The EMBO Journal - Table of Contents alert Volume 31 Issue 2

TABLE OF CONTENTS 18 January 2012 | Volume 31, Issue 2 Have you seen? Articles Also new AOP Sign up for e-alerts Recommend to your library Web feed Subscribe Have you seen? Top On epigenetics and epistasis: hybrids and their non-additive interactions Transgressive phenotypes observed in hybrids are a result of non-additive genetic interactions that lead a phenotype in the progeny that is more extreme than either parent; the molecular basis of this phenomenon is unclear. New evidence implicates small RNAs and epigenetics in this deviation from Mendelian inheritance patterns. Lisa M Smith and Detlef Weigel The EMBO Journal (2012), 31, 249 - 250; 10.1038/emboj.2011.473 Abstract | Full text | PDF Published online: 23 December 2011 The nuclear receptor signalling scaffold: insights from full-length structures Nuclear receptors are highly dynamic scaffold proteins that are regulated allosterically by ligands, DNA, or transcriptional coregulators. The first cryo-EM structure of a nuclear receptor complex suggests a key role for the hinge region between the ligand and DNA-binding domains in transmitting structural signals. Jerome C Nwachukwu and Kendall W Nettles The EMBO Journal (2012), 31, 251 - 253; 10.1038/emboj.2011.475 Abstract | Full text | PDF Published online: 18 January 2012 Extracellular matrix players in metastatic niches The identification of periostin and tenascin C offers first molecular insight into the essential support function the extracellular matrix provides as metastatic niche for disseminated tumour cells. Thordur Oskarsson and Joan Massagué The EMBO Journal (2012), 31, 254 - 256; 10.1038/emboj.2011.469 Abstract | Full text | PDF Published online: 16 December 2011 Articles Top Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs Transgressive segregation in plant hybrids leads to the formation of heritable phenotypes that are more extreme than either parent; the molecular basis of this phenomenon in unknown. This study identifies a number of small RNA loci that are more highly expressed in the hybrid than the parents, and corresponding repressed target genes that may mediate the transgressive phenotypes. Padubidri V Shivaprasad, Ruth M Dunn, Bruno ACM Santos, Andrew Bassett and David C Baulcombe The EMBO Journal (2012), 31, 257 - 266; 10.1038/emboj.2011.458 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 16 December 2011 Subject Categories: RNA | Plant Biology Cyclophilin 40 facilitates HSP90-mediated RISC assembly in plants AGO1 plays an important role in the miRNA pathway in plants; however, relatively little is known about the assembly of the AGO1–miRISC complex in this organism. This study shows that cyclophilin 40 promotes the association of HSP90–AGO1 with duplexed small RNAs, while PP5 opposes this effect. Taichiro Iki, Manabu Yoshikawa, Tetsuo Meshi and Masayuki Ishikawa The EMBO Journal (2012), 31, 267 - 278; 10.1038/emboj.2011.395 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 01 November 2011 Subject Categories: RNA | Plant Biology The structural basis of Edc3- and Scd6-mediated activation of the Dcp1:Dcp2 mRNA decapping complex 5′ mRNA caps are removed by the Dcp1:Dcp2 complex. This study provides the structural basis of the competitive interaction of two activators, Edc3 and Scd6, with Dcp2. The activators are required for full decapping activity of the complex and its localization to P-bodies. Simon A Fromm, Vincent Truffault, Julia Kamenz, Joerg E Braun, Niklas A Hoffmann, Elisa Izaurralde and Remco Sprangers The EMBO Journal (2012), 31, 279 - 290; 10.1038/emboj.2011.408 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 15 November 2011 Subject Categories: RNA | Structural Biology Structure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA The first cryo-EM structure of the complete DNA-bound retinoid X receptor (RXR)/vitamin D receptor (VDR) heterodimer, one of the smallest complexes studied with this technique, provides insight into cooperative DNA binding of a key representative of the nuclear receptor family of transcription factors. Igor Orlov, Natacha Rochel, Dino Moras and Bruno P Klaholz The EMBO Journal (2012), 31, 291 - 300; 10.1038/emboj.2011.445 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 16 December 2011 Subject Categories: Chromatin and Transcription | Structural Biology Signal-dependent incorporation of MyoD–BAF60c into Brg1-based SWI/SNF chromatin-remodelling complex The SWI/SNF chromatin-remodelling complex regulates myogenic gene expression during muscle differentiation. BAF60c, a SWI/SNF subunit, recruits the muscle determinant transcription factor MyoD to target genes, facilitates chromatin remodelling and gene activation after phosphorylation by p38α MAP-kinase. Sonia V Forcales, Sonia Albini, Lorenzo Giordani, Barbora Malecova, Luca Cignolo, Andrei Chernov, Paula Coutinho, Valentina Saccone, Silvia Consalvi, Roy Williams, Kepeng Wang, Zhenguo Wu, Svetlana Baranovskaya, Andrew Miller, F Jeffrey Dilworth and Pier Lorenzo Puri The EMBO Journal (2012), 31, 301 - 316; 10.1038/emboj.2011.391 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 08 November 2011 Subject Categories: Signal Transduction | Chromatin and Transcription An interspecies analysis reveals a key role for unmethylated CpG dinucleotides in vertebrate Polycomb complex recruitment Swapping fragments of a human locus into the mouse genome implicates polycomb complex recruitment by local, unmethylated CpG island sequences as key determinant that poises developmental regulator genes for activation. Magnus D Lynch, Andrew J H Smith, Marco De Gobbi, Maria Flenley, Jim R Hughes, Douglas Vernimmen, Helena Ayyub, Jacqueline A Sharpe, Jacqueline A Sloane-Stanley, Linda Sutherland, Stephen Meek, Tom Burdon, Richard J Gibbons, David Garrick and Douglas R Higgs The EMBO Journal (2012), 31, 317 - 329; 10.1038/emboj.2011.399 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 04 November 2011 Subject Categories: Chromatin and Transcription Human tRNA genes function as chromatin insulators The eukaryotic genome is organized into different chromatin domains. In this study, human tDNA genes are shown to function as insulators capable of blocking enhancer activity and preventing the spread of silenced chromatin. Jesse R Raab, Jonathan Chiu, Jingchun Zhu, Sol Katzman, Sreenivasulu Kurukuti, Paul A Wade, David Haussler and Rohinton T Kamakaka The EMBO Journal (2012), 31, 330 - 350; 10.1038/emboj.2011.406 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 15 November 2011 Subject Categories: Chromatin and Transcription FOG-1 and GATA-1 act sequentially to specify definitive megakaryocytic and erythroid progenitors During haematopoiesis, megakaryocytes and erythrocytes derive from a common precursor called preMegE. This study reports a role for the transcription factor FOG-1 in specification of preMegEs, while GATA-1 is subsequently required for erythroid-lineage commitment. Elena Mancini, Alejandra Sanjuan-Pla, Luisa Luciani, Susan Moore, Amit Grover, Agnes Zay, Kasper D Rasmussen, Sidinh Luc, Daniel Bilbao, Donal O'Carroll, Sten Eirik Jacobsen and Claus Nerlov The EMBO Journal (2012), 31, 351 - 365; 10.1038/emboj.2011.390 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 08 November 2011 Subject Categories: Chromatin and Transcription | Development Coreceptor gene imprinting governs thymocyte lineage fate Double-positive (CD4+CD8+) thymocytes differentiate into CD4+ helper T cells and CD8+ cytotoxic T cells. A knock-in approach replacing CD8-coding sequences with CD4 cDNA shows that it is the expression kinetics of CD8, and not the identity of the coreceptor, that governs thymocyte-lineage fate. Stanley Adoro, Thomas McCaughtry, Batu Erman, Amala Alag, François Van Laethem, Jung-Hyun Park, Xuguang Tai, Motoko Kimura, Lie Wang, Alex Grinberg, Masato Kubo, Remy Bosselut, Paul Love and Alfred Singer The EMBO Journal (2012), 31, 366 - 377; 10.1038/emboj.2011.388 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 28 October 2011 Subject Categories: Chromatin and Transcription | Immunology Synthetic biology approach to reconstituting the ubiquitylation cascade in bacteria A new system to achieve bona fide ubiquitin conjugation in E. coli circumvents specificity problems associated with previous in-vitro approaches, adding to the synthetic biology toolbox aimed at addressing the complexity of cellular ubiquitin modification. Tal Keren-Kaplan, Ilan Attali, Khatereh Motamedchaboki, Brian A Davis, Neta Tanner, Yael Reshef, Einat Laudon, Mikhail Kolot, Olga Levin-Kravets, Oded Kleifeld, Michael Glickman, Bruce F Horazdovsky, Dieter A Wolf and Gali Prag The EMBO Journal (2012), 31, 378 - 390; 10.1038/emboj.2011.397 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 11 November 2011 Subject Categories: Proteins Insights into ubiquitin-conjugating enzyme/ co-activator interactions from the structure of the Pex4p:Pex22p complex Ubiquitin conjugation by the E2 enzyme Pex4 is stimulated by tight interactions with a non-canonical co-activator, which binds the E2 at sites distant from the conserved E1- and E3-binding interfaces. Chris Williams, Marlene van den Berg, Santosh Panjikar, Will A Stanley, Ben Distel and Matthias Wilmanns The EMBO Journal (2012), 31, 391 - 402; 10.1038/emboj.2011.411 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 15 November 2011 Subject Categories: Membranes and Transport | Proteins Cdk1 promotes kinetochore bi-orientation and regulates Cdc20 expression during recovery from spindle checkpoint arrest A well-characterized cell-cycle checkpoint prevents mitotic chromosome segregation until all kinetochores are correctly attached to spindle microtubules. Here, the kinase CDK1 is implicated in the recovery from checkpoint arrest by regulating kinetochore bi-orientation and APC/C activity. Hongqing Liang, Hong Hwa Lim, Ashok Venkitaraman and Uttam Surana The EMBO Journal (2012), 31, 403 - 416; 10.1038/emboj.2011.385 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 04 November 2011 Subject Categories: Cell Cycle Nitric oxide-induced calcium release via ryanodine receptors regulates neuronal function Ryanodine receptors (RYRs) induce intracellular Ca2+ release in neurons. Nitric oxide is reported to induce Ca2+ release by S-nitrosylation of RyR1 to regulate synaptic plasticity, long-term potentiation and neuronal cell viability. Sho Kakizawa, Toshiko Yamazawa, Yili Chen, Akihiro Ito, Takashi Murayama, Hideto Oyamada, Nagomi Kurebayashi, Osamu Sato, Masahiko Watanabe, Nozomu Mori, Katsuji Oguchi, Takashi Sakurai, Hiroshi Takeshima, Nobuhito Saito and Masamitsu Iino The EMBO Journal (2012), 31, 417 - 428; 10.1038/emboj.2011.386 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 28 October 2011 Subject Categories: Signal Transduction | Neuroscience Wnt1/βcatenin injury response activates the epicardium and cardiac fibroblasts to promote cardiac repair Wnt1/βcatenin signalling plays a critical role in cardiac repair following acute cardiac injury in vivo both by inducing cardiac fibroblast proliferation and by promoting epithelial–mesenchymal transition of the epicardium to generate cardiac fibroblast. Jinzhu Duan, Costin Gherghe, Dianxin Liu, Eric Hamlett, Luxman Srikantha, Laurel Rodgers, Jenna N Regan, Mauricio Rojas, Monte Willis, Andrew Leask, Mark Majesky and Arjun Deb The EMBO Journal (2012), 31, 429 - 442; 10.1038/emboj.2011.418 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 15 November 2011 Subject Categories: Signal Transduction | Molecular Biology of Disease LRPPRC is necessary for polyadenylation and coordination of translation of mitochondrial mRNAs LRPPRC regulates mitochondrial mRNA stability and it is implicated in a neurodegenerative disorder. A heart-specific mouse knockout now reveals that LRPPRC is necessary for mRNA polyadenylation and stability, and for coordinated mitochondrial translation, resulting in respiratory chain defects and cardiomyopathy. Benedetta Ruzzenente, Metodi D Metodiev, Anna Wredenberg, Ana Bratic, Chan Bae Park, Yolanda Cámara, Dusanka Milenkovic, Volker Zickermann, Rolf Wibom, Kjell Hultenby, Hediye Erdjument-Bromage, Paul Tempst, Ulrich Brandt, James B Stewart, Claes M Gustafsson and Nils-Göran Larsson The EMBO Journal (2012), 31, 443 - 456; 10.1038/emboj.2011.392 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 01 November 2011 Subject Categories: Proteins | Cellular Metabolism Palmitoylated TMX and calnexin target to the mitochondria-associated membrane Mitochondria-associated ER membranes (MAM) recently emerged as critical for cellular signal transduction and metabolism. This study identifies palmitoylation as novel mechanism for targeted localization of ER-transmembrane proteins to MAM domains. Emily M Lynes, Michael Bui, Megan C Yap, Matthew D Benson, Bobbie Schneider, Lars Ellgaard, Luc G Berthiaume and Thomas Simmen The EMBO Journal (2012), 31, 457 - 470; 10.1038/emboj.2011.384 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 01 November 2011 Subject Categories: Membranes and Transport | Signal Transduction An indirect role for ASPP1 in limiting p53-dependent p21 expression and cellular senescence Following earlier proposal on novel functions of ASPP1, this paper reveals Yap as ASPP1's cytoplasmic target. This translates into LATS2 repression, modulating p53/p21-dependent cell-cycle arrest and cellular senescence. Arnaud M Vigneron and Karen H Vousden The EMBO Journal (2012), 31, 471 - 480; 10.1038/emboj.2011.402 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 08 November 2011 Subject Categories: Signal Transduction | Molecular Biology of Disease MYBPH, a transcriptional target of TTF-1, inhibits ROCK1, and reduces cell motility and metastasis The TTF-1 transcription factor is upregulated in lung adenocarcinomas, where it apparently suppresses malignant progression. One of its targets, MYBPH, inhibits Rho kinase 1 and hence cell motility and invasion, providing a potential explanation for the protective function of TTF-1. Yasuyuki Hosono, Tomoya Yamaguchi, Eri Mizutani, Kiyoshi Yanagisawa, Chinatsu Arima, Shuta Tomida, Yukako Shimada, Michiyo Hiraoka, Seiichi Kato, Kohei Yokoi, Motoshi Suzuki and Takashi Takahashi The EMBO Journal (2012), 31, 481 - 493; 10.1038/emboj.2011.416 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 15 November 2011 Subject Categories: Cell and Tissue Architecture Functional and structural studies of the nucleotide excision repair helicase XPD suggest a polarity for DNA translocation The first DNA-bound structure of an SF2B-type helicase reveals the DNA strand translocation polarity governing 5′-3′ directionality in this important helicase family that also includes major genome stability regulators FANCJ and RTEL. Jochen Kuper, Stefanie C Wolski, Gudrun Michels and Caroline Kisker The EMBO Journal (2012), 31, 494 - 502; 10.1038/emboj.2011.374 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 11 November 2011 Subject Categories: Genome Stability and Dynamics Regulation of translocation polarity by helicase domain 1 in SF2B helicases Biochemical and reverse footprinting studies of the nucleotide excision repair protein XPD show that opposing translocation polarity in superfamily II A and B helicases is an intrinsic property of their respective motor domains, rather than related to different relative DNA binding orientations. Robert A Pugh, Colin G Wu and Maria Spies The EMBO Journal (2012), 31, 503 - 514; 10.1038/emboj.2011.412 Abstract | Full text | PDF | Supp. info. | Review Process File Published online: 11 November 2011 Subject Categories: Genome Stability and Dynamics 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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