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Table of Contents: September 2014

Issue Image

An unbiased, systematic search for developmental regulators in the jellyfish Clytia by comparative transcriptomics of Wnt-manipulated embryos allowed identification of genes coding for both evolutionarily conserved and novel proteins. Expression analysis and knockdown studies for a subset of these confirmed their involvement in regulating embryogenesis. In this image, morpholino–mediated knockdown of the novel, hydrozoan-restricted gene WegD1 is seen to cause severe disruption of larval morphology characterized by disruption of the basal lamina between the endoderm and ectoderm layers, as demonstrated by confocal microscopy following visualization of cell contours (blue) and nuclei (purple). See Lapébie et al.

Perspective

Reviews

Out of Balance: R-loops in Human Disease

Matthias Groh, Natalia Gromak

Trans-kingdom Cross-Talk: Small RNAs on the Move

Marijn Knip, Maria E. Constantin, Hans Thordal-Christensen

Research Articles

Differential Management of the Replication Terminus Regions of the Two Vibrio cholerae Chromosomes during Cell Division

Gaëlle Demarre, Elisa Galli, Leila Muresan, Evelyne Paly, Ariane David, Christophe Possoz, François-Xavier Barre

Admixture in Latin America: Geographic Structure, Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 Individuals

Andrés Ruiz-Linares, Kaustubh Adhikari, Victor Acuña-Alonzo, Mirsha Quinto-Sanchez, Claudia Jaramillo, William Arias, Macarena Fuentes, María Pizarro, Paola Everardo, Francisco de Avila, Jorge Gómez-Valdés, Paola León-Mimila, Tábita Hunemeier, Virginia Ramallo, Caio C. Silva de Cerqueira, Mari-Wyn Burley, Esra Konca, Marcelo Zagonel de Oliveira, Mauricio Roberto Veronez, Marta Rubio-Codina, Orazio Attanasio, Sahra Gibbon, Nicolas Ray, Carla Gallo, Giovanni Poletti, Javier Rosique, Lavinia Schuler-Faccini, Francisco M. Salzano, Maria-Cátira Bortolini, Samuel Canizales-Quinteros, Francisco Rothhammer, Gabriel Bedoya, David Balding, Rolando Gonzalez-José

Dopamine Signaling Leads to Loss of Polycomb Repression and Aberrant Gene Activation in Experimental Parkinsonism

Erik Södersten, Michael Feyder, Mads Lerdrup, Ana-Luisa Gomes, Hanna Kryh, Giada Spigolon, Jocelyne Caboche, Gilberto Fisone, Klaus Hansen

The Vip1 Inositol Polyphosphate Kinase Family Regulates Polarized Growth and Modulates the Microtubule Cytoskeleton in Fungi

Jennifer Pöhlmann, Carmen Risse, Constanze Seidel, Thomas Pohlmann, Visnja Jakopec, Eva Walla, Pascal Ramrath, Norio Takeshita, Sebastian Baumann, Michael Feldbrügge, Reinhard Fischer, Ursula Fleig

Neurospora WC-1 Recruits SWI/SNF to Remodel frequency and Initiate a Circadian Cycle

Bin Wang, Arminja N. Kettenbach, Scott A. Gerber, Jennifer J. Loros, Jay C. Dunlap

Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora

Robert J. Williamson, Emily B. Josephs, Adrian E. Platts, Khaled M. Hazzouri, Annabelle Haudry, Mathieu Blanchette, Stephen I. Wright

Regulation of p53 and Rb Links the Alternative NF-κB Pathway to EZH2 Expression and Cell Senescence

Alessio Iannetti, Adeline C. Ledoux, Susan J. Tudhope, Hélène Sellier, Bo Zhao, Sophia Mowla, Adam Moore, Holger Hummerich, Benjamin E. Gewurz, Simon J. Cockell, Parmjit S. Jat, Elaine Willmore, Neil D. Perkins

SPDEF Inhibits Prostate Carcinogenesis by Disrupting a Positive Feedback Loop in Regulation of the Foxm1 Oncogene

Xin-Hua Cheng, Markaisa Black, Vladimir Ustiyan, Tien Le, Logan Fulford, Anusha Sridharan, Mario Medvedovic, Vladimir V. Kalinichenko, Jeffrey A. Whitsett, Tanya V. Kalin

Local Effect of Enhancer of Zeste-Like Reveals Cooperation of Epigenetic and cis-Acting Determinants for Zygotic Genome Rearrangements

Maoussi Lhuillier-Akakpo, Andrea Frapporti, Cyril Denby Wilkes, Mélody Matelot, Michel Vervoort, Linda Sperling, Sandra Duharcourt

Nipbl and Mediator Cooperatively Regulate Gene Expression to Control Limb Development

Akihiko Muto, Shingo Ikeda, Martha E. Lopez-Burks, Yutaka Kikuchi, Anne L. Calof, Arthur D. Lander, Thomas F. Schilling

An Evolutionarily Conserved Role for the Aryl Hydrocarbon Receptor in the Regulation of Movement

Evan G. Williams, Laurent Mouchiroud, Michael Frochaux, Ashutosh Pandey, Pénélope A. Andreux, Bart Deplancke, Johan Auwerx

Derlin-1 Regulates Mutant VCP-Linked Pathogenesis and Endoplasmic Reticulum Stress-Induced Apoptosis

Cyong-Jhih Liang, Ya-Chu Chang, Henry C. Chang, Chung-Kang Wang, Yu-Chien Hung, Ying-Er Lin, Chia-Ching Chan, Chun-Hong Chen, Hui-Yun Chang, Tzu-Kang Sang

A Genetic Assay for Transcription Errors Reveals Multilayer Control of RNA Polymerase II Fidelity

Jordan D. Irvin, Maria L. Kireeva, Deanna R. Gotte, Brenda K. Shafer, Ingold Huang, Mikhail Kashlev, Jeffrey N. Strathern

HEATR2 Plays a Conserved Role in Assembly of the Ciliary Motile Apparatus

Christine P. Diggle, Daniel J. Moore, Girish Mali, Petra zur Lage, Aouatef Ait-Lounis, Miriam Schmidts, Amelia Shoemark, Amaya Garcia Munoz, Mihail R. Halachev, Philippe Gautier, Patricia L. Yeyati, David T. Bonthron, Ian M. Carr, Bruce Hayward, Alexander F. Markham, Jilly E. Hope, Alex von Kriegsheim, Hannah M. Mitchison, Ian J. Jackson, Bénédicte Durand, Walter Reith, Eamonn Sheridan, Andrew P. Jarman, Pleasantine Mill

Differential Responses to Wnt and PCP Disruption Predict Expression and Developmental Function of Conserved and Novel Genes in a Cnidarian

Pascal Lapébie, Antonella Ruggiero, Carine Barreau, Sandra Chevalier, Patrick Chang, Philippe Dru, Evelyn Houliston, Tsuyoshi Momose

Myosin Vb Mediated Plasma Membrane Homeostasis Regulates Peridermal Cell Size and Maintains Tissue Homeostasis in the Zebrafish Epidermis

Sonal, Jaydeep Sidhaye, Mandar Phatak, Shamik Banerjee, Aditya Mulay, Ojas Deshpande, Sourabh Bhide, Tressa Jacob, Ines Gehring, Christiane Nuesslein-Volhard, Mahendra Sonawane

Interplay of dFOXO and Two ETS-Family Transcription Factors Determines Lifespan in Drosophila melanogaster

Nazif Alic, Maria E. Giannakou, Irene Papatheodorou, Matthew P. Hoddinott, T. Daniel Andrews, Ekin Bolukbasi, Linda Partridge

Clonal Expansion of Early to Mid-Life Mitochondrial DNA Point Mutations Drives Mitochondrial Dysfunction during Human Ageing

Laura C. Greaves, Marco Nooteboom, Joanna L. Elson, Helen A. L. Tuppen, Geoffrey A. Taylor, Daniel M. Commane, Ramesh P. Arasaradnam, Konstantin Khrapko, Robert W. Taylor, Thomas B. L. Kirkwood, John C. Mathers, Douglass M. Turnbull

Atkinesin-13A Modulates Cell-Wall Synthesis and Cell Expansion in Arabidopsis thaliana via the THESEUS1 Pathway

Ushio Fujikura, Lore Elsaesser, Holger Breuninger, Clara Sánchez-Rodríguez, Alexander Ivakov, Thomas Laux, Kim Findlay, Staffan Persson, Michael Lenhard

tRNA Modifying Enzymes, NSUN2 and METTL1, Determine Sensitivity to 5-Fluorouracil in HeLa Cells

Mayumi Okamoto, Mamoru Fujiwara, Masato Hori, Kaoru Okada, Futoshi Yazama, Hiroaki Konishi, Yegui Xiao, Guangying Qi, Fumio Shimamoto, Takahide Ota, Achim Temme, Masaaki Tatsuka

The Tandem Repeats Enabling Reversible Switching between the Two Phases of β-Lactamase Substrate Spectrum

Hyojeong Yi, Han Song, Junghyun Hwang, Karan Kim, William C. Nierman, Heenam Stanley Kim

The Association of the Vanin-1 N131S Variant with Blood Pressure Is Mediated by Endoplasmic Reticulum-Associated Degradation and Loss of Function

Ya-Juan Wang, Bamidele O. Tayo, Anupam Bandyopadhyay, Heming Wang, Tao Feng, Nora Franceschini, Hua Tang, Jianmin Gao, Yun Ju Sung, Robert C. Elston, Scott M. Williams, Richard S. Cooper, Ting-Wei Mu, Xiaofeng Zhu , the COGENT BP consortium

Widespread Genome Reorganization of an Obligate Virus Mutualist

Gaelen R. Burke, Kimberly K. O. Walden, James B. Whitfield, Hugh M. Robertson, Michael R. Strand

Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

Nicholas E. Banovich, Xun Lan, Graham McVicker, Bryce van de Geijn, Jacob F. Degner, John D. Blischak, Julien Roux, Jonathan K. Pritchard, Yoav Gilad

Positive Selection and Multiple Losses of the LINE-1-Derived L1TD1 Gene in Mammals Suggest a Dual Role in Genome Defense and Pluripotency

Richard N. McLaughlin Jr., Janet M. Young, Lei Yang, Rafik Neme, Holly A. Wichman, Harmit S. Malik

Genome Wide Association Studies Using a New Nonparametric Model Reveal the Genetic Architecture of 17 Agronomic Traits in an Enlarged Maize Association Panel

Ning Yang, Yanli Lu, Xiaohong Yang, Juan Huang, Yang Zhou, Farhan Ali, Weiwei Wen, Jie Liu, Jiansheng Li, Jianbing Yan

Hydroxymethylated Cytosines Are Associated with Elevated C to G Transversion Rates

Fran Supek, Ben Lehner, Petra Hajkova, Tobias Warnecke

Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics

Philipp Engel, Ramunas Stepanauskas, Nancy A. Moran

Muscular Dystrophy-Associated SUN1 and SUN2 Variants Disrupt Nuclear-Cytoskeletal Connections and Myonuclear Organization

Peter Meinke, Elisabetta Mattioli, Farhana Haque, Susumu Antoku, Marta Columbaro, Kees R. Straatman, Howard J. Worman, Gregg G. Gundersen, Giovanna Lattanzi, Manfred Wehnert, Sue Shackleton

Targeted H3R26 Deimination Specifically Facilitates Estrogen Receptor Binding by Modifying Nucleosome Structure

Michael J. Guertin, Xuesen Zhang, Lynne Anguish, Sohyoung Kim, Lyuba Varticovski, John T. Lis, Gordon L. Hager, Scott A. Coonrod

Unkempt Is Negatively Regulated by mTOR and Uncouples Neuronal Differentiation from Growth Control

Amélie Avet-Rochex, Nancy Carvajal, Christina P. Christoforou, Kelvin Yeung, Katja T. Maierbrugger, Carl Hobbs, Giovanna Lalli, Umut Cagin, Cedric Plachot, Helen McNeill, Joseph M. Bateman

BMPs Regulate msx Gene Expression in the Dorsal Neuroectoderm of Drosophila and Vertebrates by Distinct Mechanisms

Francisco F. Esteves, Alexander Springhorn, Erika Kague, Erika Taylor, George Pyrowolakis, Shannon Fisher, Ethan Bier

Identification of a Regulatory Variant That Binds FOXA1 and FOXA2 at the CDC123/CAMK1D Type 2 Diabetes GWAS Locus

Marie P. Fogarty, Maren E. Cannon, Swarooparani Vadlamudi, Kyle J. Gaulton, Karen L. Mohlke

Obesity-Linked Homologues TfAP-2 and Twz Establish Meal Frequency in Drosophila melanogaster

Michael J. Williams, Philip Goergen, Jayasimman Rajendran, Galina Zheleznyakova, Maria G. Hägglund, Emelie Perland, Sonchita Bagchi, Argyro Kalogeropoulou, Zaid Khan, Robert Fredriksson, Helgi B. Schiöth

Histone Methyltransferase MMSET/NSD2 Alters EZH2 Binding and Reprograms the Myeloma Epigenome through Global and Focal Changes in H3K36 and H3K27 Methylation

Relja Popovic, Eva Martinez-Garcia, Eugenia G. Giannopoulou, Quanwei Zhang, Qingyang Zhang, Teresa Ezponda, Mrinal Y. Shah, Yupeng Zheng, Christine M. Will, Eliza C. Small, Youjia Hua, Marinka Bulic, Yanwen Jiang, Matteo Carrara, Raffaele A. Calogero, William L. Kath, Neil L. Kelleher, Ji-Ping Wang, Olivier Elemento, Jonathan D. Licht

Meta-analysis of SHANK Mutations in Autism Spectrum Disorders: A Gradient of Severity in Cognitive Impairments

Claire S. Leblond, Caroline Nava, Anne Polge, Julie Gauthier, Guillaume Huguet, Serge Lumbroso, Fabienne Giuliano, Coline Stordeur, Christel Depienne, Kevin Mouzat, Dalila Pinto, Jennifer Howe, Nathalie Lemière, Christelle M. Durand, Jessica Guibert, Elodie Ey, Roberto Toro, Hugo Peyre, Alexandre Mathieu, Frédérique Amsellem, Maria Rastam, I. Carina Gillberg, Gudrun A. Rappold, Richard Holt, Anthony P. Monaco, Elena Maestrini, Pilar Galan, Delphine Heron, Aurélia Jacquette, Alexandra Afenjar, Agnès Rastetter, Alexis Brice, Françoise Devillard, Brigitte Assouline, Fanny Laffargue, James Lespinasse, Jean Chiesa, François Rivier, Dominique Bonneau, Beatrice Regnault, Diana Zelenika, Marc Delepine, Mark Lathrop, Damien Sanlaville, Caroline Schluth-Bolard, Patrick Edery, Laurence Perrin, Anne Claude Tabet, Michael J. Schmeisser, Tobias M. Boeckers, Mary Coleman, Daisuke Sato, Peter Szatmari, Stephen W. Scherer, Guy A. Rouleau, Catalina Betancur, Marion Leboyer, Christopher Gillberg, Richard Delorme, Thomas Bourgeron

PRO40 Is a Scaffold Protein of the Cell Wall Integrity Pathway, Linking the MAP Kinase Module to the Upstream Activator Protein Kinase C

Ines Teichert, Eva Katharina Steffens, Nicole Schnaß, Benjamin Fränzel, Christoph Krisp, Dirk A. Wolters, Ulrich Kück

The Olfactory Transcriptomes of Mice

Ximena Ibarra-Soria, Maria O. Levitin, Luis R. Saraiva, Darren W. Logan

Role for Circadian Clock Genes in Seasonal Timing: Testing the Bünning Hypothesis

Mirko Pegoraro, Joao S. Gesto, Charalambos P. Kyriacou, Eran Tauber

Genome-Wide Association Meta-analysis of Neuropathologic Features of Alzheimer's Disease and Related Dementias

Gary W. Beecham, Kara Hamilton, Adam C. Naj, Eden R. Martin, Matt Huentelman, Amanda J. Myers, Jason J. Corneveaux, John Hardy, Jean-Paul Vonsattel, Steven G. Younkin, David A. Bennett, Philip L. De Jager, Eric B. Larson, Paul K. Crane, M. Ilyas Kamboh, Julia K. Kofler, Deborah C. Mash, Linda Duque, John R. Gilbert, Harry Gwirtsman, Joseph D. Buxbaum, Patricia Kramer, Dennis W. Dickson, Lindsay A. Farrer, Matthew P. Frosch, Bernardino Ghetti, Jonathan L. Haines, Bradley T. Hyman, Walter A. Kukull, Richard P. Mayeux, Margaret A. Pericak-Vance, Julie A. Schneider, John Q. Trojanowski, Eric M. Reiman, Gerard D. Schellenberg, Thomas J. Montine , the Alzheimer's Disease Genetics Consortium (ADGC)

Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers

Han Wu, Alex S. Nord, Jennifer A. Akiyama, Malak Shoukry, Veena Afzal, Edward M. Rubin, Len A. Pennacchio, Axel Visel