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Table of Contents: March 2015

COVER

Transcription factors control comb development in chickens.

Image Credit: Ben Dorshorst and colleagues
Issue Image

There are three comb types in chickens that are each inherited independently as single gene traits: Rose, Pea and Duplex comb. Here the Duplex V-Shaped phenotype is shown to be caused by ectopic expression of the transcription factor Eomesodermin (EOMES). Previous reports have shown Rose and Pea comb to be caused by ectopic expression of transcription factors MNR2 and SOX5, respectively. Remarkably, the causal mutations for all three comb types represent structural genomic variants (duplications and inversions) that disrupt normal expression of these transcription factors and result in vastly different developmental outcomes for the comb. See Dorshorst et al.

Perspective

Research Articles

Dual-Specificity Anti-sigma Factor Reinforces Control of Cell-Type Specific Gene Expression in Bacillus subtilis

Mónica Serrano, JinXin Gao, João Bota, Ashley R. Bate, Jeffrey Meisner, Patrick Eichenberger, Charles P. Moran Jr., Adriano O. Henriques

Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast

Kristin L. Patrick, Colm J. Ryan, Jiewei Xu, Jesse J. Lipp, Kelly E. Nissen, Assen Roguev, Michael Shales, Nevan J. Krogan, Christine Guthrie

Selective and Genetic Constraints on Pneumococcal Serotype Switching

Nicholas J. Croucher, Lisa Kagedan, Claudette M. Thompson, Julian Parkhill, Stephen D. Bentley, Jonathan A. Finkelstein, Marc Lipsitch, William P. Hanage

Network Analyses Reveal Novel Aspects of ALS Pathogenesis

Mario Sanhueza, Andrea Chai, Colin Smith, Brett A. McCray, T. Ian Simpson, J. Paul Taylor, Giuseppa Pennetta

Sex Ratio Meiotic Drive as a Plausible Evolutionary Mechanism for Hybrid Male Sterility

Linbin Zhang, Tianai Sun, Fitsum Woldesellassie, Hailian Xiao, Yun Tao

Combinatorial Control of Light Induced Chromatin Remodeling and Gene Activation in Neurospora

Cigdem Sancar, Nati Ha, Rüstem Yilmaz, Rafael Tesorero, Tamas Fisher, Michael Brunner, Gencer Sancar

A Role for the Budding Yeast Separase, Esp1, in Ty1 Element Retrotransposition

Krystina L. Ho, Lina Ma, Stephanie Cheung, Savrina Manhas, Nancy Fang, Kaiqian Wang, Barry Young, Christopher Loewen, Thibault Mayor, Vivien Measday

Arabidopsis BREVIPEDICELLUS Interacts with the SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA to Regulate KNAT2 and KNAT6 Expression in Control of Inflorescence Architecture

Minglei Zhao, Songguang Yang, Chia-Yang Chen, Chenlong Li, Wei Shan, Wangjin Lu, Yuhai Cui, Xuncheng Liu, Keqiang Wu

Unsaturation of Very-Long-Chain Ceramides Protects Plant from Hypoxia-Induced Damages by Modulating Ethylene Signaling in Arabidopsis

Li-Juan Xie, Qin-Fang Chen, Mo-Xian Chen, Lu-Jun Yu, Li Huang, Liang Chen, Feng-Zhu Wang, Fan-Nv Xia, Tian-Ren Zhu, Jian-Xin Wu, Jian Yin, Bin Liao, Jianxin Shi, Jian-Hua Zhang, Asaph Aharoni, Nan Yao, Wensheng Shu, Shi Xiao

Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs

Aaron M. Nuss, Ann Kathrin Heroven, Barbara Waldmann, Jan Reinkensmeier, Michael Jarek, Michael Beckstette, Petra Dersch

Mutation in MRPS34 Compromises Protein Synthesis and Causes Mitochondrial Dysfunction

Tara R. Richman, Judith A. Ermer, Stefan M. K. Davies, Kara L. Perks, Helena M. Viola, Anne-Marie J. Shearwood, Livia C. Hool, Oliver Rackham, Aleksandra Filipovska

Mitochondrial Dysfunction Reveals the Role of mRNA Poly(A) Tail Regulation in Oculopharyngeal Muscular Dystrophy Pathogenesis

Aymeric Chartier, Pierre Klein, Stéphanie Pierson, Nicolas Barbezier, Teresa Gidaro, François Casas, Steven Carberry, Paul Dowling, Laurie Maynadier, Maëlle Bellec, Martine Oloko, Claude Jardel, Bodo Moritz, George Dickson, Vincent Mouly, Kay Ohlendieck, Gillian Butler-Browne, Capucine Trollet, Martine Simonelig

GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters

Nicholas J. Fuda, Michael J. Guertin, Sumeet Sharma, Charles G. Danko, André L. Martins, Adam Siepel, John T. Lis

Systems Biology of Tissue-Specific Response to Anaplasma phagocytophilum Reveals Differentiated Apoptosis in the Tick Vector Ixodes scapularis

Nieves Ayllón, Margarita Villar, Ruth C. Galindo, Katherine M. Kocan, Radek Šíma, Juan A. López, Jesús Vázquez, Pilar Alberdi, Alejandro Cabezas-Cruz, Petr Kopáček, José de la Fuente

HOMER2, a Stereociliary Scaffolding Protein, Is Essential for Normal Hearing in Humans and Mice

Hela Azaiez, Amanda R. Decker, Kevin T. Booth, Allen C. Simpson, A. Eliot Shearer, Patrick L. M. Huygen, Fengxiao Bu, Michael S. Hildebrand, Paul T. Ranum, Seiji B. Shibata, Ann Turner, Yuzhou Zhang, William J. Kimberling, Robert A. Cornell, Richard J. H. Smith

A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations

Emile R. Chimusa, Ayton Meintjies, Milaine Tchanga, Nicola Mulder, Cathal Seioghe, Himla Soodyall, Rajkumar Ramesar

Osteopetrorickets due to Snx10 Deficiency in Mice Results from Both Failed Osteoclast Activity and Loss of Gastric Acid-Dependent Calcium Absorption

Liang Ye, Leslie R. Morse, Li Zhang, Hajime Sasaki, Jason C. Mills, Paul R. Odgren, Greg Sibbel, James R. L. Stanley, Gee Wong, Ariane Zamarioli, Ricardo A. Battaglino

A RecA Protein Surface Required for Activation of DNA Polymerase V

Angela J. Gruber, Aysen L. Erdem, Grzegorz Sabat, Kiyonobu Karata, Malgorzata M. Jaszczur, Dan D. Vo, Tayla M. Olsen, Roger Woodgate, Myron F. Goodman, Michael M. Cox

Tertiary siRNAs Mediate Paramutation in C. elegans

Alexandra Sapetschnig, Peter Sarkies, Nicolas J. Lehrbach, Eric A. Miska

NLRC5 Exclusively Transactivates MHC Class I and Related Genes through a Distinctive SXY Module

Kristina Ludigs, Queralt Seguín-Estévez, Sylvain Lemeille, Isabel Ferrero, Giorgia Rota, Sonia Chelbi, Chantal Mattmann, H. Robson MacDonald, Walter Reith, Greta Guarda

Mutations of Human NARS2, Encoding the Mitochondrial Asparaginyl-tRNA Synthetase, Cause Nonsyndromic Deafness and Leigh Syndrome

Mariella Simon, Elodie M. Richard, Xinjian Wang, Mohsin Shahzad, Vincent H. Huang, Tanveer A. Qaiser, Prasanth Potluri, Sarah E. Mahl, Antonio Davila, Sabiha Nazli, Saege Hancock, Margret Yu, Jay Gargus, Richard Chang, Nada Al-sheqaih, William G. Newman, Jose Abdenur, Arnold Starr, Rashmi Hegde, Thomas Dorn, Anke Busch, Eddie Park, Jie Wu, Hagen Schwenzer, Adrian Flierl, Catherine Florentz, Marie Sissler, Shaheen N. Khan, Ronghua Li, Min-Xin Guan, Thomas B. Friedman, Doris K. Wu, Vincent Procaccio, Sheikh Riazuddin, Douglas C. Wallace, Zubair M. Ahmed, Taosheng Huang, Saima Riazuddin

Opposite Phenotypes of Muscle Strength and Locomotor Function in Mouse Models of Partial Trisomy and Monosomy 21 for the Proximal Hspa13-App Region

Véronique Brault, Arnaud Duchon, Caroline Romestaing, Ignasi Sahun, Stéphanie Pothion, Mona Karout, Christelle Borel, Doulaye Dembele, Jean-Charles Bizot, Nadia Messaddeq, Andrew J. Sharp, Damien Roussel, Stylianos E Antonarakis, Mara Dierssen, Yann Hérault

Accumulation of Glucosylceramide in the Absence of the Beta-Glucosidase GBA2 Alters Cytoskeletal Dynamics

Diana Raju, Sophie Schonauer, Hussein Hamzeh, Kevin C. Flynn, Frank Bradke, Katharina vom Dorp, Peter Dörmann, Yildiz Yildiz, Christian Trötschel, Ansgar Poetsch, Bernadette Breiden, Konrad Sandhoff, Heinz G. Körschen, Dagmar Wachten

Genome-Wide Association Studies in Dogs and Humans Identify ADAMTS20 as a Risk Variant for Cleft Lip and Palate

Zena T. Wolf, Harrison A. Brand, John R. Shaffer, Elizabeth J. Leslie, Boaz Arzi, Cali E. Willet, Timothy C. Cox, Toby McHenry, Nicole Narayan, Eleanor Feingold, Xioajing Wang, Saundra Sliskovic, Nili Karmi, Noa Safra, Carla Sanchez, Frederic W. B. Deleyiannis, Jeffrey C. Murray, Claire M. Wade, Mary L. Marazita, Danika L. Bannasch

The Fun30 Chromatin Remodeler Fft3 Controls Nuclear Organization and Chromatin Structure of Insulators and Subtelomeres in Fission Yeast

Babett Steglich, Annelie Strålfors, Olga Khorosjutina, Jenna Persson, Agata Smialowska, Jean-Paul Javerzat, Karl Ekwall

Bacterial Infection Drives the Expression Dynamics of microRNAs and Their isomiRs

Katherine J. Siddle, Ludovic Tailleux, Matthieu Deschamps, Yong-Hwee Eddie Loh, Cécile Deluen, Brigitte Gicquel, Christophe Antoniewski, Luis B. Barreiro, Laurent Farinelli, Lluís Quintana-Murci

Neurospora Importin α Is Required for Normal Heterochromatic Formation and DNA Methylation

Andrew D. Klocko, Michael R. Rountree, Paula L. Grisafi, Shan M. Hays, Keyur K. Adhvaryu, Eric U. Selker

Zinc Finger Independent Genome-Wide Binding of Sp2 Potentiates Recruitment of Histone-Fold Protein Nf-y Distinguishing It from Sp1 and Sp3

Sara Völkel, Bastian Stielow, Florian Finkernagel, Thorsten Stiewe, Andrea Nist, Guntram Suske

A Genomic Duplication is Associated with Ectopic Eomesodermin Expression in the Embryonic Chicken Comb and Two Duplex-comb Phenotypes

Ben Dorshorst, Mohammad Harun-Or-Rashid, Alireza Jian Bagherpoor, Carl-Johan Rubin, Chris Ashwell, David Gourichon, Michèle Tixier-Boichard, Finn Hallböök, Leif Andersson

Small Regulatory RNA-Induced Growth Rate Heterogeneity of Bacillus subtilis

Ruben A. T. Mars, Pierre Nicolas, Mariano Ciccolini, Ewoud Reilman, Alexander Reder, Marc Schaffer, Ulrike Mäder, Uwe Völker, Jan Maarten van Dijl, Emma L. Denham

Phenotype Specific Analyses Reveal Distinct Regulatory Mechanism for Chronically Activated p53

Kristina Kirschner, Shamith A. Samarajiwa, Jonathan M. Cairns, Suraj Menon, Pedro A. Pérez-Mancera, Kosuke Tomimatsu, Camino Bermejo-Rodriguez, Yoko Ito, Tamir Chandra, Masako Narita, Scott K. Lyons, Andy G. Lynch, Hiroshi Kimura, Tetsuya Ohbayashi, Simon Tavaré, Masashi Narita

A Meta-analysis of Gene Expression Signatures of Blood Pressure and Hypertension

Tianxiao Huan, Tõnu Esko, Marjolein J. Peters, Luke C. Pilling, Katharina Schramm, Claudia Schurmann, Brian H. Chen, Chunyu Liu, Roby Joehanes, Andrew D. Johnson, Chen Yao, Sai-xia Ying, Paul Courchesne, Lili Milani, Nalini Raghavachari, Richard Wang, Poching Liu, Eva Reinmaa, Abbas Dehghan, Albert Hofman, André G. Uitterlinden, Dena G. Hernandez, Stefania Bandinelli, Andrew Singleton, David Melzer, Andres Metspalu, Maren Carstensen, Harald Grallert, Christian Herder, Thomas Meitinger, Annette Peters, Michael Roden, Melanie Waldenberger, Marcus Dörr, Stephan B. Felix, Tanja Zeller, Ramachandran Vasan, Christopher J. O'Donnell, Peter J. Munson, Xia Yang, Holger Prokisch, Uwe Völker, Joyce B. J. van Meurs, Luigi Ferrucci, Daniel Levy , International Consortium for Blood Pressure GWAS (ICBP)

Escape from X Inactivation Varies in Mouse Tissues

Joel B. Berletch, Wenxiu Ma, Fan Yang, Jay Shendure, William S. Noble, Christine M. Disteche, Xinxian Deng

Male-Biased Aganglionic Megacolon in the TashT Mouse Line Due to Perturbation of Silencer Elements in a Large Gene Desert of Chromosome 10

Karl-F. Bergeron, Tatiana Cardinal, Aboubacrine M. Touré, Mélanie Béland, Diana L. Raiwet, David W. Silversides, Nicolas Pilon

Examining the Evolution of the Regulatory Circuit Controlling Secondary Metabolism and Development in the Fungal Genus Aspergillus

Abigail L. Lind, Jennifer H. Wisecaver, Timothy D. Smith, Xuehuan Feng, Ana M. Calvo, Antonis Rokas

Exome Sequencing in an Admixed Isolated Population Indicates NFXL1 Variants Confer a Risk for Specific Language Impairment

Pía Villanueva, Ron Nudel, Alexander Hoischen, María Angélica Fernández, Nuala H. Simpson, Christian Gilissen, Rose H. Reader, Lillian Jara, Maria Magdalena Echeverry, Clyde Francks, Gillian Baird, Gina Conti-Ramsden, Anne O’Hare, Patrick F. Bolton, Elizabeth R. Hennessy, Hernán Palomino, Luis Carvajal-Carmona, Joris A. Veltman, Jean-Baptiste Cazier, Zulema De Barbieri, Simon E. Fisher, Dianne F. Newbury , the SLI Consortium

Gene Networks Underlying Convergent and Pleiotropic Phenotypes in a Large and Systematically-Phenotyped Cohort with Heterogeneous Developmental Disorders

Tallulah Andrews, Stephen Meader, Anneke Vulto-van Silfhout, Avigail Taylor, Julia Steinberg, Jayne Hehir-Kwa, Rolph Pfundt, Nicole de Leeuw, Bert B. A. de Vries, Caleb Webber

LRGUK-1 Is Required for Basal Body and Manchette Function during Spermatogenesis and Male Fertility

Yan Liu, Kathleen DeBoer, David M. de Kretser, Liza O’Donnell, Anne E. O’Connor, D. Jo Merriner, Hidenobu Okuda, Belinda Whittle, David A. Jans, Athina Efthymiadis, Robert I. McLachlan, Christopher J. Ormandy, Chris C. Goodnow, Duangporn Jamsai, Moira K. O’Bryan

Linking Aβ42-Induced Hyperexcitability to Neurodegeneration, Learning and Motor Deficits, and a Shorter Lifespan in an Alzheimer’s Model

Yong Ping, Eu-Teum Hahm, Girma Waro, Qian Song, Dai-An Vo-Ba, Ashley Licursi, Han Bao, Logan Ganoe, Kelly Finch, Susan Tsunoda

The Nuclear Receptor DAF-12 Regulates Nutrient Metabolism and Reproductive Growth in Nematodes

Zhu Wang, Jonathan Stoltzfus, Young-jai You, Najju Ranjit, Hao Tang, Yang Xie, James B. Lok, David J. Mangelsdorf, Steven A. Kliewer

Methyl Farnesoate Plays a Dual Role in Regulating Drosophila Metamorphosis

Di Wen, Crisalejandra Rivera-Perez, Mohamed Abdou, Qiangqiang Jia, Qianyu He, Xi Liu, Ola Zyaan, Jingjing Xu, William G. Bendena, Stephen S. Tobe, Fernando G. Noriega, Subba R. Palli, Jian Wang, Sheng Li

Hyperdiverse Gene Cluster in Snail Host Conveys Resistance to Human Schistosome Parasites

Jacob A. Tennessen, André Théron, Melanie Marine, Jan-Ying Yeh, Anne Rognon, Michael S. Blouin

The ATM Signaling Cascade Promotes Recombination-Dependent Pachytene Arrest in Mouse Spermatocytes

Sarai Pacheco, Marina Marcet-Ortega, Julian Lange, Maria Jasin, Scott Keeney, Ignasi Roig

A Zinc Finger Motif-Containing Protein Is Essential for Chloroplast RNA Editing

Tao Sun, Xiaowen Shi, Giulia Friso, Klaas Van Wijk, Stephane Bentolila, Maureen R. Hanson

Reproductive Isolation of Hybrid Populations Driven by Genetic Incompatibilities

Molly Schumer, Rongfeng Cui, Gil G. Rosenthal, Peter Andolfatto

The Role of China in the Global Spread of the Current Cholera Pandemic

Xavier Didelot, Bo Pang, Zhemin Zhou, Angela McCann, Peixiang Ni, Dongfang Li, Mark Achtman, Biao Kan

Clonality and Evolutionary History of Rhabdomyosarcoma

Li Chen, Jack F. Shern, Jun S. Wei, Marielle E. Yohe, Young K. Song, Laura Hurd, Hongling Liao, Daniel Catchpoole, Stephen X. Skapek, Frederic G. Barr, Douglas S. Hawkins, Javed Khan

RECG Maintains Plastid and Mitochondrial Genome Stability by Suppressing Extensive Recombination between Short Dispersed Repeats

Masaki Odahara, Yuichi Masuda, Mayuko Sato, Mayumi Wakazaki, Chizuru Harada, Kiminori Toyooka, Yasuhiko Sekine

Seizures Are Regulated by Ubiquitin-specific Peptidase 9 X-linked (USP9X), a De-Ubiquitinase

Lily Paemka, Vinit B. Mahajan, Salleh N. Ehaideb, Jessica M. Skeie, Men Chee Tan, Shu Wu, Allison J. Cox, Levi P. Sowers, Jozef Gecz, Lachlan Jolly, Polly J. Ferguson, Benjamin Darbro, Amy Schneider, Ingrid E. Scheffer, Gemma L. Carvill, Heather C. Mefford, Hatem El-Shanti, Stephen A. Wood, J. Robert Manak, Alexander G. Bassuk

Genome-wide Association Study and Meta-Analysis Identify ISL1 as Genome-wide Significant Susceptibility Gene for Bladder Exstrophy

Markus Draaken, Michael Knapp, Tracie Pennimpede, Johanna M. Schmidt, Anne-Karolin Ebert, Wolfgang Rösch, Raimund Stein, Boris Utsch, Karin Hirsch, Thomas M. Boemers, Elisabeth Mangold, Stefanie Heilmann, Kerstin U. Ludwig, Ekkehart Jenetzky, Nadine Zwink, Susanne Moebus, Bernhard G. Herrmann, Manuel Mattheisen, Markus M. Nöthen, Michael Ludwig, Heiko Reutter

The Complex Contributions of Genetics and Nutrition to Immunity in Drosophila melanogaster

Robert L. Unckless, Susan M. Rottschaefer, Brian P. Lazzaro

The Contribution of Alu Elements to Mutagenic DNA Double-Strand Break Repair

Maria E. Morales, Travis B. White, Vincent A. Streva, Cecily B. DeFreece, Dale J. Hedges, Prescott L. Deininger

Effects on Murine Behavior and Lifespan of Selectively Decreasing Expression of Mutant Huntingtin Allele by Supt4h Knockdown

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Complex Genomic Rearrangements at the PLP1 Locus Include Triplication and Quadruplication

Christine R. Beck, Claudia M. B. Carvalho, Linda Banser, Tomasz Gambin, Danielle Stubbolo, Bo Yuan, Karen Sperle, Suzanne M. McCahan, Marco Henneke, Pavel Seeman, James Y. Garbern, Grace M. Hobson, James R. Lupski

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Carrie L. Flood, Gina P. Rodriguez, Gaobin Bao, Arthur H. Shockley, Yoke Wah Kow, Gray F. Crouse

Rapid Evolution of Recombinant Saccharomyces cerevisiae for Xylose Fermentation through Formation of Extra-chromosomal Circular DNA

Mekonnen M. Demeke, María R. Foulquié-Moreno, Françoise Dumortier, Johan M. Thevelein

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Yueh-Chiang Hu, Peter K. Nicholls, Y. Q. Shirleen Soh, Joseph R. Daniele, Jan Philipp Junker, Alexander van Oudenaarden, David C. Page

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Jose Sebastian, Kook Hui Ryu, Jing Zhou, Danuše Tarkowská, Petr Tarkowski, Young-Hee Cho, Sang-Dong Yoo, Eun-Sol Kim, Ji-Young Lee