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Table of Contents: June 2012

COVER

Behavioral genes impact metabolic physiology.

Image Credit: Christofer Bang (Arizona State University).
Issue Image

A newborn honey bee worker (Apis mellifera) breaks free from her nursery chamber in the colony nest. A few weeks later, she will leave the hive in search of nectar and pollen to feed her siblings and mother queen. The genes vitellogenin and ultraspiracle, which regulate the bees' behavioral transition to foraging tasks, also coordinate their carbohydrate metabolism, blood sugar levels, sweet taste, and several metabolic genes in adipose tissue. When vitellogenin and ultraspiracle are simultaneously suppressed in adipose cells, the bees develop a metabolic syndrome similar to type 1 diabetes. See Wang et al.

Perspectives

Found: The Elusive ANTAR Transcription Antiterminator

Valley Stewart, Herman van Tilbeurgh

Research Articles

Fuzzy Tandem Repeats Containing p53 Response Elements May Define Species-Specific p53 Target Genes

Iva Simeonova, Vincent Lejour, Boris Bardot, Rachida Bouarich-Bourimi, Aurélie Morin, Ming Fang, Laure Charbonnier, Franck Toledo

In Vivo Control of CpG and Non-CpG DNA Methylation by DNA Methyltransferases

Julia Arand, David Spieler, Tommy Karius, Miguel R. Branco, Daniela Meilinger, Alexander Meissner, Thomas Jenuwein, Guoliang Xu, Heinrich Leonhardt, Verena Wolf, Jörn Walter

G Protein Activation without a GEF in the Plant Kingdom

Daisuke Urano, Janice C. Jones, Hao Wang, Melissa Matthews, William Bradford, Jeffrey L. Bennetzen, Alan M. Jones

The Rose-comb Mutation in Chickens Constitutes a Structural Rearrangement Causing Both Altered Comb Morphology and Defective Sperm Motility

Freyja Imsland, Chungang Feng, Henrik Boije, Bertrand Bed'hom, Valérie Fillon, Ben Dorshorst, Carl-Johan Rubin, Ranran Liu, Yu Gao, Xiaorong Gu, Yanqiang Wang, David Gourichon, Michael C. Zody, William Zecchin, Agathe Vieaud, Michèle Tixier-Boichard, Xiaoxiang Hu, Finn Hallböök, Ning Li, Leif Andersson

Global Regulatory Functions of the Staphylococcus aureus Endoribonuclease III in Gene Expression

Efthimia Lioliou, Cynthia M. Sharma, Isabelle Caldelari, Anne-Catherine Helfer, Pierre Fechter, François Vandenesch, Jörg Vogel, Pascale Romby

Quantifying the Adaptive Potential of an Antibiotic Resistance Enzyme

Martijn F. Schenk, Ivan G. Szendro, Joachim Krug, J. Arjan G. M. de Visser

Selection-Driven Gene Loss in Bacteria

Sanna Koskiniemi, Song Sun, Otto G. Berg, Dan I. Andersson

Parallel Evolution of Auditory Genes for Echolocation in Bats and Toothed Whales

Yong-Yi Shen, Lu Liang, Gui-Sheng Li, Robert W. Murphy, Ya-Ping Zhang

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

Yoichiro Shibata, Nathan C. Sheffield, Olivier Fedrigo, Courtney C. Babbitt, Matthew Wortham, Alok K. Tewari, Darin London, Lingyun Song, Bum-Kyu Lee, Vishwanath R. Iyer, Stephen C. J. Parker, Elliott H. Margulies, Gregory A. Wray, Terrence S. Furey, Gregory E. Crawford

Gene Expression Profiles in Parkinson Disease Prefrontal Cortex Implicate FOXO1 and Genes under Its Transcriptional Regulation

Alexandra Dumitriu, Jeanne C. Latourelle, Tiffany C. Hadzi, Nathan Pankratz, Dan Garza, John P. Miller, Jeffery M. Vance, Tatiana Foroud, Thomas G. Beach, Richard H. Myers

Incompatibility and Competitive Exclusion of Genomic Segments between Sibling Drosophila Species

Shu Fang, Roman Yukilevich, Ying Chen, David A. Turissini, Kai Zeng, Ian A. Boussy, Chung-I. Wu

The Rad4TopBP1 ATR-Activation Domain Functions in G1/S Phase in a Chromatin-Dependent Manner

Su-Jiun Lin, Christopher P. Wardlaw, Takashi Morishita, Izumi Miyabe, Charly Chahwan, Thomas Caspari, Ulrike Schmidt, Antony M. Carr, Valerie Garcia

Genome-Wide Identification of Ampicillin Resistance Determinants in Enterococcus faecium

Xinglin Zhang, Fernanda L. Paganelli, Damien Bierschenk, Annemarie Kuipers, Marc J. M. Bonten, Rob J. L. Willems, Willem van Schaik

Phylogenomic Analysis Reveals Dynamic Evolutionary History of the Drosophila Heterochromatin Protein 1 (HP1) Gene Family

Mia T. Levine, Connor McCoy, Danielle Vermaak, Yuh Chwen G. Lee, Mary Alice Hiatt, Frederick A. Matsen, Harmit S. Malik

Rare Copy Number Variants Observed in Hereditary Breast Cancer Cases Disrupt Genes in Estrogen Signaling and TP53 Tumor Suppression Network

Katri Pylkäs, Mikko Vuorela, Meeri Otsukka, Anne Kallioniemi, Arja Jukkola-Vuorinen, Robert Winqvist

Adaptive Introgression across Species Boundaries in Heliconius Butterflies

Carolina Pardo-Diaz, Camilo Salazar, Simon W. Baxter, Claire Merot, Wilsea Figueiredo-Ready, Mathieu Joron, W. Owen McMillan, Chris D. Jiggins

Geographic Differences in Genetic Susceptibility to IgA Nephropathy: GWAS Replication Study and Geospatial Risk Analysis

Krzysztof Kiryluk, Yifu Li, Simone Sanna-Cherchi, Mersedeh Rohanizadegan, Hitoshi Suzuki, Frank Eitner, Holly J. Snyder, Murim Choi, Ping Hou, Francesco Scolari, Claudia Izzi, Maddalena Gigante, Loreto Gesualdo, Silvana Savoldi, Antonio Amoroso, Daniele Cusi, Pasquale Zamboli, Bruce A. Julian, Jan Novak, Robert J. Wyatt, Krzysztof Mucha, Markus Perola, Kati Kristiansson, Alexander Viktorin, Patrik K. Magnusson, Gudmar Thorleifsson, Unnur Thorsteinsdottir, Kari Stefansson, Anne Boland, Marie Metzger, Lise Thibaudin, Christoph Wanner, Kitty J. Jager, Shin Goto, Dita Maixnerova, Hussein H. Karnib, Judit Nagy, Ulf Panzer, Jingyuan Xie, Nan Chen, Vladimir Tesar, Ichiei Narita, Francois Berthoux, Jürgen Floege, Benedicte Stengel, Hong Zhang, Richard P. Lifton, Ali G. Gharavi

Preferential Genome Targeting of the CBP Co-Activator by Rel and Smad Proteins in Early Drosophila melanogaster Embryos

Per-Henrik Holmqvist, Ann Boija, Philge Philip, Filip Crona, Per Stenberg, Mattias Mannervik

Genome-Wide Location Analysis Reveals Distinct Transcriptional Circuitry by Paralogous Regulators Foxa1 and Foxa2

Irina M. Bochkis, Jonathan Schug, Diana Z. Ye, Svitlana Kurinna, Sabrina A. Stratton, Michelle C. Barton, Klaus H. Kaestner

The CCR4-NOT Complex Is Implicated in the Viability of Aneuploid Yeasts

Yoshie Tange, Atsushi Kurabayashi, Bunshiro Goto, Kwang-Lae Hoe, Dong-Uk Kim, Han-Oh Park, Jacqueline Hayles, Yuji Chikashige, Chihiro Tsutumi, Yasushi Hiraoka, Fumiaki Yamao, Paul Nurse, Osami Niwa

Stretching the Rules: Monocentric Chromosomes with Multiple Centromere Domains

Pavel Neumann, Alice Navrátilová, Elizabeth Schroeder-Reiter, Andrea Koblížková, Veronika Steinbauerová, Eva Chocholová, Petr Novák, Gerhard Wanner, Jiří Macas

Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia

Altuna Akalin, Francine E. Garrett-Bakelman, Matthias Kormaksson, Jennifer Busuttil, Lu Zhang, Irina Khrebtukova, Thomas A. Milne, Yongsheng Huang, Debabrata Biswas, Jay L. Hess, C. David Allis, Robert G. Roeder, Peter J. M. Valk, Bob Löwenberg, Ruud Delwel, Hugo F. Fernandez, Elisabeth Paietta, Martin S. Tallman, Gary P. Schroth, Christopher E. Mason, Ari Melnick, Maria E. Figueroa

Stimulation of Host Immune Defenses by a Small Molecule Protects C. elegans from Bacterial Infection

Read Pukkila-Worley, Rhonda Feinbaum, Natalia V. Kirienko, Jonah Larkins-Ford, Annie L. Conery, Frederick M. Ausubel

The NSL Complex Regulates Housekeeping Genes in Drosophila

Kin Chung Lam, Friederike Mühlpfordt, Juan M. Vaquerizas, Sunil Jayaramaiah Raja, Herbert Holz, Nicholas M. Luscombe, Thomas Manke, Asifa Akhtar

Cohesin Proteins Promote Ribosomal RNA Production and Protein Translation in Yeast and Human Cells

Tania Bose, Kenneth K. Lee, Shuai Lu, Baoshan Xu, Bethany Harris, Brian Slaughter, Jay Unruh, Alexander Garrett, William McDowell, Andrew Box, Hua Li, Allison Peak, Sree Ramachandran, Chris Seidel, Jennifer L. Gerton

sox9b Is a Key Regulator of Pancreaticobiliary Ductal System Development

Marion Delous, Chunyue Yin, Donghun Shin, Nikolay Ninov, Juliana Debrito Carten, Luyuan Pan, Taylur P. Ma, Steven A. Farber, Cecilia B. Moens, Didier Y. R. Stainier

Polymorphisms in the Mitochondrial Ribosome Recycling Factor EF-G2mt/MEF2 Compromise Cell Respiratory Function and Increase Atorvastatin Toxicity

Sylvie Callegari, Philip A. Gregory, Matthew J. Sykes, Jennifer Bellon, Stuart Andrews, Ross A. McKinnon, Miguel A. de Barros Lopes

A SEL1L Mutation Links a Canine Progressive Early-Onset Cerebellar Ataxia to the Endoplasmic Reticulum–Associated Protein Degradation (ERAD) Machinery

Kaisa Kyöstilä, Sigitas Cizinauskas, Eija H. Seppälä, Esko Suhonen, Janis Jeserevics, Antti Sukura, Pernilla Syrjä, Hannes Lohi

Protective Coupling of Mitochondrial Function and Protein Synthesis via the eIF2α Kinase GCN-2

Brooke M. Baker, Amrita M. Nargund, Tiffany Sun, Cole M. Haynes

The Histone Demethylase Jhdm1a Regulates Hepatic Gluconeogenesis

Dongning Pan, Chunxiao Mao, Tie Zou, Annie Y. Yao, Marcus P. Cooper, Victor Boyartchuk, Yong-Xu Wang

Diverse CRISPRs Evolving in Human Microbiomes

Mina Rho, Yu-Wei Wu, Haixu Tang, Thomas G. Doak, Yuzhen Ye

The Mechanism for RNA Recognition by ANTAR Regulators of Gene Expression

Arati Ramesh, Sruti DebRoy, Jonathan R. Goodson, Kristina A. Fox, Herbey Faz, Danielle A. Garsin, Wade C. Winkler

Decreased Mitochondrial DNA Mutagenesis in Human Colorectal Cancer

Nolan G. Ericson, Mariola Kulawiec, Marc Vermulst, Kieran Sheahan, Jacintha O'Sullivan, Jesse J. Salk, Jason H. Bielas

Genome-Wide Functional Profiling Identifies Genes and Processes Important for Zinc-Limited Growth of Saccharomyces cerevisiae

Matthew North, Janet Steffen, Alex V. Loguinov, Ginelle R. Zimmerman, Chris D. Vulpe, David J. Eide

Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants

Fanggeng Zou, High Seng Chai, Curtis S. Younkin, Mariet Allen, Julia Crook, V. Shane Pankratz, Minerva M. Carrasquillo, Christopher N. Rowley, Asha A. Nair, Sumit Middha, Sooraj Maharjan, Thuy Nguyen, Li Ma, Kimberly G. Malphrus, Ryan Palusak, Sarah Lincoln, Gina Bisceglio, Constantin Georgescu, Naomi Kouri, Christopher P. Kolbert, Jin Jen, Jonathan L. Haines, Richard Mayeux, Margaret A. Pericak-Vance, Lindsay A. Farrer, Gerard D. Schellenberg, Ronald C. Petersen, Neill R. Graff-Radford, Dennis W. Dickson, Steven G. Younkin, Nilüfer Ertekin-Taner , Alzheimer's Disease Genetics Consortium

RNA Methylation by the MIS Complex Regulates a Cell Fate Decision in Yeast

Sudeep D. Agarwala, Hannah G. Blitzblau, Andreas Hochwagen, Gerald R. Fink

Uracil-Containing DNA in Drosophila: Stability, Stage-Specific Accumulation, and Developmental Involvement

Villő Muha, András Horváth, Angéla Békési, Mária Pukáncsik, Barbara Hodoscsek, Gábor Merényi, Gergely Róna, Júlia Batki, István Kiss, Ferenc Jankovics, Péter Vilmos, Miklós Erdélyi, Beáta G. Vértessy

MicroRNA93 Regulates Proliferation and Differentiation of Normal and Malignant Breast Stem Cells

Suling Liu, Shivani H. Patel, Christophe Ginestier, Ingrid Ibarra, Rachel Martin-Trevino, Shoumin Bai, Sean P. McDermott, Li Shang, Jia Ke, Sing J. Ou, Amber Heath, Kevin J. Zhang, Hasan Korkaya, Shawn G. Clouthier, Emmanuelle Charafe-Jauffret, Daniel Birnbaum, Gregory J. Hannon, Max S. Wicha

Genetic Variants on Chromosome 1q41 Influence Ocular Axial Length and High Myopia

Qiao Fan, Veluchamy A. Barathi, Ching-Yu Cheng, Xin Zhou, Akira Meguro, Isao Nakata, Chiea-Chuen Khor, Liang-Kee Goh, Yi-Ju Li, Wan'e Lim, Candice E. H. Ho, Felicia Hawthorne, Yingfeng Zheng, Daniel Chua, Hidetoshi Inoko, Kenji Yamashiro, Kyoko Ohno-Matsui, Keitaro Matsuo, Fumihiko Matsuda, Eranga Vithana, Mark Seielstad, Nobuhisa Mizuki, Roger W. Beuerman, E.-Shyong Tai, Nagahisa Yoshimura, Tin Aung, Terri L. Young, Tien-Yin Wong, Yik-Ying Teo, Seang-Mei Saw