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Table of Contents: August 2012

COVER

Butterfly eyespots.

Image Credit: Jeffrey C. Oliver (Yale University).
Issue Image

Many species in the butterfly family Nymphalidae are characterized by conspicuous eyespot patterns on their wings. In this issue, Oliver et al. show that these eyespots and the expression of associated developmental genes evolved once, approximately 90 million years ago. In some lineages however, gene expression underwent significant changes, with many genes being turned off without a corresponding loss of eyespots. These data suggest that the origin of novel traits proceeds via the co-option of complex, preexisting gene regulatory networks that later become streamlined for their novel function.

Perspectives

It's All in the Timing: Too Much E2F Is a Bad Thing

Brandon N. Nicolay, Nicholas J. Dyson

Review

Research Articles

Dynamic Distribution of Linker Histone H1.5 in Cellular Differentiation

Jing-Yu Li, Michaela Patterson, Hanna K. A. Mikkola, William E. Lowry, Siavash K. Kurdistani

Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)

Fabian Staubach, Anna Lorenc, Philipp W. Messer, Kun Tang, Dmitri A. Petrov, Diethard Tautz

Genetic Modulation of Lipid Profiles following Lifestyle Modification or Metformin Treatment: The Diabetes Prevention Program

Toni I. Pollin, Tamara Isakova, Kathleen A. Jablonski, Paul I. W. de Bakker, Andrew Taylor, Jarred McAteer, Qing Pan, Edward S. Horton, Linda M. Delahanty, David Altshuler, Alan R. Shuldiner, Ronald B. Goldberg, Jose C. Florez, Paul W. Franks , Diabetes Prevention Program Research Group

The PARN Deadenylase Targets a Discrete Set of mRNAs for Decay and Regulates Cell Motility in Mouse Myoblasts

Jerome E. Lee, Ju Youn Lee, Jarrett Trembly, Jeffrey Wilusz, Bin Tian, Carol J. Wilusz

Reprogramming to Pluripotency Can Conceal Somatic Cell Chromosomal Instability

Masakazu Hamada, Liviu A. Malureanu, Tobias Wijshake, Wei Zhou, Jan M. van Deursen

A Sexual Ornament in Chickens Is Affected by Pleiotropic Alleles at HAO1 and BMP2, Selected during Domestication

Martin Johnsson, Ida Gustafson, Carl-Johan Rubin, Anna-Stina Sahlqvist, Kenneth B. Jonsson, Susanne Kerje, Olov Ekwall, Olle Kämpe, Leif Andersson, Per Jensen, Dominic Wright

Role of Mex67-Mtr2 in the Nuclear Export of 40S Pre-Ribosomes

Marius B. Faza, Yiming Chang, Laura Occhipinti, Stefan Kemmler, Vikram G. Panse

Experimental Evolution of a Novel Sexually Antagonistic Allele

Rebecca Dean, Jennifer C. Perry, Tommaso Pizzari, Judith E. Mank, Stuart Wigby

Loss of Axonal Mitochondria Promotes Tau-Mediated Neurodegeneration and Alzheimer's Disease–Related Tau Phosphorylation Via PAR-1

Kanae Iijima-Ando, Michiko Sekiya, Akiko Maruko-Otake, Yosuke Ohtake, Emiko Suzuki, Bingwei Lu, Koichi M. Iijima

ATXN2-CAG42 Sequesters PABPC1 into Insolubility and Induces FBXW8 in Cerebellum of Old Ataxic Knock-In Mice

Ewa Damrath, Melanie V. Heck, Suzana Gispert, Mekhman Azizov, Joachim Nowock, Carola Seifried, Udo Rüb, Michael Walter, Georg Auburger

Ccdc94 Protects Cells from Ionizing Radiation by Inhibiting the Expression of p53

Shelly Sorrells, Seth Carbonneau, Erik Harrington, Aye T. Chen, Bridgid Hast, Brett Milash, Ujwal Pyati, Michael B. Major, Yi Zhou, Leonard I. Zon, Rodney A. Stewart, A. Thomas Look, Cicely Jette

Drosophila melanogaster Acetyl-CoA-Carboxylase Sustains a Fatty Acid–Dependent Remote Signal to Waterproof the Respiratory System

Jean-Philippe Parvy, Laura Napal, Thomas Rubin, Mickael Poidevin, Laurent Perrin, Claude Wicker-Thomas, Jacques Montagne

Phylogenetic and Transcriptomic Analysis of Chemosensory Receptors in a Pair of Divergent Ant Species Reveals Sex-Specific Signatures of Odor Coding

Xiaofan Zhou, Jesse D. Slone, Antonis Rokas, Shelley L. Berger, Jürgen Liebig, Anandasankar Ray, Danny Reinberg, Laurence J. Zwiebel

Combining Comparative Proteomics and Molecular Genetics Uncovers Regulators of Synaptic and Axonal Stability and Degeneration In Vivo

Thomas M. Wishart, Timothy M. Rooney, Douglas J. Lamont, Ann K. Wright, A. Jennifer Morton, Mandy Jackson, Marc R. Freeman, Thomas H. Gillingwater

Reduced Prostasin (CAP1/PRSS8) Activity Eliminates HAI-1 and HAI-2 Deficiency–Associated Developmental Defects by Preventing Matriptase Activation

Roman Szabo, Katiuchia Uzzun Sales, Peter Kosa, Natalia A. Shylo, Sine Godiksen, Karina K. Hansen, Stine Friis, J. Silvio Gutkind, Lotte K. Vogel, Edith Hummler, Eric Camerer, Thomas H. Bugge

SLX-1 Is Required for Maintaining Genomic Integrity and Promoting Meiotic Noncrossovers in the Caenorhabditis elegans Germline

Takamune T. Saito, Firaz Mohideen, Katherine Meyer, J. Wade Harper, Monica P. Colaiácovo

SCS3 and YFT2 Link Transcription of Phospholipid Biosynthetic Genes to ER Stress and the UPR

Robyn D. Moir, David A. Gross, David L. Silver, Ian M. Willis

SEMA3A, a Gene Involved in Axonal Pathfinding, Is Mutated in Patients with Kallmann Syndrome

Naresh Kumar Hanchate, Paolo Giacobini, Pierre Lhuillier, Jyoti Parkash, Cécile Espy, Corinne Fouveaut, Chrystel Leroy, Stéphanie Baron, Céline Campagne, Charlotte Vanacker, Francis Collier, Corinne Cruaud, Vincent Meyer, Alfons García-Piñero, Didier Dewailly, Christine Cortet-Rudelli, Ksenija Gersak, Chantal Metz, Gérard Chabrier, Michel Pugeat, Jacques Young, Jean-Pierre Hardelin, Vincent Prevot, Catherine Dodé

Polysome Profiling in Liver Identifies Dynamic Regulation of Endoplasmic Reticulum Translatome by Obesity and Fasting

Suneng Fu, Jason Fan, Joshua Blanco, Alfredo Gimenez-Cassina, Nika N. Danial, Steve M. Watkins, Gökhan S. Hotamisligil

Retrovolution: HIV–Driven Evolution of Cellular Genes and Improvement of Anticancer Drug Activation

Paola Rossolillo, Flore Winter, Etienne Simon-Loriere, Sarah Gallois-Montbrun, Matteo Negroni

Chemical Genetics Reveals a Specific Requirement for Cdk2 Activity in the DNA Damage Response and Identifies Nbs1 as a Cdk2 Substrate in Human Cells

Lara Wohlbold, Karl A. Merrick, Saurav De, Ramon Amat, Jun Hyun Kim, Stéphane Larochelle, Jasmina J. Allen, Chao Zhang, Kevan M. Shokat, John H. J. Petrini, Robert P. Fisher

Cell-Nonautonomous Signaling of FOXO/DAF-16 to the Stem Cells of Caenorhabditis elegans

Wenjing Qi, Xu Huang, Elke Neumann-Haefelin, Ekkehard Schulze, Ralf Baumeister

Rates of Gyrase Supercoiling and Transcription Elongation Control Supercoil Density in a Bacterial Chromosome

Nikolay Rovinskiy, Andrews Akwasi Agbleke, Olga Chesnokova, Zhenhua Pang, N. Patrick Higgins

Simple Methods for Generating and Detecting Locus-Specific Mutations Induced with TALENs in the Zebrafish Genome

Timothy J. Dahlem, Kazuyuki Hoshijima, Michael J. Jurynec, Derrick Gunther, Colby G. Starker, Alexandra S. Locke, Allison M. Weis, Daniel F. Voytas, David Jonah Grunwald

Experimental Relocation of the Mitochondrial ATP9 Gene to the Nucleus Reveals Forces Underlying Mitochondrial Genome Evolution

Maïlis Bietenhader, Alexandre Martos, Emmanuel Tetaud, Raeka S. Aiyar, Carole H. Sellem, Roza Kucharczyk, Sandra Clauder-Münster, Marie-France Giraud, François Godard, Bénédicte Salin, Isabelle Sagot, Julien Gagneur, Michelle Déquard-Chablat, Véronique Contamine, Sylvie Hermann-Le Denmat, Annie Sainsard-Chanet, Lars M. Steinmetz, Jean-Paul di Rago

Transgene Induced Co-Suppression during Vegetative Growth in Cryptococcus neoformans

Xuying Wang, Ping Wang, Sheng Sun, Sabrina Darwiche, Alexander Idnurm, Joseph Heitman

The Genetic Basis of Pollinator Adaptation in a Sexually Deceptive Orchid

Shuqing Xu, Philipp M. Schlüter, Ueli Grossniklaus, Florian P. Schiestl

A Single Origin for Nymphalid Butterfly Eyespots Followed by Widespread Loss of Associated Gene Expression

Jeffrey C. Oliver, Xiao-Ling Tong, Lawrence F. Gall, William H. Piel, Antónia Monteiro

Identification of Human Proteins That Modify Misfolding and Proteotoxicity of Pathogenic Ataxin-1

Spyros Petrakis, Tamás Raskó, Jenny Russ, Ralf P. Friedrich, Martin Stroedicke, Sean-Patrick Riechers, Katja Muehlenberg, Angeli Möller, Anita Reinhardt, Arunachalam Vinayagam, Martin H. Schaefer, Michael Boutros, Hervé Tricoire, Miguel A. Andrade-Navarro, Erich E. Wanker

Melanophore Migration and Survival during Zebrafish Adult Pigment Stripe Development Require the Immunoglobulin Superfamily Adhesion Molecule Igsf11

Dae Seok Eom, Shinya Inoue, Larissa B. Patterson, Tiffany N. Gordon, Rebecca Slingwine, Shigeru Kondo, Masakatsu Watanabe, David M. Parichy

Stromal Liver Kinase B1 [STK11] Signaling Loss Induces Oviductal Adenomas and Endometrial Cancer by Activating Mammalian Target of Rapamycin Complex 1

Pradeep S. Tanwar, Tomoko Kaneko-Tarui, LiHua Zhang, Yoshihiro Tanaka, Christopher P. Crum, Jose M. Teixeira

Novel Loci for Metabolic Networks and Multi-Tissue Expression Studies Reveal Genes for Atherosclerosis

Michael Inouye, Samuli Ripatti, Johannes Kettunen, Leo-Pekka Lyytikäinen, Niku Oksala, Pirkka-Pekka Laurila, Antti J. Kangas, Pasi Soininen, Markku J. Savolainen, Jorma Viikari, Mika Kähönen, Markus Perola, Veikko Salomaa, Olli Raitakari, Terho Lehtimäki, Marja-Riitta Taskinen, Marjo-Riitta Järvelin, Mika Ala-Korpela, Aarno Palotie, Paul I. W. de Bakker

Use of Allele-Specific FAIRE to Determine Functional Regulatory Polymorphism Using Large-Scale Genotyping Arrays

Andrew J. P. Smith, Philip Howard, Sonia Shah, Per Eriksson, Stefan Stender, Claudia Giambartolomei, Lasse Folkersen, Anne Tybjærg-Hansen, Meena Kumari, Jutta Palmen, Aroon D. Hingorani, Philippa J. Talmud, Steve E. Humphries

A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins

Alice Barkan, Margarita Rojas, Sota Fujii, Aaron Yap, Yee Seng Chong, Charles S. Bond, Ian Small

Dissecting the Gene Network of Dietary Restriction to Identify Evolutionarily Conserved Pathways and New Functional Genes

Daniel Wuttke, Richard Connor, Chintan Vora, Thomas Craig, Yang Li, Shona Wood, Olga Vasieva, Robert Shmookler Reis, Fusheng Tang, João Pedro de Magalhães

Rescuing Alu: Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion

Bradley J. Wagstaff, Dale J. Hedges, Rebecca S. Derbes, Rebeca Campos Sanchez, Francesca Chiaromonte, Kateryna D. Makova, Astrid M. Roy-Engel

Rare Copy Number Variations in Adults with Tetralogy of Fallot Implicate Novel Risk Gene Pathways

Candice K. Silversides, Anath C. Lionel, Gregory Costain, Daniele Merico, Ohsuke Migita, Ben Liu, Tracy Yuen, Jessica Rickaby, Bhooma Thiruvahindrapuram, Christian R. Marshall, Stephen W. Scherer, Anne S. Bassett

Mutations in a P-Type ATPase Gene Cause Axonal Degeneration

Xianjun Zhu, Richard T. Libby, Wilhelmine N. de Vries, Richard S. Smith, Dana L. Wright, Roderick T. Bronson, Kevin L. Seburn, Simon W. M. John

Modulating the Strength and Threshold of NOTCH Oncogenic Signals by mir-181a-1/b-1

Rita Fragoso, Tin Mao, Song Wang, Steven Schaffert, Xue Gong, Sibiao Yue, Richard Luong, Hyeyoung Min, Yumi Yashiro-Ohtani, Mark Davis, Warren Pear, Chang-Zheng Chen

Cohesin Rings Devoid of Scc3 and Pds5 Maintain Their Stable Association with the DNA

Irina Kulemzina, Martin R. Schumacher, Vikash Verma, Jochen Reiter, Janina Metzler, Antonio Virgilio Failla, Christa Lanz, Vipin T. Sreedharan, Gunnar Rätsch, Dmitri Ivanov

Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling

Donghyuk Kim, Jay Sung-Joong Hong, Yu Qiu, Harish Nagarajan, Joo-Hyun Seo, Byung-Kwan Cho, Shih-Feng Tsai, Bernhard Ø. Palsson

Fine-Mapping and Initial Characterization of QT Interval Loci in African Americans

Christy L. Avery, Praveen Sethupathy, Steven Buyske, Qianchuan He, Dan-Yu Lin, Dan E. Arking, Cara L. Carty, David Duggan, Megan D. Fesinmeyer, Lucia A. Hindorff, Janina M. Jeff, Liviu Klein, Kristen K. Patton, Ulrike Peters, Ralph V. Shohet, Nona Sotoodehnia, Alicia M. Young, Charles Kooperberg, Christopher A. Haiman, Karen L. Mohlke, Eric A. Whitsel, Kari E. North

Mutational Signatures of De-Differentiation in Functional Non-Coding Regions of Melanoma Genomes

Stephen C. J. Parker, Jared Gartner, Isabel Cardenas-Navia, Xiaomu Wei, Hatice Ozel Abaan, Subramanian S. Ajay, Nancy F. Hansen, Lingyun Song, Umesh K. Bhanot, J. Keith Killian, Yevgeniy Gindin, Robert L. Walker, Paul S. Meltzer, James C. Mullikin, Terrence S. Furey, Gregory E. Crawford, Steven A. Rosenberg, Yardena Samuels, Elliott H. Margulies

Uncovering the Genome-Wide Transcriptional Responses of the Filamentous Fungus Aspergillus niger to Lignocellulose Using RNA Sequencing

Stéphane Delmas, Steven T. Pullan, Sanyasi Gaddipati, Matthew Kokolski, Sunir Malla, Martin J. Blythe, Roger Ibbett, Maria Campbell, Susan Liddell, Aziz Aboobaker, Gregory A. Tucker, David B. Archer

The Drosophila Mi-2 Chromatin-Remodeling Factor Regulates Higher-Order Chromatin Structure and Cohesin Dynamics In Vivo

Barbara Fasulo, Renate Deuring, Magdalena Murawska, Maria Gause, Kristel M. Dorighi, Cheri A. Schaaf, Dale Dorsett, Alexander Brehm, John W. Tamkun

HAL-2 Promotes Homologous Pairing during Caenorhabditis elegans Meiosis by Antagonizing Inhibitory Effects of Synaptonemal Complex Precursors

Weibin Zhang, Natasha Miley, Michael S. Zastrow, Amy J. MacQueen, Aya Sato, Kentaro Nabeshima, Enrique Martinez-Perez, Susanna Mlynarczyk-Evans, Peter M. Carlton, Anne M. Villeneuve

Cryptocephal, the Drosophila melanogaster ATF4, Is a Specific Coactivator for Ecdysone Receptor Isoform B2

Sebastien A. Gauthier, Eric VanHaaften, Lucy Cherbas, Peter Cherbas, Randall S. Hewes

Components of a Fanconi-Like Pathway Control Pso2-Independent DNA Interstrand Crosslink Repair in Yeast

Thomas A. Ward, Zuzana Dudášová, Sovan Sarkar, Mangesh R. Bhide, Danuša Vlasáková, Miroslav Chovanec, Peter J. McHugh

The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits

Benjamin F. Voight, Hyun Min Kang, Jun Ding, Cameron D. Palmer, Carlo Sidore, Peter S. Chines, Noël P. Burtt, Christian Fuchsberger, Yanming Li, Jeanette Erdmann, Timothy M. Frayling, Iris M. Heid, Anne U. Jackson, Toby Johnson, Tuomas O. Kilpeläinen, Cecilia M. Lindgren, Andrew P. Morris, Inga Prokopenko, Joshua C. Randall, Richa Saxena, Nicole Soranzo, Elizabeth K. Speliotes, Tanya M. Teslovich, Eleanor Wheeler, Jared Maguire, Melissa Parkin, Simon Potter, N. William Rayner, Neil Robertson, Kathleen Stirrups, Wendy Winckler, Serena Sanna, Antonella Mulas, Ramaiah Nagaraja, Francesco Cucca, Inês Barroso, Panos Deloukas, Ruth J. F. Loos, Sekar Kathiresan, Patricia B. Munroe, Christopher Newton-Cheh, Arne Pfeufer, Nilesh J. Samani, Heribert Schunkert, Joel N. Hirschhorn, David Altshuler, Mark I. McCarthy, Gonçalo R. Abecasis, Michael Boehnke

A Positive Feedback Loop Links Opposing Functions of P-TEFb/Cdk9 and Histone H2B Ubiquitylation to Regulate Transcript Elongation in Fission Yeast

Miriam Sansó, Karen M. Lee, Laia Viladevall, Pierre-Étienne Jacques, Viviane Pagé, Stephen Nagy, Ariane Racine, Courtney V. St. Amour, Chao Zhang, Kevan M. Shokat, Beate Schwer, François Robert, Robert P. Fisher, Jason C. Tanny

Inheritance Beyond Plain Heritability: Variance-Controlling Genes in Arabidopsis thaliana

Xia Shen, Mats Pettersson, Lars Rönnegård, Örjan Carlborg

Epigenetic Remodeling of Meiotic Crossover Frequency in Arabidopsis thaliana DNA Methyltransferase Mutants

Nataliya E. Yelina, Kyuha Choi, Liudmila Chelysheva, Malcolm Macaulay, Bastiaan de Snoo, Erik Wijnker, Nigel Miller, Jan Drouaud, Mathilde Grelon, Gregory P. Copenhaver, Christine Mezard, Krystyna A. Kelly, Ian R. Henderson

A General G1/S-Phase Cell-Cycle Control Module in the Flowering Plant Arabidopsis thaliana

Xin'Ai Zhao, Hirofumi Harashima, Nico Dissmeyer, Stefan Pusch, Annika K. Weimer, Jonathan Bramsiepe, Daniel Bouyer, Svenja Rademacher, Moritz K. Nowack, Bela Novak, Stefanie Sprunck, Arp Schnittger

Variation of BMP3 Contributes to Dog Breed Skull Diversity

Jeffrey J. Schoenebeck, Sarah A. Hutchinson, Alexandra Byers, Holly C. Beale, Blake Carrington, Daniel L. Faden, Maud Rimbault, Brennan Decker, Jeffrey M. Kidd, Raman Sood, Adam R. Boyko, John W. Fondon III, Robert K. Wayne, Carlos D. Bustamante, Brian Ciruna, Elaine A. Ostrander

A Luminal Glycoprotein Drives Dose-Dependent Diameter Expansion of the Drosophila melanogaster Hindgut Tube

Zulfeqhar A. Syed, Anne-Laure Bougé, Sunitha Byri, Tina M. Chavoshi, Erika Tång, Hervé Bouhin, Iris F. van Dijk-Härd, Anne Uv

Human Developmental Enhancers Conserved between Deuterostomes and Protostomes

Shoa L. Clarke, Julia E. VanderMeer, Aaron M. Wenger, Bruce T. Schaar, Nadav Ahituv, Gill Bejerano

Minibrain/Dyrk1a Regulates Food Intake through the Sir2-FOXO-sNPF/NPY Pathway in Drosophila and Mammals

Seung-Hyun Hong, Kyu-Sun Lee, Su-Jin Kwak, Ae-Kyeong Kim, Hua Bai, Min-Su Jung, O-Yu Kwon, Woo-Joo Song, Marc Tatar, Kweon Yu

Rapid-Throughput Skeletal Phenotyping of 100 Knockout Mice Identifies 9 New Genes That Determine Bone Strength

J. H. Duncan Bassett, Apostolos Gogakos, Jacqueline K. White, Holly Evans, Richard M. Jacques, Anne H. van der Spek, Ramiro Ramirez-Solis, Edward Ryder, David Sunter, Alan Boyde, Michael J. Campbell, Peter I. Croucher, Graham R. Williams , Sanger Mouse Genetics Project

Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medicae

Brendan Epstein, Antoine Branca, Joann Mudge, Arvind K. Bharti, Roman Briskine, Andrew D. Farmer, Masayuki Sugawara, Nevin D. Young, Michael J. Sadowsky, Peter Tiffin

Comparative Analysis of the Genomes of Two Field Isolates of the Rice Blast Fungus Magnaporthe oryzae

Minfeng Xue, Jun Yang, Zhigang Li, Songnian Hu, Nan Yao, Ralph A. Dean, Wensheng Zhao, Mi Shen, Haiwang Zhang, Chao Li, Liyuan Liu, Lei Cao, Xiaowen Xu, Yunfei Xing, Tom Hsiang, Ziding Zhang, Jin-Rong Xu, You-Liang Peng