EMBO reports Table of Contents for December 2015; Vol. 16, No. 12

December 2015 | Volume 16, Number 12 Submit Table of Contents Correspondence Opinion Science & Society Reviews Scientific Report Articles Volume 16, Number 12 Correspondence PDE6D binds to the C‐terminus of RPGR in a prenylation‐dependent manner Contrary to the prior studies, PDE6D was found to bind more preferentially to the C‐terminal prenyl moiety than the N‐terminal region of RPGR in mammalian cells. This RPGR–PDE6D interaction is also dependent on the amino acid adjacent to the prenylation motif, providing an explanation as to how the specificity of PDE6D and prenylated protein interaction is determined. Je‐Jung Lee and Seongjin Seo Published online 09.11.2015 The N‐ and C‐terminal ends of RPGR can bind to PDE6δ This study shows that the prenylated C‐terminus of RPGR can bind to PDE6δ with high affinity, suggesting two distinct binding sites of the RPGR/PDE6δ complex. The serine residue at the −3 position relative to the prenylated cysteine seems to play a key role in defining the selectivity of PDE6δ towards ciliary prenylated cargo. Eyad Kalawy Fansa, Nicola J O'Reilly, Shehab Ismail, and Alfred Wittinghofer Published online 09.11.2015 Opinion When gain‐of‐function research is not “gain‐of‐function” research The recent publication of an influenza high‐yield vaccine backbone again raises questions about the regulation of gain‐of‐function research with dangerous pathogens. It shows that the current classification system based on select pathogens needs a more fine‐grained distinction to better identify those pathogens and their strains that have pandemic potential. Andy Kilianski and Randall S Murch Published online 04.11.2015 Science & Society Social influence and peer review: Why traditional peer review is no longer adapted, and how it should evolve There is growing unhappiness with the role of peer review in scientific assessment for grants and publications. While only a few critics would abandon peer review altogether, it is clear that scientific assessment has to evolve to keep serving scientists and the public. Daniel Fisher and Nikolaos Parisis Published online 11.11.2015 Are scientists a workforce? – Or, how Dr. Frankenstein made biomedical research sick: A proposed plan to rescue US biomedical research from its current ‘malaise’ will not be effective as it misdiagnoses the root cause of the disease A group of prominent scientists and science administrators recently published a plan for rescuing US biomedical research from what they have identified as an incapacitating and widespread malaise. The plan is unlikely to work because it misdiagnoses the root cause of the disease. The author suggests a new diagnosis. Yuri Lazebnik Published online 13.11.2015 The radical openness of science and innovation: Why uncertainty is inherent in the openness towards the future To meet the pressing challenges for Europe, EU Commissioner Carlos Moedas proposed more openness in science, innovation and towards the world. But society and its decision‐makers should embrace the notion that science is even more radically open towards the future. It thrives on the cusp of uncertainty. Helga Nowotny Published online 09.11.2015 Essentially deadly: living with toxic elements: Humans and plants have evolved various mechanisms to deal with and even adopt toxic heavy metals Organisms have evolved to deal with or make use of toxic metals. Understanding these mechanisms could help to protect the health of mine workers, tackle malnourishment, or improve ways to clean up polluted environments. Philip Hunter Published online 09.11.2015 Reviews “Histones and Chromatin” Review series: Chromatin remodeling and bivalent histone modifications in embryonic stem cells This review discusses the emerging link between bivalent histone modifications and ATP‐dependent chromatin remodeling in pluripotent ESCs. Arigela Harikumar and Eran Meshorer Published online 09.11.2015 “Histones and Chromatin” Review Series: Histone demethylases in chromatin biology and beyond Histone demethylases regulate chromatin biology and shape the epigenome. This review focuses on the mechanisms underlying histone demethylase function in a variety of cellular processes, including enzymatic activity‐independent roles and non‐histone substrates. Emilia Dimitrova, Anne H Turberfield, and Robert J Klose Published online 12.11.2015 The pathogenicity of splicing defects: mechanistic insights into pre‐mRNA processing inform novel therapeutic approaches Mutations affecting pre‐mRNA splicing have been linked to various human pathologies. This review discusses recent insights into the molecular mechanisms of disease‐causing splicing defects, which may inform future therapies and enhance our understanding of complex splicing processes. Elisabeth Daguenet, Gwendal Dujardin, and Juan Valcárcel Published online 13.11.2015 Scientific Report Human TLR8 senses UR/URR motifs in bacterial and mitochondrial RNA This study shows that human monocyte TLR8 senses bacterial ribosomal and transfer RNA, as well as mitochondrial RNA. TLR8 recognizes a UR/URR RNA‐ligand consensus motif in contrast to the bacteria‐borne 10‐mer motif detected by its murine TLR13 counterpart. Anne Krüger, Marina Oldenburg, Chiranjeevi Chebrolu, Daniela Beisser, Julia Kolter, Anna M Sigmund, Jörg Steinmann, Simon Schäfer, Hubertus Hochrein, Sven Rahmann, Hermann Wagner, Philipp Henneke, Veit Hornung, Jan Buer, and Carsten J Kirschning Published online 06.11.2015 Articles JAK/STAT signaling in Drosophila muscles controls the cellular immune response against parasitoid infection This study shows that JAK/STAT signaling in Drosophila muscles regulates the cellular immune response to wasp infection. Cytokines Upd2 and Upd3 secreted from circulating hemocytes trigger the JAK/STAT pathway in somatic muscles. Hairu Yang, Jesper Kronhamn, Jens‐Ola Ekström, Gül Gizem Korkut, and Dan Hultmark Published online 27.09.2015 The Paf1 complex factors Leo1 and Paf1 promote local histone turnover to modulate chromatin states in fission yeast Components of the transcription elongation complex Paf1C promote transitions between heterochromatin and euchromatin by replacing histones during RNA polymerase II‐mediated transcription. By evicting chromatin‐bound histones, the epigenetic memory is locally reset. Laia Sadeghi, Punit Prasad, Karl Ekwall, Amikam Cohen, and J Peter Svensson Published online 29.10.2015 A conformational RNA zipper promotes intron ejection during non‐conventional XBP1 mRNA splicing Unconventional splicing of XBP1 mRNA by IRE1 and tRNA ligase is a key regulatory step in the UPR. This study shows that RNA‐intrinsic conformational changes are a prerequisite for the completion of the reaction, defining an active role for XBP1 mRNA in its splicing reaction. Jirka Peschek, Diego Acosta‐Alvear, Aaron S Mendez, and Peter Walter Published online 19.10.2015 Ubiquitin‐Activated Interaction Traps (UBAITs) identify E3 ligase binding partners This study reports the development of UBAITs, tools to identify ubiquitin E3 ligase‐interacting proteins through covalent trapping, enabling co‐purification. H2A.Z is identified as a new RNF168 substrate. Hazel F O'Connor, Nancy Lyon, Justin W Leung, Poonam Agarwal, Caleb D Swaim, Kyle M Miller, and Jon M Huibregtse Published online 27.10.2015 Deconstruction of O‐glycosylation—GalNAc‐T isoforms direct distinct subsets of the O‐glycoproteome This study shows that the O‐glycoproteome of a cell is differentially regulated by the repertoire of polypeptide GalNAc‐transferases expressed, and that individual polypeptide GalNAc‐transferases modify distinct subsets of the proteome that likely impact different pathways and processes. Katrine T Schjoldager, Hiren J Joshi, Yun Kong, Christoffer K Goth, Sarah Louise King, Hans H Wandall, Eric P Bennett, Sergey Y Vakhrushev, and Henrik Clausen Published online 13.11.2015 Myc coordinates transcription and translation to enhance transformation and suppress invasiveness This study reports the effect of Myc induction on gene expression at the levels of transcription, translation and protein amounts at a genomic scale, and uncovers novel facets of regulation carried out by this major proto‐oncogene. Ran Elkon, Fabricio Loayza‐Puch, Gozde Korkmaz, Rui Lopes, Pieter C van Breugel, Onno B Bleijerveld, AF Maarten Altelaar, Elmar Wolf, Francesca Lorenzin, Martin Eilers, and Reuven Agami Published online 04.11.2015   Unsubscribe from or edit your subscription for this service. Or by mail: Customer Service * 425 Broadway St * Redwood City, CA 94063 * U.S.A. Copyright © 2015 by the European Molecular Biology Organisation.