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Table of Contents: October 2011

COVER

A bulldog.

Image Credit: User Nokdie at flickr.com
Issue Image

There are hundreds of breeds of domestic dog, which each have unique characteristics. The huge phenotypic variability of dogs results from strong artificial selection. Vaysse et al. identified footprints of selection in the dog's genome.

Perspectives

Research Articles

Insights into Hox Protein Function from a Large Scale Combinatorial Analysis of Protein Domains

Samir Merabet, Isma Litim-Mecheri, Daniel Karlsson, Richa Dixit, Mehdi Saadaoui, Bruno Monier, Christine Brun, Stefan Thor, K. Vijayraghavan, Laurent Perrin, Jacques Pradel, Yacine Graba

Role of Exonic Variation in Chemokine Receptor Genes on AIDS: CCRL2 F167Y Association with Pneumocystis Pneumonia

Ping An, Rongling Li, Ji Ming Wang, Teizo Yoshimura, Munehisa Takahashi, Ram Samudralal, Stephen J. O'Brien, John Phair, James J. Goedert, Gregory D. Kirk, Jennifer L. Troyer, Efe Sezgin, Susan P. Buchbinder, Sharyne Donfield, George W. Nelson, Cheryl A. Winkler

Association of NCF2, IKZF1, IRF8, IFIH1, and TYK2 with Systemic Lupus Erythematosus

Deborah S. Cunninghame Graham, David L. Morris, Tushar R. Bhangale, Lindsey A. Criswell, Ann-Christine Syvänen, Lars Rönnblom, Timothy W. Behrens, Robert R. Graham, Timothy J. Vyse

Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis

Christopher A. Desjardins, Mia D. Champion, Jason W. Holder, Anna Muszewska, Jonathan Goldberg, Alexandre M. Bailão, Marcelo Macedo Brigido, Márcia Eliana da Silva Ferreira, Ana Maria Garcia, Marcin Grynberg, Sharvari Gujja, David I. Heiman, Matthew R. Henn, Chinnappa D. Kodira, Henry León-Narváez, Larissa V. G. Longo, Li-Jun Ma, Iran Malavazi, Alisson L. Matsuo, Flavia V. Morais, Maristela Pereira, Sabrina Rodríguez-Brito, Sharadha Sakthikumar, Silvia M. Salem-Izacc, Sean M. Sykes, Marcus Melo Teixeira, Milene C. Vallejo, Maria Emília Machado Telles Walter, Chandri Yandava, Sarah Young, Qiandong Zeng, Jeremy Zucker, Maria Sueli Felipe, Gustavo H. Goldman, Brian J. Haas, Juan G. McEwen, Gustavo Nino-Vega, Rosana Puccia, Gioconda San-Blas, Celia Maria de Almeida Soares, Bruce W. Birren, Christina A. Cuomo

A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila

Charless C. Fowlkes, Kelly B. Eckenrode, Meghan D. Bragdon, Miriah Meyer, Zeba Wunderlich, Lisa Simirenko, Cris L. Luengo Hendriks, Soile V. E. Keränen, Clara Henriquez, David W. Knowles, Mark D. Biggin, Michael B. Eisen, Angela H. DePace

Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation

Hironori Waki, Masahiro Nakamura, Toshimasa Yamauchi, Ken-ichi Wakabayashi, Jing Yu, Lisa Hirose-Yotsuya, Kazumi Take, Wei Sun, Masato Iwabu, Miki Okada-Iwabu, Takanori Fujita, Tomohisa Aoyama, Shuichi Tsutsumi, Kohjiro Ueki, Tatsuhiko Kodama, Juro Sakai, Hiroyuki Aburatani, Takashi Kadowaki

Identification of Widespread Ultra-Edited Human RNAs

Shai Carmi, Itamar Borukhov, Erez Y. Levanon

Genetic Interaction between MTMR2 and FIG4 Phospholipid Phosphatases Involved in Charcot-Marie-Tooth Neuropathies

Ilaria Vaccari, Giorgia Dina, Hélène Tronchère, Emily Kaufman, Gaëtan Chicanne, Federica Cerri, Lawrence Wrabetz, Bernard Payrastre, Angelo Quattrini, Lois S. Weisman, Miriam H. Meisler, Alessandra Bolino

Transforming Growth Factor β Receptor Type 1 Is Essential for Female Reproductive Tract Integrity and Function

Qinglei Li, Julio E. Agno, Mark A. Edson, Ankur K. Nagaraja, Takashi Nagashima, Martin M. Matzuk

Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1

Tyler J. Creamer, Miranda M. Darby, Nuttara Jamonnak, Paul Schaughency, Haiping Hao, Sarah J. Wheelan, Jeffry L. Corden

Feed-Forward Microprocessing and Splicing Activities at a MicroRNA–Containing Intron

Maja M. Janas, Mehdi Khaled, Steffen Schubert, Jacob G. Bernstein, David Golan, Rosa A. Veguilla, David E. Fisher, Noam Shomron, Carmit Levy, Carl D. Novina

Genetic Rearrangements Can Modify Chromatin Features at Epialleles

Andrea M. Foerster, Huy Q. Dinh, Laura Sedman, Bonnie Wohlrab, Ortrun Mittelsten Scheid

A Systems Biology Approach Reveals the Role of a Novel Methyltransferase in Response to Chemical Stress and Lipid Homeostasis

Elena Lissina, Brian Young, Malene L. Urbanus, Xue Li Guan, Jonathan Lowenson, Shawn Hoon, Anastasia Baryshnikova, Isabelle Riezman, Magali Michaut, Howard Riezman, Leah E. Cowen, Markus R. Wenk, Steven G. Clarke, Guri Giaever, Corey Nislow

A Genome-Wide Screen for Interactions Reveals a New Locus on 4p15 Modifying the Effect of Waist-to-Hip Ratio on Total Cholesterol

Ida Surakka, Aaron Isaacs, Lennart C. Karssen, Pirkka-Pekka P. Laurila, Rita P. S. Middelberg, Emmi Tikkanen, Janina S. Ried, Claudia Lamina, Massimo Mangino, Wilmar Igl, Jouke-Jan Hottenga, Vasiliki Lagou, Pim van der Harst, Irene Mateo Leach, Tõnu Esko, Zoltán Kutalik, Nicholas W. Wainwright, Maksim V. Struchalin, Antti-Pekka Sarin, Antti J. Kangas, Jorma S. Viikari, Markus Perola, Taina Rantanen, Ann-Kristin Petersen, Pasi Soininen, Åsa Johansson, Nicole Soranzo, Andrew C. Heath, Theodore Papamarkou, Inga Prokopenko, Anke Tönjes, Florian Kronenberg, Angela Döring, Fernando Rivadeneira, Grant W. Montgomery, John B. Whitfield, Mika Kähönen, Terho Lehtimäki, Nelson B. Freimer, Gonneke Willemsen, Eco J. C. de Geus, Aarno Palotie, Manj S. Sandhu, Dawn M. Waterworth, Andres Metspalu, Michael Stumvoll, André G. Uitterlinden, Antti Jula, Gerjan Navis, Cisca Wijmenga, Bruce H. R. Wolffenbuttel, Marja-Riitta Taskinen, Mika Ala-Korpela, Jaakko Kaprio, Kirsten O. Kyvik, Dorret I. Boomsma, Nancy L. Pedersen, Ulf Gyllensten, James F. Wilson, Igor Rudan, Harry Campbell, Peter P. Pramstaller, Tim D. Spector, Jacqueline C. M. Witteman, Johan G. Eriksson, Veikko Salomaa, Ben A. Oostra, Olli T. Raitakari, H.-Erich Wichmann, Christian Gieger, Marjo-Riitta Järvelin, Nicholas G. Martin, Albert Hofman, Mark I. McCarthy, Leena Peltonen, Cornelia M. van Duijn, Yurii S. Aulchenko, Samuli Ripatti , for the ENGAGE Consortium

HIF–VEGF Pathways Are Critical for Chronic Otitis Media in Junbo and Jeff Mouse Mutants

Michael T. Cheeseman, Hayley E. Tyrer, Debbie Williams, Tertius A. Hough, Paras Pathak, Maria R. Romero, Helen Hilton, Sulzhan Bali, Andrew Parker, Lucie Vizor, Tom Purnell, Kate Vowell, Sara Wells, Mahmood F. Bhutta, Paul K. Potter, Steve D. M. Brown

Oxr1 Is Essential for Protection against Oxidative Stress-Induced Neurodegeneration

Peter L. Oliver, Mattéa J. Finelli, Benjamin Edwards, Emmanuelle Bitoun, Darcy L. Butts, Esther B. E. Becker, Michael T. Cheeseman, Ben Davies, Kay E. Davies

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo

Chung-Yi Nien, Hsiao-Lan Liang, Stephen Butcher, Yujia Sun, Shengbo Fu, Tenzin Gocha, Nikolai Kirov, J. Robert Manak, Christine Rushlow

Novel Function of Distal-less as a Gap Gene during Spider Segmentation

Matthias Pechmann, Sara Khadjeh, Natascha Turetzek, Alistair P. McGregor, Wim G. M. Damen, Nikola-Michael Prpic

Preventing Dangerous Nonsense: Selection for Robustness to Transcriptional Error in Human Genes

Brian P. Cusack, Peter F. Arndt, Laurent Duret, Hugues Roest Crollius

A One Base Pair Deletion in the Canine ATP13A2 Gene Causes Exon Skipping and Late-Onset Neuronal Ceroid Lipofuscinosis in the Tibetan Terrier

Anne Wöhlke, Ute Philipp, Patricia Bock, Andreas Beineke, Peter Lichtner, Thomas Meitinger, Ottmar Distl

Von Hippel-Lindau (VHL) Inactivation in Sporadic Clear Cell Renal Cancer: Associations with Germline VHL Polymorphisms and Etiologic Risk Factors

Lee E. Moore, Michael L. Nickerson, Paul Brennan, Jorge R. Toro, Erich Jaeger, Jessica Rinsky, Summer S. Han, David Zaridze, Vsevolod Matveev, Vladimir Janout, Hellena Kollarova, Vladimir Bencko, Marie Navratilova, Neonilia Szeszenia-Dabrowska, Dana Mates, Laura S. Schmidt, Petra Lenz, Sara Karami, W. Marston Linehan, Maria Merino, Stephen Chanock, Paolo Boffetta, Wong-Ho Chow, Frederic M. Waldman, Nathaniel Rothman

Three Structure-Selective Endonucleases Are Essential in the Absence of BLM Helicase in Drosophila

Sabrina L. Andersen, H. Kenny Kuo, Daniel Savukoski, Michael H. Brodsky, Jeff Sekelsky

Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping

Amaury Vaysse, Abhirami Ratnakumar, Thomas Derrien, Erik Axelsson, Gerli Rosengren Pielberg, Snaevar Sigurdsson, Tove Fall, Eija H. Seppälä, Mark S. T. Hansen, Cindy T. Lawley, Elinor K. Karlsson, Danika Bannasch, Carles Vilà, Hannes Lohi, Francis Galibert, Merete Fredholm, Jens Häggström, Åke Hedhammar, Catherine André, Kerstin Lindblad-Toh, Christophe Hitte, Matthew T. Webster , The LUPA Consortium

The Thermoanaerobacter Glycobiome Reveals Mechanisms of Pentose and Hexose Co-Utilization in Bacteria

Lu Lin, Houhui Song, Qichao Tu, Yujia Qin, Aifen Zhou, Wenbin Liu, Zhili He, Jizhong Zhou, Jian Xu

Macroautophagy Is Regulated by the UPR–Mediator CHOP and Accentuates the Phenotype of SBMA Mice

Zhigang Yu, Adrienne M. Wang, Hiroaki Adachi, Masahisa Katsuno, Gen Sobue, Zhenyu Yue, Diane M. Robins, Andrew P. Lieberman

A Phenomics-Based Strategy Identifies Loci on APOC1, BRAP, and PLCG1 Associated with Metabolic Syndrome Phenotype Domains

Christy L. Avery, Qianchuan He, Kari E. North, Jose L. Ambite, Eric Boerwinkle, Myriam Fornage, Lucia A. Hindorff, Charles Kooperberg, James B. Meigs, James S. Pankow, Sarah A. Pendergrass, Bruce M. Psaty, Marylyn D. Ritchie, Jerome I. Rotter, Kent D. Taylor, Lynne R. Wilkens, Gerardo Heiss, Dan Yu Lin

The Bicoid Stability Factor Controls Polyadenylation and Expression of Specific Mitochondrial mRNAs in Drosophila melanogaster

Ana Bratic, Anna Wredenberg, Sebastian Grönke, James B. Stewart, Arnaud Mourier, Benedetta Ruzzenente, Christian Kukat, Rolf Wibom, Bianca Habermann, Linda Partridge, Nils-Göran Larsson

Whole-Exome Sequencing Identifies Homozygous AFG3L2 Mutations in a Spastic Ataxia-Neuropathy Syndrome Linked to Mitochondrial m-AAA Proteases

Tyler Mark Pierson, David Adams, Florian Bonn, Paola Martinelli, Praveen F. Cherukuri, Jamie K. Teer, Nancy F. Hansen, Pedro Cruz, James C. Mullikin for the NISC Comparative Sequencing Program, Robert W. Blakesley, Gretchen Golas, Justin Kwan, Anthony Sandler, Karin Fuentes Fajardo, Thomas Markello, Cynthia Tifft, Craig Blackstone, Elena I. Rugarli, Thomas Langer, William A. Gahl, Camilo Toro

Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome

Kirk E. Lohmueller, Anders Albrechtsen, Yingrui Li, Su Yeon Kim, Thorfinn Korneliussen, Nicolas Vinckenbosch, Geng Tian, Emilia Huerta-Sanchez, Alison F. Feder, Niels Grarup, Torben Jørgensen, Tao Jiang, Daniel R. Witte, Annelli Sandbæk, Ines Hellmann, Torsten Lauritzen, Torben Hansen, Oluf Pedersen, Jun Wang, Rasmus Nielsen

MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains

Hai Yang Hu, Song Guo, Jiang Xi, Zheng Yan, Ning Fu, Xiaoyu Zhang, Corinna Menzel, Hongyu Liang, Hongyi Yang, Min Zhao, Rong Zeng, Wei Chen, Svante Pääbo, Philipp Khaitovich

Mutations in a Guanylate Cyclase GCY-35/GCY-36 Modify Bardet-Biedl Syndrome–Associated Phenotypes in Caenorhabditis elegans

Calvin A. Mok, Michael P. Healey, Tanvi Shekhar, Michel R. Leroux, Elise Héon, Mei Zhen

Dynamic Replacement of Histone H3 Variants Reprograms Epigenetic Marks in Early Mouse Embryos

Tomohiko Akiyama, Osamu Suzuki, Junichiro Matsuda, Fugaku Aoki

Mutator Suppression and Escape from Replication Error–Induced Extinction in Yeast

Alan J. Herr, Masanori Ogawa, Nicole A. Lawrence, Lindsey N. Williams, Julie M. Eggington, Mallika Singh, Robert A. Smith, Bradley D. Preston

A Barcode Screen for Epigenetic Regulators Reveals a Role for the NuB4/HAT-B Histone Acetyltransferase Complex in Histone Turnover

Kitty F. Verzijlbergen, Tibor van Welsem, Daoud Sie, Tineke L. Lenstra, Daniel J. Turner, Frank C. P. Holstege, Ron M. Kerkhoven, Fred van Leeuwen

Identification, Replication, and Fine-Mapping of Loci Associated with Adult Height in Individuals of African Ancestry

Amidou N'Diaye, Gary K. Chen, Cameron D. Palmer, Bing Ge, Bamidele Tayo, Rasika A. Mathias, Jingzhong Ding, Michael A. Nalls, Adebowale Adeyemo, Véronique Adoue, Christine B. Ambrosone, Larry Atwood, Elisa V. Bandera, Lewis C. Becker, Sonja I. Berndt, Leslie Bernstein, William J. Blot, Eric Boerwinkle, Angela Britton, Graham Casey, Stephen J. Chanock, Ellen Demerath, Sandra L. Deming, W. Ryan Diver, Caroline Fox, Tamara B. Harris, Dena G. Hernandez, Jennifer J. Hu, Sue A. Ingles, Esther M. John, Craig Johnson, Brendan Keating, Rick A. Kittles, Laurence N. Kolonel, Stephen B. Kritchevsky, Loic Le Marchand, Kurt Lohman, Jiankang Liu, Robert C. Millikan, Adam Murphy, Solomon Musani, Christine Neslund-Dudas, Kari E. North, Sarah Nyante, Adesola Ogunniyi, Elaine A. Ostrander, George Papanicolaou, Sanjay Patel, Curtis A. Pettaway, Michael F. Press, Susan Redline, Jorge L. Rodriguez-Gil, Charles Rotimi, Benjamin A. Rybicki, Babatunde Salako, Pamela J. Schreiner, Lisa B. Signorello, Andrew B. Singleton, Janet L. Stanford, Alex H. Stram, Daniel O. Stram, Sara S. Strom, Bhoom Suktitipat, Michael J. Thun, John S. Witte, Lisa R. Yanek, Regina G. Ziegler, Wei Zheng, Xiaofeng Zhu, Joseph M. Zmuda, Alan B. Zonderman, Michele K. Evans, Yongmei Liu, Diane M. Becker, Richard S. Cooper, Tomi Pastinen, Brian E. Henderson, Joel N. Hirschhorn, Guillaume Lettre, Christopher A. Haiman

CtIP Mutations Cause Seckel and Jawad Syndromes

Per Qvist, Pablo Huertas, Sonia Jimeno, Mette Nyegaard, Muhammad J. Hassan, Stephen P. Jackson, Anders D. Børglum

Genetic Determinants of Serum Testosterone Concentrations in Men

Claes Ohlsson, Henri Wallaschofski, Kathryn L. Lunetta, Lisette Stolk, John R. B. Perry, Annemarie Koster, Ann-Kristin Petersen, Joel Eriksson, Terho Lehtimäki, Ilpo T. Huhtaniemi, Geoffrey L. Hammond, Marcello Maggio, Andrea D. Coviello, Luigi Ferrucci, Margit Heier, Albert Hofman, Kate L. Holliday, John-Olov Jansson, Mika Kähönen, David Karasik, Magnus K. Karlsson, Douglas P. Kiel, Yongmei Liu, Östen Ljunggren, Mattias Lorentzon, Leo-Pekka Lyytikäinen, Thomas Meitinger, Dan Mellström, David Melzer, Iva Miljkovic, Matthias Nauck, Maria Nilsson, Brenda Penninx, Stephen R. Pye, Ramachandran S. Vasan, Martin Reincke, Fernando Rivadeneira, Abdelouahid Tajar, Alexander Teumer, André G. Uitterlinden, Jagadish Ulloor, Jorma Viikari, Uwe Völker, Henry Völzke, H. Erich Wichmann, Tsung-Sheng Wu, Wei Vivian Zhuang, Elad Ziv, Frederick C. W. Wu, Olli Raitakari, Anna Eriksson, Martin Bidlingmaier, Tamara B. Harris, Anna Murray, Frank H. de Jong, Joanne M. Murabito, Shalender Bhasin, Liesbeth Vandenput, Robin Haring , EMAS Study Group

Developmental Stability: A Major Role for Cyclin G in Drosophila melanogaster

Vincent Debat, Sébastien Bloyer, Floria Faradji, Nelly Gidaszewski, Nicolas Navarro, Pablo Orozco-terWengel, Valérie Ribeiro, Christian Schlötterer, Jean S. Deutsch, Frédérique Peronnet

Positional Cloning of a Type 2 Diabetes Quantitative Trait Locus; Tomosyn-2, a Negative Regulator of Insulin Secretion

Sushant Bhatnagar, Angie T. Oler, Mary E. Rabaglia, Donald S. Stapleton, Kathryn L. Schueler, Nathan A. Truchan, Sara L. Worzella, Jonathan P. Stoehr, Susanne M. Clee, Brian S. Yandell, Mark P. Keller, Debbie C. Thurmond, Alan D. Attie