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Table of Contents: December 2011

COVER

A Chinese Silkie rooster exhibiting fibromelanosis.

Image Credit: Freyja Imsland (Uppsala University)
Issue Image

The study of Dorshorst et al. shows that fibromelanosis (intense pigmentation of the dermal layer of skin and pigmented connective tissue) is caused by a complex genomic rearrangement that leads to upregulated expression of the Endothelin 3 gene located within the rearranged region. The study illustrates how structural changes have contributed to rapid phenotypic evolution in domestic animals.

Interview

Perspective

An Anti-Checkpoint Activity for Rif1

Yaniv Harari, Linda Rubinstein, Martin Kupiec

Research Articles

Transcription Is Required to Establish Maternal Imprinting at the Prader-Willi Syndrome and Angelman Syndrome Locus

Emily Y. Smith, Christopher R. Futtner, Stormy J. Chamberlain, Karen A. Johnstone, James L. Resnick

Substitutions in the Amino-Terminal Tail of Neurospora Histone H3 Have Varied Effects on DNA Methylation

Keyur K. Adhvaryu, Emanuela Berge, Hisashi Tamaru, Michael Freitag, Eric U. Selker

Autosomal Recessive Dilated Cardiomyopathy due to DOLK Mutations Results from Abnormal Dystroglycan O-Mannosylation

Dirk J. Lefeber, Arjan P. M. de Brouwer, Eva Morava, Moniek Riemersma, Janneke H. M. Schuurs-Hoeijmakers, Birgit Absmanner, Kiek Verrijp, Willem M. R. van den Akker, Karin Huijben, Gerry Steenbergen, Jeroen van Reeuwijk, Adam Jozwiak, Nili Zucker, Avraham Lorber, Martin Lammens, Carlos Knopf, Hans van Bokhoven, Stephanie Grünewald, Ludwig Lehle, Livia Kapusta, Hanna Mandel, Ron A. Wevers

MAPK/ERK Signaling Regulates Insulin Sensitivity to Control Glucose Metabolism in Drosophila

Wei Zhang, Barry J. Thompson, Ville Hietakangas, Stephen M. Cohen

The RNA Silencing Enzyme RNA Polymerase V Is Required for Plant Immunity

Ana López, Vicente Ramírez, Javier García-Andrade, Victor Flors, Pablo Vera

Interspecific Sex in Grass Smuts and the Genetic Diversity of Their Pheromone-Receptor System

Ronny Kellner, Evelyn Vollmeister, Michael Feldbrügge, Dominik Begerow

A Genetic Screening Strategy Identifies Novel Regulators of the Proteostasis Network

M. Catarina Silva, Susan Fox, Monica Beam, Happy Thakkar, Margarida D. Amaral, Richard I. Morimoto

Common Variants Show Predicted Polygenic Effects on Height in the Tails of the Distribution, Except in Extremely Short Individuals

Yingleong Chan, Oddgeir L. Holmen, Andrew Dauber, Lars Vatten, Aki S. Havulinna, Frank Skorpen, Kirsti Kvaløy, Kaisa Silander, Thutrang T. Nguyen, Cristen Willer, Michael Boehnke, Markus Perola, Aarno Palotie, Veikko Salomaa, Kristian Hveem, Timothy M. Frayling, Joel N. Hirschhorn, Michael N. Weedon

DNA Methylation of the Gonadal Aromatase (cyp19a) Promoter Is Involved in Temperature-Dependent Sex Ratio Shifts in the European Sea Bass

Laia Navarro-Martín, Jordi Viñas, Laia Ribas, Noelia Díaz, Arantxa Gutiérrez, Luciano Di Croce, Francesc Piferrer

Acute Multiple Organ Failure in Adult Mice Deleted for the Developmental Regulator Wt1

You-Ying Chau, David Brownstein, Heidi Mjoseng, Wen-Chin Lee, Natalija Buza-Vidas, Claus Nerlov, Sten Eirik Jacobsen, Paul Perry, Rachel Berry, Anna Thornburn, David Sexton, Nik Morton, Peter Hohenstein, Elisabeth Freyer, Kay Samuel, Rob van't Hof, Nicholas Hastie

A Complex Genomic Rearrangement Involving the Endothelin 3 Locus Causes Dermal Hyperpigmentation in the Chicken

Ben Dorshorst, Anna-Maja Molin, Carl-Johan Rubin, Anna M. Johansson, Lina Strömstedt, Manh-Hung Pham, Chih-Feng Chen, Finn Hallböök, Chris Ashwell, Leif Andersson

Histone H3K9 Trimethylase Eggless Controls Germline Stem Cell Maintenance and Differentiation

Xiaoxi Wang, Lei Pan, Su Wang, Jian Zhou, William McDowell, Jungeun Park, Jeff Haug, Karen Staehling, Hong Tang, Ting Xie

Ror2 Enhances Polarity and Directional Migration of Primordial Germ Cells

Diana J. Laird, Svetlana Altshuler-Keylin, Michael D. Kissner, Xin Zhou, Kathryn V. Anderson

Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments

Florence Wisniewski-Dyé, Kirill Borziak, Gurusahai Khalsa-Moyers, Gladys Alexandre, Leonid O. Sukharnikov, Kristin Wuichet, Gregory B. Hurst, W. Hayes McDonald, Jon S. Robertson, Valérie Barbe, Alexandra Calteau, Zoé Rouy, Sophie Mangenot, Claire Prigent-Combaret, Philippe Normand, Mickaël Boyer, Patricia Siguier, Yves Dessaux, Claudine Elmerich, Guy Condemine, Ganisan Krishnen, Ivan Kennedy, Andrew H. Paterson, Victor González, Patrick Mavingui, Igor B. Zhulin

Identification of Evolutionarily Conserved Exons as Regulated Targets for the Splicing Activator Tra2β in Development

Sushma Grellscheid, Caroline Dalgliesh, Markus Storbeck, Andrew Best, Yilei Liu, Miriam Jakubik, Ylva Mende, Ingrid Ehrmann, Tomaz Curk, Kristina Rossbach, Cyril F. Bourgeois, James Stévenin, David Grellscheid, Michael S. Jackson, Brunhilde Wirth, David J. Elliott

Drosophila Ribosomal Protein Mutants Control Tissue Growth Non-Autonomously via Effects on the Prothoracic Gland and Ecdysone

Jane I. Lin, Naomi C. Mitchell, Marina Kalcina, Elly Tchoubrieva, Mary J. Stewart, Steven J. Marygold, Cherryl D. Walker, George Thomas, Sally J. Leevers, Richard B. Pearson, Leonie M. Quinn, Ross D. Hannan

Plasticity of BRCA2 Function in Homologous Recombination: Genetic Interactions of the PALB2 and DNA Binding Domains

Nicolas Siaud, Maria A. Barbera, Akinori Egashira, Isabel Lam, Nicole Christ, Katharina Schlacher, Bing Xia, Maria Jasin

Ancestral Components of Admixed Genomes in a Mexican Cohort

Nicholas A. Johnson, Marc A. Coram, Mark D. Shriver, Isabelle Romieu, Gregory S. Barsh, Stephanie J. London, Hua Tang

A Functional Phylogenomic View of the Seed Plants

Ernest K. Lee, Angelica Cibrian-Jaramillo, Sergios-Orestis Kolokotronis, Manpreet S. Katari, Alexandros Stamatakis, Michael Ott, Joanna C. Chiu, Damon P. Little, Dennis Wm. Stevenson, W. Richard McCombie, Robert A. Martienssen, Gloria Coruzzi, Rob DeSalle

Target Site Recognition by a Diversity-Generating Retroelement

Huatao Guo, Longping V. Tse, Angela W. Nieh, Elizabeth Czornyj, Steven Williams, Sabrina Oukil, Vincent B. Liu, Jeff F. Miller

A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures

Chia Huey Ooi, Hue Kian Oh, Hannah Zhu'Ai Wang, Angie Lay Keng Tan, Jeanie Wu, Minghui Lee, Sun Young Rha, Hyun Cheol Chung, David Marc Virshup, Patrick Tan

A Novel Checkpoint and RPA Inhibitory Pathway Regulated by Rif1

Yuan Xue, Michael D. Rushton, Laura Maringele

Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types

Michael J. Ziller, Fabian Müller, Jing Liao, Yingying Zhang, Hongcang Gu, Christoph Bock, Patrick Boyle, Charles B. Epstein, Bradley E. Bernstein, Thomas Lengauer, Andreas Gnirke, Alexander Meissner

Mining the LIPG Allelic Spectrum Reveals the Contribution of Rare and Common Regulatory Variants to HDL Cholesterol

Sumeet A. Khetarpal, Andrew C. Edmondson, Avanthi Raghavan, Hemanth Neeli, Weijun Jin, Karen O. Badellino, Serkalem Demissie, Alisa K. Manning, Stephanie L. DerOhannessian, Megan L. Wolfe, L. Adrienne Cupples, Mingyao Li, Sekar Kathiresan, Daniel J. Rader

Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes

Laure Escoubet-Lozach, Christopher Benner, Minna U. Kaikkonen, Jean Lozach, Sven Heinz, Nathan J. Spann, Andrea Crotti, Josh Stender, Serena Ghisletti, Donna Reichart, Christine S. Cheng, Rosa Luna, Colleen Ludka, Roman Sasik, Ivan Garcia-Bassets, Alexander Hoffmann, Shankar Subramaniam, Gary Hardiman, Michael G. Rosenfeld, Christopher K. Glass

Age-Related Neuronal Degeneration: Complementary Roles of Nucleotide Excision Repair and Transcription-Coupled Repair in Preventing Neuropathology

Dick Jaarsma, Ingrid van der Pluijm, Monique C. de Waard, Elize D. Haasdijk, Renata Brandt, Marcel Vermeij, Yvonne Rijksen, Alex Maas, Harry van Steeg, Jan H. J. Hoeijmakers, Gijsbertus T. J. van der Horst

A Comprehensive Analysis of Shared Loci between Systemic Lupus Erythematosus (SLE) and Sixteen Autoimmune Diseases Reveals Limited Genetic Overlap

Paula S. Ramos, Lindsey A. Criswell, Kathy L. Moser, Mary E. Comeau, Adrienne H. Williams, Nicholas M. Pajewski, Sharon A. Chung, Robert R. Graham, Raphael Zidovetzki, Jennifer A. Kelly, Kenneth M. Kaufman, Chaim O. Jacob, Timothy J. Vyse, Betty P. Tsao, Robert P. Kimberly, Patrick M. Gaffney, Marta E. Alarcón-Riquelme, John B. Harley, Carl D. Langefeld , for The International Consortium on the Genetics of Systemic Erythematosus (SLEGEN)

An Assessment of the Individual and Collective Effects of Variants on Height Using Twins and a Developmentally Informative Study Design

Scott I. Vrieze, Matt McGue, Michael B. Miller, Lisa N. Legrand, Nicholas J. Schork, William G. Iacono

Integrating Genome-Wide Genetic Variations and Monocyte Expression Data Reveals Trans-Regulated Gene Modules in Humans

Maxime Rotival, Tanja Zeller, Philipp S. Wild, Seraya Maouche, Silke Szymczak, Arne Schillert, Raphaele Castagné, Arne Deiseroth, Carole Proust, Jessy Brocheton, Tiphaine Godefroy, Claire Perret, Marine Germain, Medea Eleftheriadis, Christoph R. Sinning, Renate B. Schnabel, Edith Lubos, Karl J. Lackner, Heidi Rossmann, Thomas Münzel, Augusto Rendon, Cardiogenics Consortium, Jeanette Erdmann, Panos Deloukas, Christian Hengstenberg, Patrick Diemert, Gilles Montalescot, Willem H. Ouwehand, Nilesh J. Samani, Heribert Schunkert, David-Alexandre Tregouet, Andreas Ziegler, Alison H. Goodall, François Cambien, Laurence Tiret, Stefan Blankenberg

SREBP Coordinates Iron and Ergosterol Homeostasis to Mediate Triazole Drug and Hypoxia Responses in the Human Fungal Pathogen Aspergillus fumigatus

Michael Blatzer, Bridget M. Barker, Sven D. Willger, Nicola Beckmann, Sara J. Blosser, Elizabeth J. Cornish, Aurelien Mazurie, Nora Grahl, Hubertus Haas, Robert A. Cramer

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

A. P. Jason de Koning, Wanjun Gu, Todd A. Castoe, Mark A. Batzer, David D. Pollock

Genome Instability and Transcription Elongation Impairment in Human Cells Depleted of THO/TREX

María S. Domínguez-Sánchez, Sonia Barroso, Belén Gómez-González, Rosa Luna, Andrés Aguilera

A Population Genetics-Phylogenetics Approach to Inferring Natural Selection in Coding Sequences

Daniel J. Wilson, Ryan D. Hernandez, Peter Andolfatto, Molly Przeworski

Targeted Proteolysis of Plectin Isoform 1a Accounts for Hemidesmosome Dysfunction in Mice Mimicking the Dominant Skin Blistering Disease EBS-Ogna

Gernot Walko, Nevena Vukasinovic, Karin Gross, Irmgard Fischer, Sabrina Sibitz, Peter Fuchs, Siegfried Reipert, Ute Jungwirth, Walter Berger, Ulrich Salzer, Oliviero Carugo, Maria J. Castañón, Gerhard Wiche

Charcot-Marie-Tooth–Linked Mutant GARS Is Toxic to Peripheral Neurons Independent of Wild-Type GARS Levels

William W. Motley, Kevin L. Seburn, Mir Hussain Nawaz, Kathy E. Miers, Jun Cheng, Anthony Antonellis, Eric D. Green, Kevin Talbot, Xiang-Lei Yang, Kenneth H. Fischbeck, Robert W. Burgess

Genome-Wide Meta-Analysis of Five Asian Cohorts Identifies PDGFRA as a Susceptibility Locus for Corneal Astigmatism

Qiao Fan, Xin Zhou, Chiea-Chuen Khor, Ching-Yu Cheng, Liang-Kee Goh, Xueling Sim, Wan-Ting Tay, Yi-Ju Li, Rick Twee-Hee Ong, Chen Suo, Belinda Cornes, Mohammad Kamran Ikram, Kee-Seng Chia, Mark Seielstad, Jianjun Liu, Eranga Vithana, Terri L. Young, E.-Shyong Tai, Tien-Yin Wong, Tin Aung, Yik-Ying Teo, Seang-Mei Saw

The RNA–Methyltransferase Misu (NSun2) Poises Epidermal Stem Cells to Differentiate

Sandra Blanco, Agata Kurowski, Jennifer Nichols, Fiona M. Watt, Salvador Aznar Benitah, Michaela Frye