyk and colleagues uncover a transient subset of CD11c+ microglia that regulate CNS myelination via IGF-1 expression. These findings represent not only the first evidence for a microglial role in myelinogenesis, but the first for a functionally distinct, genetically defined subpopulation of microglia. (Source: EMBO Journal)
Source: EMBO Journal - November 15, 2017 Category: Molecular Biology Authors: Bennett, M. L., Barres, B. A. Tags: Immunology, Neuroscience News [amp ] Views Source Type: research

Crosstalk between PKA and PKG controls pH-dependent host cell egress of Toxoplasma gondii
Toxoplasma gondii encodes three protein kinase A catalytic (PKAc1-3) and one regulatory (PKAr) subunits to integrate cAMP-dependent signals. Here, we show that inactive PKAc1 is maintained at the parasite pellicle by interacting with acylated PKAr. Either a conditional knockdown of PKAr or the overexpression of PKAc1 blocks parasite division. Conversely, down-regulation of PKAc1 or stabilisation of a dominant-negative PKAr isoform that does not bind cAMP triggers premature parasite egress from infected cells followed by serial invasion attempts leading to host cell lysis. This untimely egress depends on host cell acidifica...
Source: EMBO Journal - November 2, 2017 Category: Molecular Biology Authors: Jia, Y., Marq, J.-B., Bisio, H., Jacot, D., Mueller, C., Yu, L., Choudhary, J., Brochet, M., Soldati-Favre, D. Tags: Microbiology, Virology & Host Pathogen Interaction, Signal Transduction Articles Source Type: research

RBPJ/CBF1 interacts with L3MBTL3/MBT1 to promote repression of Notch signaling via histone demethylase KDM1A/LSD1
Notch signaling is an evolutionarily conserved signal transduction pathway that is essential for metazoan development. Upon ligand binding, the Notch intracellular domain (NOTCH ICD) translocates into the nucleus and forms a complex with the transcription factor RBPJ (also known as CBF1 or CSL) to activate expression of Notch target genes. In the absence of a Notch signal, RBPJ acts as a transcriptional repressor. Using a proteomic approach, we identified L3MBTL3 (also known as MBT1) as a novel RBPJ interactor. L3MBTL3 competes with NOTCH ICD for binding to RBPJ. In the absence of NOTCH ICD, RBPJ recruits L3MBTL3 and the h...
Source: EMBO Journal - November 2, 2017 Category: Molecular Biology Authors: Xu, T., Park, S.-S., Giaimo, B. D., Hall, D., Ferrante, F., Ho, D. M., Hori, K., Anhezini, L., Ertl, I., Bartkuhn, M., Zhang, H., Milon, E., Ha, K., Conlon, K. P., Kuick, R., Govindarajoo, B., Zhang, Y., Sun, Y., Dou, Y., Basrur, V., Elenitoba-Johnson, K. Tags: Signal Transduction, Transcription Articles Source Type: research

Initiation of DNA replication requires actin dynamics and formin activity
Nuclear actin regulates transcriptional programmes in a manner dependent on its levels and polymerisation state. This dynamics is determined by the balance of nucleocytoplasmic shuttling, formin- and redox-dependent filament polymerisation. Here, using Xenopus egg extracts and human somatic cells, we show that actin dynamics and formins are essential for DNA replication. In proliferating cells, formin inhibition abolishes nuclear transport and initiation of DNA replication, as well as general transcription. In replicating nuclei from transcriptionally silent Xenopus egg extracts, we identified numerous actin regulators, an...
Source: EMBO Journal - November 2, 2017 Category: Molecular Biology Authors: Parisis, N., Krasinska, L., Harker, B., Urbach, S., Rossignol, M., Camasses, A., Dewar, J., Morin, N., Fisher, D. Tags: Cell Adhesion, Polarity & Cytoskeleton, DNA Replication, Repair & Recombination Articles Source Type: research

Aubergine and piRNAs promote germline stem cell self-renewal by repressing the proto-oncogene Cbl
This study reveals the role of piRNAs and PIWI proteins in controlling stem cell homeostasis via translational repression and highlights piRNAs as major post-transcriptional regulators in key developmental decisions. (Source: EMBO Journal)
Source: EMBO Journal - November 2, 2017 Category: Molecular Biology Authors: Rojas-Rios, P., Chartier, A., Pierson, S., Simonelig, M. Tags: Development & Differentiation, RNA Biology, Stem Cells Articles Source Type: research

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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