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The EMBO Journal

Cover image for Vol. 31 Issue 3

February 1, 2012

Volume 31, Issue 3

Pages 515–779

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      RNA driving the epigenetic bus (pages 515–516)

      John S Mattick

      Article first published online: 1 FEB 2012 | DOI: 10.1038/emboj.2011.479

      Data on the biological significance of long non-coding RNAs remain scarce. Recent work functionally annotated long non-coding RNAs in both mice and humans with an emphasis on pluripotency and neural differentiation.

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      Rac1 gets fattier (pages 517–518)

      Frederick D Tsai and Mark R Philips

      Article first published online: 1 FEB 2012 | DOI: 10.1038/emboj.2011.481

      The identification of Rac1 palmitoylation reveals how Rac1 changes subcellular localization to modulate its signalling function.

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      A structural road map to unveil basal body composition and assembly (pages 519–521)

      Swadhin C Jana, Pedro Machado and Mónica Bettencourt-Dias

      Article first published online: 1 FEB 2012 | DOI: 10.1038/emboj.2011.474

      The Basal Body is the template for the axoneme, the internal scaffolding of cilia andflagella. Bettencourt-Dias and colleagues comment on an article by DavidAgard's group, in which they characterize the structure of the basal body byelectron cryo-tomography and reveal new clues into its biogenesis and function.

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      Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors (pages 522–533)

      Shi-Yan Ng, Rory Johnson and Lawrence W Stanton

      Article first published online: 23 DEC 2011 | DOI: 10.1038/emboj.2011.459

      An array-based approach identifies hESC-specific novel long non-coding RNAs (lncRNAs) that are essential for the maintenance of pluripotency and indispensable for neuronal differentiation. A number of these lncRNAs directly interact with the pluripotency regulators SOX2 and PRC2.

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      A palmitoylation switch mechanism regulates Rac1 function and membrane organization (pages 534–551)

      Inmaculada Navarro-Lérida, Sara Sánchez-Perales, María Calvo, Carles Rentero, Yi Zheng, Carlos Enrich and Miguel A Del Pozo

      Article first published online: 9 DEC 2011 | DOI: 10.1038/emboj.2011.446

      Activity of the small GTPase Rac1 is linked to its membrane recruitment. Like Rho GTPases, Rac1 is palmitoylated, targeting it to membrane microdomains and promoting its activity, thus contributing to the spatial regulation of actin dynamics.

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      Three-dimensional structure of basal body triplet revealed by electron cryo-tomography (pages 552–562)

      Sam Li, Jose-Jesus Fernandez, Wallace F Marshall and David A Agard

      Article first published online: 13 DEC 2011 | DOI: 10.1038/emboj.2011.460

      The basal body, derived from the centriole, is a microtubule-organizing organelle that nucleates the cilium in non-dividing cells. Cryo-electron tomography reveals the overall structure of this organelle, and provides insights its biogenesis and function.

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      H2O2 stress-specific regulation of S. pombe MAPK Sty1 by mitochondrial protein phosphatase Ptc4 (pages 563–575)

      Yujun Di, Emily J Holmes, Amna Butt, Keren Dawson, Aleksandr Mironov, Vassilios N Kotiadis, Campbell W Gourlay, Nic Jones and Caroline R M Wilkinson

      Article first published online: 2 DEC 2011 | DOI: 10.1038/emboj.2011.438

      The PP2C phosphatase Ptc4 regulates the MAPK Sty1 upon oxidative stress. With Ptc4 localizing to the mitochondria by a targeting sequence that is cleaved upon import, the study proposes the regulation of MAPKs by specific phosphatases to also take place within mitochondria.

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      Positive regulation of p53 stability and activity by the deubiquitinating enzyme Otubain 1 (pages 576–592)

      Xiao-Xin Sun, Kishore B Challagundla and Mu-Shui Dai

      Article first published online: 29 NOV 2011 | DOI: 10.1038/emboj.2011.434

      The deubiquitinating enzyme Otubain 1 regulates MDM2-mediated p53 ubiquitination in a non-catalytic manner, by binding and suppressing the activity of MDM2's cognate ubiquitin-conjugating enzyme UbcH5.

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      NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression (pages 593–605)

      Nicola Reynolds, Mali Salmon-Divon, Heidi Dvinge, Antony Hynes-Allen, Gayan Balasooriya, Donna Leaford, Axel Behrens, Paul Bertone and Brian Hendrich

      Article first published online: 2 DEC 2011 | DOI: 10.1038/emboj.2011.431

      The NURD and Polycomb complexes PRC1 and PRC2 have been implicated in stem cell differentiation although their molecular roles are unclear. This study identifies a common set of genes that are sequentially regulated by these complexes, the NURD complex deacetylates H3K27 as a prerequisite for subsequent methylation by PRC2.

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      Transcription and histone methylation changes correlate with imprint acquisition in male germ cells (pages 606–615)

      Amandine Henckel, Karim Chebli, Satya K Kota, Philippe Arnaud and Robert Feil

      Article first published online: 25 NOV 2011 | DOI: 10.1038/emboj.2011.425

      The changes in chromatin state associated with the establishment of paternal genomic imprints in male germ cells are currently unclear. This study describes a correlation between histone H3 lysine methylation, active transcription and the establishment of DNA methylation at imprinted loci in male germ cells.

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      The histone methyltransferase Setd8 acts in concert with c-Myc and is required to maintain skin (pages 616–629)

      Iwona Driskell, Hisanobu Oda, Sandra Blanco, Elisabete Nascimento, Peter Humphreys and Michaela Frye

      Article first published online: 25 NOV 2011 | DOI: 10.1038/emboj.2011.421

      Keratinocyte-specific ablation of the histone H4K20 methyltransferase Setd8 reveals its essential role in embryonic and postnatal skin homeostasis. Molecularly, the c-myc target gene Setd8 regulates proliferation/differentiation by controlling p63 function.

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      Factor-independent transcription pausing caused by recognition of the RNA–DNA hybrid sequence (pages 630–639)

      Aleksandra Bochkareva, Yulia Yuzenkova, Vasisht R Tadigotla and Nikolay Zenkin

      Article first published online: 29 NOV 2011 | DOI: 10.1038/emboj.2011.432

      RNA polymerase pausing during transcription is implicated in controlling gene expression. This study identifies a new type of pausing mechanism, by which the RNAP core recognizes the shape of base pairs of the RNA–DNA hybrid, which determines the rate of translocation and the nucleotide addition cycle. The expression of a number of viral and bacterial genes is shown to be subject to this mechanism.

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      Differential regulation of motor control and response to dopaminergic drugs by D1R and D2R neurons in distinct dorsal striatum subregions (pages 640–653)

      Pierre F Durieux, Serge N Schiffmann and Alban de Kerchove d'Exaerde

      Article first published online: 8 NOV 2011 | DOI: 10.1038/emboj.2011.400

      A diphtheria toxin receptor-mediated cell ablation strategy reveals cell type-selective involvement of dorsal striatum subregions in motor control and skill learning.

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      Endocytosis and intracellular trafficking contribute to necrotic neurodegeneration in C. elegans (pages 654–666)

      Kostoula Troulinaki and Nektarios Tavernarakis

      Article first published online: 9 DEC 2011 | DOI: 10.1038/emboj.2011.447

      Clathrin-mediated endocytosis synergizes with autophagy and lysosomal proteolytic mechanisms to mediate necrotic cell death and neurodegeneration in C. elegans.

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      Monoamines and neuropeptides interact to inhibit aversive behaviour in Caenorhabditis elegans (pages 667–678)

      Holly Mills, Rachel Wragg, Vera Hapiak, Michelle Castelletto, Jeffrey Zahratka, Gareth Harris, Philip Summers, Amanda Korchnak, Wenjing Law, Bruce Bamber and Richard Komuniecki

      Article first published online: 29 NOV 2011 | DOI: 10.1038/emboj.2011.422

      Octopamine (OA), the invertebrate counterpart of the neurotransmitter norepinephrine that is involved in pain modulation, affects avoidance behaviour in C. elegans. This effect is mediated via three OA receptors that either inhibit nociceptive neurons or stimulate the release of inhibitory neuropeptides that activate receptors on sensory neurons mediating attraction.

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      Optimal functional levels of activation-induced deaminase specifically require the Hsp40 DnaJa1 (pages 679–691)

      Alexandre Orthwein, Astrid Zahn, Stephen P Methot, David Godin, Silvestro G Conticello, Kazutoyo Terada and Javier M Di Noia

      Article first published online: 15 NOV 2011 | DOI: 10.1038/emboj.2011.417

      AID deaminates deoxycytidine at immunoglobulin genes to generate an antibody response. AID misregulation can contribute to cancer and autoimmune disease. Here, the chaperone DnaJa1 is shown to determine AID protein levels and biological activity during the murine immune response.

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      The NF-κB1 transcription factor prevents the intrathymic development of CD8 T cells with memory properties (pages 692–706)

      Raffi Gugasyan, Elisha Horat, Sarah A Kinkel, Fiona Ross, George Grigoriadis, Daniel Gray, Meredith O'Keeffe, Stuart P Berzins, Gabrielle T Belz, Raelene J Grumont, Ashish Banerjee, Andreas Strasser, Dale I Godfrey, Philip N Tsichlis and Steve Gerondakis

      Article first published online: 29 NOV 2011 | DOI: 10.1038/emboj.2011.435

      Mice deleted for the transcription factor NF-κB1 exhibit aberrant T-cell selection leading to increases in conventional single-positive CD8 T cells with memory-like characteristics.

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      Tail-anchor targeting by a Get3 tetramer: the structure of an archaeal homologue (pages 707–719)

      Christian JM Suloway, Michael E Rome and William M Clemons Jr

      Article first published online: 29 NOV 2011 | DOI: 10.1038/emboj.2011.433

      The delivery of tail-anchored (TA) proteins to the endoplasmic reticulum depends on the GET pathway. The structure of the ATPase Get3 is complemented by low-resolution X-ray scattering data of a Get3/TA protein complex, suggesting a model for the membrane insertion step based on binding of TA proteins to a hydrophobic interaction chamber formed by Get3 tetramers.

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      Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle (pages 720–730)

      Yao Cong, Gunnar F Schröder, Anne S Meyer, Joanita Jakana, Boxue Ma, Matthew T Dougherty, Michael F Schmid, Stefanie Reissmann, Michael Levitt, Steven L Ludtke, Judith Frydman and Wah Chiu

      Article first published online: 1 NOV 2011 | DOI: 10.1038/emboj.2011.366

      Chaperonins are multisubunit entities that are composed of two stacked rings enclosing a central chamber for ATP-dependent protein folding. A series of cryo-EM structures of the eukaryotic group II chaperonin TRiC/CCT reveal the conformational changes during the ATPase cycle and provide insight into how the subunits cooperate to close the lid.

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      Mechanism of nucleotide sensing in group II chaperonins (pages 731–740)

      Jose H Pereira, Corie Y Ralston, Nicholai R Douglas, Ramya Kumar, Tom Lopez, Ryan P McAndrew, Kelly M Knee, Jonathan A King, Judith Frydman and Paul D Adams

      Article first published online: 23 DEC 2011 | DOI: 10.1038/emboj.2011.468

      Group II chaperonins mediate ATP-dependent protein folding in eukaryotes and archaea. A series of crystal structures and functional studies of an archaeal chaperonin identify a nucleotide-sensing loop that is involved in the timing of the protein folding cycle.

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      A viral deubiquitylating enzyme targets viral RNA-dependent RNA polymerase and affects viral infectivity (pages 741–753)

      Mélanie Chenon, Laurent Camborde, Soizic Cheminant and Isabelle Jupin

      Article first published online: 25 NOV 2011 | DOI: 10.1038/emboj.2011.424

      Turnip Yellow Mosaic Virus protects its replicative polymerase from degradation by the host cell ubiquitin-proteasome system, employing deubiquitination activity of a processing protease with resemblance to OTU domain DUBs.

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      ACBD3-mediated recruitment of PI4KB to picornavirus RNA replication sites (pages 754–766)

      Jun Sasaki, Kumiko Ishikawa, Minetaro Arita and Koki Taniguchi

      Article first published online: 29 NOV 2011 | DOI: 10.1038/emboj.2011.429

      Picornavirus genome replication occurs on intracellular membranes, to which the polymerase localizes by binding the lipid PI4P. Aichi virus proteins interact with the Golgi protein ACBD3, which in turn recruits PI4-kinase to stimulate PI4P synthesis, thus promoting replication.

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      Structural insights into the neutralization mechanism of a higher primate antibody against dengue virus (pages 767–779)

      Joseph JB Cockburn, M Erika Navarro Sanchez, Ana P Goncalvez, Elena Zaitseva, Enrico A Stura, Carlos M Kikuti, Stéphane Duquerroy, Philippe Dussart, Leonid V Chernomordik, Ching-Juh Lai and Felix A Rey

      Article first published online: 2 DEC 2011 | DOI: 10.1038/emboj.2011.439

      The envelope (E) protein of Dengue virus is essential for virus entry, and various neutralizing antibodies have been identified that target this protein. Structural analysis of a chimpanzee antibody in complex with the E protein elucidates its mechanism of inhibition, providing a potential basis for vaccine design.

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