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Table of Contents: July 2012

COVER

Fungal development.

Image Credit: Özgür Bayram and Gerhard H. Braus (Georg–August–Universität).
Issue Image

The mold Aspergillus nidulans grows as filaments (yellow) with the potential for several developmental pathways: asexual spores (green) will be released into the air, and sexual spores are produced within fruiting bodies (purple), which are nursed by round Hülle cells (brown). In this issue, Bayram et al. demonstrate that the Fus3 mitogen-activated protein kinase (MAPK) of this filamentous fungus controls nuclear regulators to coordinate sexual development and secondary metabolism. Signal transduction requires that several kinases migrate as the MAPK module from the membrane to the nuclear envelope where only Fus3 enters the nucleus.

Editorial

Guidelines for Genome-Wide Association Studies

Gregory S. Barsh, Gregory P. Copenhaver, Greg Gibson, Scott M. Williams

Perspectives

Oocyte Family Trees: Old Branches or New Stems?

Dori C. Woods, Evelyn E. Telfer, Jonathan L. Tilly

Review

Genomic Data Reveal a Complex Making of Humans

Isabel Alves, Anna Šrámková Hanulová, Matthieu Foll, Laurent Excoffier

Research Articles

Histone H2A Mono-Ubiquitination Is a Crucial Step to Mediate PRC1-Dependent Repression of Developmental Genes to Maintain ES Cell Identity

Mitsuhiro Endoh, Takaho A. Endo, Tamie Endoh, Kyo-ichi Isono, Jafar Sharif, Osamu Ohara, Tetsuro Toyoda, Takashi Ito, Ragnhild Eskeland, Wendy A. Bickmore, Miguel Vidal, Bradley E. Bernstein, Haruhiko Koseki

Intact p53-Dependent Responses in miR-34–Deficient Mice

Carla P. Concepcion, Yoon-Chi Han, Ping Mu, Ciro Bonetti, Evelyn Yao, Aleco D'Andrea, Joana A. Vidigal, William P. Maughan, Paul Ogrodowski, Andrea Ventura

The Arabidopsis HEI10 Is a New ZMM Protein Related to Zip3

Liudmila Chelysheva, Daniel Vezon, Aurélie Chambon, Ghislaine Gendrot, Lucie Pereira, Afef Lemhemdi, Nathalie Vrielynck, Sylvia Le Guin, Maria Novatchkova, Mathilde Grelon

Large-Scale Introgression Shapes the Evolution of the Mating-Type Chromosomes of the Filamentous Ascomycete Neurospora tetrasperma

Yu Sun, Pádraic Corcoran, Audrius Menkis, Carrie A. Whittle, Siv G. E. Andersson, Hanna Johannesson

Let-7b/c Enhance the Stability of a Tissue-Specific mRNA during Mammalian Organogenesis as Part of a Feedback Loop Involving KSRP

Emanuela Repetto, Paola Briata, Nathalie Kuziner, Brian D. Harfe, Michael T. McManus, Roberto Gherzi, Michael G. Rosenfeld, Michele Trabucchi

Lipoproteins in Drosophila melanogaster—Assembly, Function, and Influence on Tissue Lipid Composition

Wilhelm Palm, Julio L. Sampaio, Marko Brankatschk, Maria Carvalho, Ali Mahmoud, Andrej Shevchenko, Suzanne Eaton

Identification of Chromatin-Associated Regulators of MSL Complex Targeting in Drosophila Dosage Compensation

Erica Larschan, Marcela M. L. Soruco, Ok-Kyung Lee, Shouyong Peng, Eric Bishop, Jessica Chery, Karen Goebel, Jessica Feng, Peter J. Park, Mitzi I. Kuroda

Drosophila Fatty Acid Transport Protein Regulates Rhodopsin-1 Metabolism and Is Required for Photoreceptor Neuron Survival

Pierre Dourlen, Benjamin Bertin, Gilles Chatelain, Marion Robin, Francesco Napoletano, Michel J. Roux, Bertrand Mollereau

Brain-Specific Rescue of Clock Reveals System-Driven Transcriptional Rhythms in Peripheral Tissue

Michael E. Hughes, Hee-Kyung Hong, Jason L. Chong, Alejandra A. Indacochea, Samuel S. Lee, Michael Han, Joseph S. Takahashi, John B. Hogenesch

Recent Loss of Self-Incompatibility by Degradation of the Male Component in Allotetraploid Arabidopsis kamchatica

Takashi Tsuchimatsu, Pascal Kaiser, Chow-Lih Yew, Julien B. Bachelier, Kentaro K. Shimizu

Pregnancy-Induced Noncoding RNA (PINC) Associates with Polycomb Repressive Complex 2 and Regulates Mammary Epithelial Differentiation

Amy N. Shore, Elena B. Kabotyanski, Kevin Roarty, Martin A. Smith, Yiqun Zhang, Chad J. Creighton, Marcel E. Dinger, Jeffrey M. Rosen

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

Claudia Kutter, Stephen Watt, Klara Stefflova, Michael D. Wilson, Angela Goncalves, Chris P. Ponting, Duncan T. Odom, Ana C. Marques

The SCFDia2 Ubiquitin E3 Ligase Ubiquitylates Sir4 and Functions in Transcriptional Silencing

Rebecca J. Burgess, Hui Zhou, Junhong Han, Qing Li, Zhiguo Zhang

F-Box Protein Specificity for G1 Cyclins Is Dictated by Subcellular Localization

Benjamin D. Landry, John P. Doyle, David P. Toczyski, Jennifer A. Benanti

Genetic Variants in REC8, RNF212, and PRDM9 Influence Male Recombination in Cattle

Cynthia Sandor, Wanbo Li, Wouter Coppieters, Tom Druet, Carole Charlier, Michel Georges

OSD1 Promotes Meiotic Progression via APC/C Inhibition and Forms a Regulatory Network with TDM and CYCA1;2/TAM

Laurence Cromer, Jefri Heyman, Sandra Touati, Hirofumi Harashima, Emilie Araou, Chloe Girard, Christine Horlow, Katja Wassmann, Arp Schnittger, Lieven De Veylder, Raphael Mercier

Evidence of Inbreeding Depression on Human Height

Ruth McQuillan, Niina Eklund, Nicola Pirastu, Maris Kuningas, Brian P. McEvoy, Tõnu Esko, Tanguy Corre, Gail Davies, Marika Kaakinen, Leo-Pekka Lyytikäinen, Kati Kristiansson, Aki S. Havulinna, Martin Gögele, Veronique Vitart, Albert Tenesa, Yurii Aulchenko, Caroline Hayward, Åsa Johansson, Mladen Boban, Sheila Ulivi, Antonietta Robino, Vesna Boraska, Wilmar Igl, Sarah H. Wild, Lina Zgaga, Najaf Amin, Evropi Theodoratou, Ozren Polašek, Giorgia Girotto, Lorna M. Lopez, Cinzia Sala, Jari Lahti, Tiina Laatikainen, Inga Prokopenko, Mart Kals, Jorma Viikari, Jian Yang, Anneli Pouta, Karol Estrada, Albert Hofman, Nelson Freimer, Nicholas G. Martin, Mika Kähönen, Lili Milani, Markku Heliövaara, Erkki Vartiainen, Katri Räikkönen, Corrado Masciullo, John M. Starr, Andrew A. Hicks, Laura Esposito, Ivana Kolčić, Susan M. Farrington, Ben Oostra, Tatijana Zemunik, Harry Campbell, Mirna Kirin, Marina Pehlic, Flavio Faletra, David Porteous, Giorgio Pistis, Elisabeth Widén, Veikko Salomaa, Seppo Koskinen, Krista Fischer, Terho Lehtimäki, Andrew Heath, Mark I. McCarthy, Fernando Rivadeneira, Grant W. Montgomery, Henning Tiemeier, Anna-Liisa Hartikainen, Pamela A. F. Madden, Pio d'Adamo, Nicholas D. Hastie, Ulf Gyllensten, Alan F. Wright, Cornelia M. van Duijn, Malcolm Dunlop, Igor Rudan, Paolo Gasparini, Peter P. Pramstaller, Ian J. Deary, Daniela Toniolo, Johan G. Eriksson, Antti Jula, Olli T. Raitakari, Andres Metspalu, Markus Perola, Marjo-Riitta Järvelin, André Uitterlinden, Peter M. Visscher, James F. Wilson , on behalf of the ROHgen Consortium

Differential Impact of the HEN1 Homolog HENN-1 on 21U and 26G RNAs in the Germline of Caenorhabditis elegans

Leonie M. Kamminga, Josien C. van Wolfswinkel, Maartje J. Luteijn, Lucas J. T. Kaaij, Marloes P. Bagijn, Alexandra Sapetschnig, Eric A. Miska, Eugene Berezikov, René F. Ketting

The Chicken Frizzle Feather Is Due to an α-Keratin (KRT75) Mutation That Causes a Defective Rachis

Chen Siang Ng, Ping Wu, John Foley, Anne Foley, Merry-Lynn McDonald, Wen-Tau Juan, Chih-Jen Huang, Yu-Ting Lai, Wen-Sui Lo, Chih-Feng Chen, Suzanne M. Leal, Huanmin Zhang, Randall B. Widelitz, Pragna I. Patel, Wen-Hsiung Li, Cheng-Ming Chuong

Loss of ATRX, Genome Instability, and an Altered DNA Damage Response Are Hallmarks of the Alternative Lengthening of Telomeres Pathway

Courtney A. Lovejoy, Wendi Li, Steven Reisenweber, Supawat Thongthip, Joanne Bruno, Titia de Lange, Saurav De, John H. J. Petrini, Patricia A. Sung, Maria Jasin, Joseph Rosenbluh, Yaara Zwang, Barbara A. Weir, Charlie Hatton, Elena Ivanova, Laura Macconaill, Megan Hanna, William C. Hahn, Neal F. Lue, Roger R. Reddel, Yuchen Jiao, Kenneth Kinzler, Bert Vogelstein, Nickolas Papadopoulos, Alan K. Meeker , for the ALT Starr Cancer Consortium

A Genome-Wide Association Meta-Analysis of Circulating Sex Hormone–Binding Globulin Reveals Multiple Loci Implicated in Sex Steroid Hormone Regulation

Andrea D. Coviello, Robin Haring, Melissa Wellons, Dhananjay Vaidya, Terho Lehtimäki, Sarah Keildson, Kathryn L. Lunetta, Chunyan He, Myriam Fornage, Vasiliki Lagou, Massimo Mangino, N. Charlotte Onland-Moret, Brian Chen, Joel Eriksson, Melissa Garcia, Yong Mei Liu, Annemarie Koster, Kurt Lohman, Leo-Pekka Lyytikäinen, Ann-Kristin Petersen, Jennifer Prescott, Lisette Stolk, Liesbeth Vandenput, Andrew R. Wood, Wei Vivian Zhuang, Aimo Ruokonen, Anna-Liisa Hartikainen, Anneli Pouta, Stefania Bandinelli, Reiner Biffar, Georg Brabant, David G. Cox, Yuhui Chen, Steven Cummings, Luigi Ferrucci, Marc J. Gunter, Susan E. Hankinson, Hannu Martikainen, Albert Hofman, Georg Homuth, Thomas Illig, John-Olov Jansson, Andrew D. Johnson, David Karasik, Magnus Karlsson, Johannes Kettunen, Douglas P. Kiel, Peter Kraft, Jingmin Liu, Östen Ljunggren, Mattias Lorentzon, Marcello Maggio, Marcello R. P. Markus, Dan Mellström, Iva Miljkovic, Daniel Mirel, Sarah Nelson, Laure Morin Papunen, Petra H. M. Peeters, Inga Prokopenko, Leslie Raffel, Martin Reincke, Alex P. Reiner, Kathryn Rexrode, Fernando Rivadeneira, Stephen M. Schwartz, David Siscovick, Nicole Soranzo, Doris Stöckl, Shelley Tworoger, André G. Uitterlinden, Carla H. van Gils, Ramachandran S. Vasan, H.-Erich Wichmann, Guangju Zhai, Shalender Bhasin, Martin Bidlingmaier, Stephen J. Chanock, Immaculata De Vivo, Tamara B. Harris, David J. Hunter, Mika Kähönen, Simin Liu, Pamela Ouyang, Tim D. Spector, Yvonne T. van der Schouw, Jorma Viikari, Henri Wallaschofski, Mark I. McCarthy, Timothy M. Frayling, Anna Murray, Steve Franks, Marjo-Riitta Järvelin, Frank H. de Jong, Olli Raitakari, Alexander Teumer, Claes Ohlsson, Joanne M. Murabito, John R. B. Perry

Balancing Selection at the Tomato RCR3 Guardee Gene Family Maintains Variation in Strength of Pathogen Defense

Anja C. Hörger, Muhammad Ilyas, Wolfgang Stephan, Aurélien Tellier, Renier A. L. van der Hoorn, Laura E. Rose

RsfA (YbeB) Proteins Are Conserved Ribosomal Silencing Factors

Roman Häuser, Markus Pech, Jaroslaw Kijek, Hiroshi Yamamoto, Björn Titz, Florian Naeve, Andrey Tovchigrechko, Kaori Yamamoto, Witold Szaflarski, Nono Takeuchi, Thorsten Stellberger, Markus E. Diefenbacher, Knud H. Nierhaus, Peter Uetz

The Aspergillus nidulans MAPK Module AnSte11-Ste50-Ste7-Fus3 Controls Development and Secondary Metabolism

Özgür Bayram, Özlem Sarikaya Bayram, Yasar Luqman Ahmed, Jun-ichi Maruyama, Oliver Valerius, Silvio O. Rizzoli, Ralf Ficner, Stefan Irniger, Gerhard H. Braus

Histone H2B Monoubiquitination Facilitates the Rapid Modulation of Gene Expression during Arabidopsis Photomorphogenesis

Clara Bourbousse, Ikhlak Ahmed, François Roudier, Gérald Zabulon, Eddy Blondet, Sandrine Balzergue, Vincent Colot, Chris Bowler, Fredy Barneche

Reversal of PCNA Ubiquitylation by Ubp10 in Saccharomyces cerevisiae

Alfonso Gallego-Sánchez, Sonia Andrés, Francisco Conde, Pedro A. San-Segundo, Avelino Bueno

The Caenorhabditis elegans Gene mfap-1 Encodes a Nuclear Protein That Affects Alternative Splicing

Long Ma, Xiaoyang Gao, Jintao Luo, Liange Huang, Yanling Teng, H. Robert Horvitz

GRHL3/GET1 and Trithorax Group Members Collaborate to Activate the Epidermal Progenitor Differentiation Program

Amelia Soto Hopkin, William Gordon, Rachel Herndon Klein, Francisco Espitia, Kenneth Daily, Michael Zeller, Pierre Baldi, Bogi Andersen

Detecting Individual Sites Subject to Episodic Diversifying Selection

Ben Murrell, Joel O. Wertheim, Sasha Moola, Thomas Weighill, Konrad Scheffler, Sergei L. Kosakovsky Pond

Three Dopamine Pathways Induce Aversive Odor Memories with Different Stability

Yoshinori Aso, Andrea Herb, Maite Ogueta, Igor Siwanowicz, Thomas Templier, Anja B. Friedrich, Kei Ito, Henrike Scholz, Hiromu Tanimoto

CED-10/Rac1 Regulates Endocytic Recycling through the RAB-5 GAP TBC-2

Lin Sun, Ou Liu, Jigar Desai, Farhad Karbassi, Marc-André Sylvain, Anbing Shi, Zheng Zhou, Christian E. Rocheleau, Barth D. Grant

GWAS Identifies Novel Susceptibility Loci on 6p21.32 and 21q21.3 for Hepatocellular Carcinoma in Chronic Hepatitis B Virus Carriers

Shengping Li, Ji Qian, Yuan Yang, Wanting Zhao, Juncheng Dai, Jin-Xin Bei, Jia Nee Foo, Paul J. McLaren, Zhiqiang Li, Jingmin Yang, Feng Shen, Li Liu, Jiamei Yang, Shuhong Li, Shandong Pan, Yi Wang, Wenjin Li, Xiangjun Zhai, Boping Zhou, Lehua Shi, Xinchun Chen, Minjie Chu, Yiqun Yan, Jun Wang, Shuqun Cheng, Jiawei Shen, Weihua Jia, Jibin Liu, Jiahe Yang, Zujia Wen, Aijun Li, Ying Zhang, Guoliang Zhang, Xianrong Luo, Hongbo Qin, Minshan Chen, Hua Wang, Li Jin, Dongxin Lin, Hongbing Shen, Lin He, Paul I. W. de Bakker, Hongyang Wang, Yi-Xin Zeng, Mengchao Wu, Zhibin Hu, Yongyong Shi, Jianjun Liu, Weiping Zhou

A Trans-Species Missense SNP in Amhr2 Is Associated with Sex Determination in the Tiger Pufferfish, Takifugu rubripes (Fugu)

Takashi Kamiya, Wataru Kai, Satoshi Tasumi, Ayumi Oka, Takayoshi Matsunaga, Naoki Mizuno, Masashi Fujita, Hiroaki Suetake, Shigenori Suzuki, Sho Hosoya, Sumanty Tohari, Sydney Brenner, Toshiaki Miyadai, Byrappa Venkatesh, Yuzuru Suzuki, Kiyoshi Kikuchi

A Key Role for Chd1 in Histone H3 Dynamics at the 3′ Ends of Long Genes in Yeast

Marta Radman-Livaja, Tiffani K. Quan, Lourdes Valenzuela, Jennifer A. Armstrong, Tibor van Welsem, TaeSoo Kim, Laura J. Lee, Stephen Buratowski, Fred van Leeuwen, Oliver J. Rando, Grant A. Hartzog

Allelic Heterogeneity and Trade-Off Shape Natural Variation for Response to Soil Micronutrient

Seifollah Poormohammad Kiani, Charlotte Trontin, Matthew Andreatta, Matthieu Simon, Thierry Robert, David E. Salt, Olivier Loudet

Cellular Variability of RpoS Expression Underlies Subpopulation Activation of an Integrative and Conjugative Element

Ryo Miyazaki, Marco Minoia, Nicolas Pradervand, Sandra Sulser, Friedrich Reinhard, Jan Roelof van der Meer

Functional Evolution of Mammalian Odorant Receptors

Kaylin A. Adipietro, Joel D. Mainland, Hiroaki Matsunami

Meta-Analysis of Genome-Wide Scans for Total Body BMD in Children and Adults Reveals Allelic Heterogeneity and Age-Specific Effects at the WNT16 Locus

Carolina Medina-Gomez, John P. Kemp, Karol Estrada, Joel Eriksson, Jeff Liu, Sjur Reppe, David M. Evans, Denise H. M. Heppe, Liesbeth Vandenput, Lizbeth Herrera, Susan M. Ring, Claudia J. Kruithof, Nicholas J. Timpson, M. Carola Zillikens, Ole K. Olstad, Hou-Feng Zheng, J. Brent Richards, Beate St. Pourcain, Albert Hofman, Vincent W. V. Jaddoe, George Davey Smith, Mattias Lorentzon, Kaare M. Gautvik, André G. Uitterlinden, Robert Brommage, Claes Ohlsson, Jonathan H. Tobias, Fernando Rivadeneira

WNT16 Influences Bone Mineral Density, Cortical Bone Thickness, Bone Strength, and Osteoporotic Fracture Risk

Hou-Feng Zheng, Jon H. Tobias, Emma Duncan, David M. Evans, Joel Eriksson, Lavinia Paternoster, Laura M. Yerges-Armstrong, Terho Lehtimäki, Ulrica Bergström, Mika Kähönen, Paul J. Leo, Olli Raitakari, Marika Laaksonen, Geoffrey C. Nicholson, Jorma Viikari, Martin Ladouceur, Leo-Pekka Lyytikäinen, Carolina Medina-Gomez, Fernando Rivadeneira, Richard L. Prince, Harri Sievanen, William D. Leslie, Dan Mellström, John A. Eisman, Sofia Movérare-Skrtic, David Goltzman, David A. Hanley, Graeme Jones, Beate St. Pourcain, Yongjun Xiao, Nicholas J. Timpson, George Davey Smith, Ian R. Reid, Susan M. Ring, Philip N. Sambrook, Magnus Karlsson, Elaine M. Dennison, John P. Kemp, Patrick Danoy, Adrian Sayers, Scott G. Wilson, Maria Nethander, Eugene McCloskey, Liesbeth Vandenput, Richard Eastell, Jeff Liu, Tim Spector, Braxton D. Mitchell, Elizabeth A. Streeten, Robert Brommage, Ulrika Pettersson-Kymmer, Matthew A. Brown, Claes Ohlsson, J. Brent Richards, Mattias Lorentzon

A Regulatory Loop Involving PAX6, MITF, and WNT Signaling Controls Retinal Pigment Epithelium Development

Kapil Bharti, Melanie Gasper, Jingxing Ou, Martha Brucato, Katharina Clore-Gronenborn, James Pickel, Heinz Arnheiter

Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions

Joyce E. Loper, Karl A. Hassan, Dmitri V. Mavrodi, Edward W. Davis II, Chee Kent Lim, Brenda T. Shaffer, Liam D. H. Elbourne, Virginia O. Stockwell, Sierra L. Hartney, Katy Breakwell, Marcella D. Henkels, Sasha G. Tetu, Lorena I. Rangel, Teresa A. Kidarsa, Neil L. Wilson, Judith E. van de Mortel, Chunxu Song, Rachel Blumhagen, Diana Radune, Jessica B. Hostetler, Lauren M. Brinkac, A. Scott Durkin, Daniel A. Kluepfel, W. Patrick Wechter, Anne J. Anderson, Young Cheol Kim, Leland S. Pierson III, Elizabeth A. Pierson, Steven E. Lindow, Donald Y. Kobayashi, Jos M. Raaijmakers, David M. Weller, Linda S. Thomashow, Andrew E. Allen, Ian T. Paulsen

FANCJ/BACH1 Acetylation at Lysine 1249 Regulates the DNA Damage Response

Jenny Xie, Min Peng, Shawna Guillemette, Steven Quan, Stephanie Maniatis, Yuliang Wu, Aditya Venkatesh, Scott A. Shaffer, Robert M. Brosh Jr., Sharon B. Cantor

TDP-1/TDP-43 Regulates Stress Signaling and Age-Dependent Proteotoxicity in Caenorhabditis elegans

Alexandra Vaccaro, Arnaud Tauffenberger, Peter E. A. Ash, Yari Carlomagno, Leonard Petrucelli, J. Alex Parker

DNA Methyltransferases Are Required to Induce Heterochromatic Re-Replication in Arabidopsis

Hume Stroud, Christopher J. Hale, Suhua Feng, Elena Caro, Yannick Jacob, Scott D. Michaels, Steven E. Jacobsen

The Role of Rice HEI10 in the Formation of Meiotic Crossovers

Kejian Wang, Mo Wang, Ding Tang, Yi Shen, Chunbo Miao, Qing Hu, Tiegang Lu, Zhukuan Cheng

Phosphorylation-Dependent Interactions between Crb2 and Chk1 Are Essential for DNA Damage Checkpoint

Meng Qu, Bing Yang, Li Tao, John R. Yates III, Paul Russell, Meng-Qiu Dong, Li-Lin Du

Genome-Wide Association Analysis in Asthma Subjects Identifies SPATS2L as a Novel Bronchodilator Response Gene

Blanca E. Himes, Xiaofeng Jiang, Ruoxi Hu, Ann C. Wu, Jessica A. Lasky-Su, Barbara J. Klanderman, John Ziniti, Jody Senter-Sylvia, John J. Lima, Charles G. Irvin, Stephen P. Peters, Deborah A. Meyers, Eugene R. Bleecker, Michiaki Kubo, Mayumi Tamari, Yusuke Nakamura, Stanley J. Szefler, Robert F. Lemanske Jr., Robert S. Zeiger, Robert C. Strunk, Fernando D. Martinez, John P. Hanrahan, Gerard H. Koppelman, Dirkje S. Postma, Maartje A. E. Nieuwenhuis, Judith M. Vonk, Reynold A. Panettieri Jr., Amy Markezich, Elliot Israel, Vincent J. Carey, Kelan G. Tantisira, Augusto A. Litonjua, Quan Lu, Scott T. Weiss