The EMBO Journal - Table of Contents alert Volume 31 Issue 3

TABLE OF CONTENTS 01 February 2012 | Volume 31, Issue 3 Have you seen? Articles Sign up for e-alerts Recommend to your library Web feed Subscribe Advertisement Rockland Celebrates 50 Years Rockland, a leader in the production of the highest quality antibodies and assays, marks 50 years of providing reagents for Cancer, Cell Biology, Cell Signaling and Neuroscience research. Manufactured near Philadelphia, PA, Rockland products are guaranteed to give predictable, repeatable results. Protect your experiments with Rockland antibodies. Compromise elsewhere. Visit our content-rich website at www.rockland-inc.com Have you seen? Top RNA driving the epigenetic bus 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. John S Mattick The EMBO Journal (2012), 31, 515 - 516; 10.1038/emboj.2011.479 Abstract | Full text | PDF Published online: 01 February 2012 Rac1 gets fattier The identification of Rac1 palmitoylation reveals how Rac1 changes subcellular localization to modulate its signalling function. Frederick D Tsai and Mark R Philips The EMBO Journal (2012), 31, 517 - 518; 10.1038/emboj.2011.481 Abstract | Full text | PDF Published online: 01 February 2012 A structural road map to unveil basal body composition and assembly The Basal Body is the template for the axoneme, the internal scaffolding of cilia and flagella. Bettencourt-Dias and colleagues comment on an article by David Agard's group, in which they characterize the structure of the basal body by electron cryo-tomography and reveal new clues into its biogenesis and function. Swadhin C Jana, Pedro Machado and Mónica Bettencourt-Dias The EMBO Journal (2012), 31, 519 - 521; 10.1038/emboj.2011.474 Abstract | Full text | PDF Published online: 01 February 2012 Articles Top Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors 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. Shi-Yan Ng, Rory Johnson and Lawrence W Stanton The EMBO Journal (2012), 31, 522 - 533; 10.1038/emboj.2011.459 Abstract | Full text | PDF | Supp. info. Published online: 23 December 2011 Subject Categories: Chromatin and Transcription | RNA | Neuroscience A palmitoylation switch mechanism regulates Rac1 function and membrane organization 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. Inmaculada Navarro-Lérida, Miguel A Del Pozo, and colleagues The EMBO Journal (2012), 31, 534 - 551; 10.1038/emboj.2011.446 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 09 December 2011 Subject Categories: Cell and Tissue Architecture Three-dimensional structure of basal body triplet revealed by electron cryo-tomography 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. Sam Li, Jose-Jesus Fernandez, Wallace F Marshall and David A Agard The EMBO Journal (2012), 31, 552 - 562; 10.1038/emboj.2011.460 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 13 December 2011 Subject Categories: Cell and Tissue Architecture | Structural Biology H2O2 stress-specific regulation of S. pombe MAPK Sty1 by mitochondrial protein phosphatase Ptc4 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. Yujun Di, Caroline R M Wilkinson, and colleagues The EMBO Journal (2012), 31, 563 - 575; 10.1038/emboj.2011.438 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 02 December 2011 Subject Categories: Membranes and Transport | Signal Transduction Positive regulation of p53 stability and activity by the deubiquitinating enzyme Otubain 1 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. Xiao-Xin Sun, Kishore B Challagundla and Mu-Shui Dai The EMBO Journal (2012), 31, 576 - 592; 10.1038/emboj.2011.434 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 29 November 2011 Subject Categories: Signal Transduction | Proteins NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression 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. Nicola Reynolds, Brian Hendrich, and colleagues The EMBO Journal (2012), 31, 593 - 605; 10.1038/emboj.2011.431 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 02 December 2011 Subject Categories: Chromatin and Transcription | Development Transcription and histone methylation changes correlate with imprint acquisition in male germ cells 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. Amandine Henckel, Karim Chebli, Satya K Kota, Philippe Arnaud and Robert Feil The EMBO Journal (2012), 31, 606 - 615; 10.1038/emboj.2011.425 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 25 November 2011 Subject Categories: Chromatin and Transcription | Development The histone methyltransferase Setd8 acts in concert with c-Myc and is required to maintain skin 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. Iwona Driskell, Michaela Frye, and colleagues The EMBO Journal (2012), 31, 616 - 629; 10.1038/emboj.2011.421 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 25 November 2011 Subject Categories: Signal Transduction | Development | Differentiation and Death Factor-independent transcription pausing caused by recognition of the RNA–DNA hybrid sequence 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. Aleksandra Bochkareva, Yulia Yuzenkova, Vasisht R Tadigotla and Nikolay Zenkin The EMBO Journal (2012), 31, 630 - 639; 10.1038/emboj.2011.432 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 29 November 2011 Subject Categories: Chromatin and Transcription Differential regulation of motor control and response to dopaminergic drugs by D1R and D2R neurons in distinct dorsal striatum subregions A diphtheria toxin receptor-mediated cell ablation strategy reveals cell type-selective involvement of dorsal striatum subregions in motor control and skill learning. Pierre F Durieux, Serge N Schiffmann and Alban de Kerchove d'Exaerde The EMBO Journal (2012), 31, 640 - 653; 10.1038/emboj.2011.400 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 08 November 2011 Subject Categories: Neuroscience Endocytosis and intracellular trafficking contribute to necrotic neurodegeneration in C. elegans Clathrin-mediated endocytosis synergizes with autophagy and lysosomal proteolytic mechanisms to mediate necrotic cell death and neurodegeneration in C. elegans. Kostoula Troulinaki and Nektarios Tavernarakis The EMBO Journal (2012), 31, 654 - 666; 10.1038/emboj.2011.447 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 09 December 2011 Subject Categories: Membranes and Transport | Neuroscience Monoamines and neuropeptides interact to inhibit aversive behaviour in Caenorhabditis elegans 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. Holly Mills, Richard Komuniecki, and colleagues The EMBO Journal (2012), 31, 667 - 678; 10.1038/emboj.2011.422 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 29 November 2011 Subject Categories: Neuroscience Optimal functional levels of activation-induced deaminase specifically require the Hsp40 DnaJa1 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. Alexandre Orthwein, Javier M Di Noia, and colleagues The EMBO Journal (2012), 31, 679 - 691; 10.1038/emboj.2011.417 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 15 November 2011 Subject Categories: Immunology The NF-κB1 transcription factor prevents the intrathymic development of CD8 T cells with memory properties 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. Raffi Gugasyan, Steve Gerondakis, and colleagues The EMBO Journal (2012), 31, 692 - 706; 10.1038/emboj.2011.435 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 29 November 2011 Subject Categories: Immunology Tail-anchor targeting by a Get3 tetramer: the structure of an archaeal homologue 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. Christian JM Suloway, Michael E Rome and William M Clemons Jr The EMBO Journal (2012), 31, 707 - 719; 10.1038/emboj.2011.433 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 29 November 2011 Subject Categories: Membranes and Transport | Structural Biology Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle 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. Yao Cong, Wah Chiu, and colleagues The EMBO Journal (2012), 31, 720 - 730; 10.1038/emboj.2011.366 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 01 November 2011 Subject Categories: Proteins | Structural Biology Mechanism of nucleotide sensing in group II chaperonins 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. Jose H Pereira, Paul D Adams, and colleagues The EMBO Journal (2012), 31, 731 - 740; 10.1038/emboj.2011.468 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 23 December 2011 Subject Categories: Proteins | Structural Biology A viral deubiquitylating enzyme targets viral RNA-dependent RNA polymerase and affects viral infectivity 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. Mélanie Chenon, Laurent Camborde, Soizic Cheminant and Isabelle Jupin The EMBO Journal (2012), 31, 741 - 753; 10.1038/emboj.2011.424 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 25 November 2011 Subject Categories: Proteins | Microbiology and Pathogens ACBD3-mediated recruitment of PI4KB to picornavirus RNA replication sites 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. Jun Sasaki, Kumiko Ishikawa, Minetaro Arita and Koki Taniguchi The EMBO Journal (2012), 31, 754 - 766; 10.1038/emboj.2011.429 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 29 November 2011 Subject Categories: Microbiology and Pathogens Structural insights into the neutralization mechanism of a higher primate antibody against dengue virus 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. Joseph JB Cockburn, Felix A Rey, and colleagues The EMBO Journal (2012), 31, 767 - 779; 10.1038/emboj.2011.439 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 02 December 2011 Subject Categories: Microbiology and Pathogens | Structural Biology Please note that you need to be a subscriber or site-licence holder to enjoy full-text access to The EMBO Journal. In order to do so, please purchase a subscription. You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at: www.nature.com/nams/svc/myaccount (You will need to log in to be recognised as a nature.com registrant). For further technical assistance, please contact our registration department. For print subscription enquiries, please contact our subscription department. For other enquiries, please contact our customer feedback department. 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