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Table of Contents: July 2014

COVER

Common alleles of an immunity gene reduce plant compatibility.

Image Credit: Marco Todesco and Detlef Weigel, Max Planck Institute for Developmental Biology
Issue Image

Crosses between different plants can sometimes result in progeny that is compromised in growth and fertility, but at the same time resists pathogens more vigorously. Both are consequences of an autonomous activation of the immune system, associated with the hybrid necrosis syndrome, in which endogenous factors are accidentally recognized as non-self. Interactions between alleles of a single defense-related gene were found to be responsible for several hybrid necrosis cases in Arabidopsis thaliana. These interacting alleles co-exist and form hybrids in natural populations. See Todesco et al.

Research Articles

The Coding and Noncoding Architecture of the Caulobacter crescentus Genome

Jared M. Schrader, Bo Zhou, Gene-Wei Li, Keren Lasker, W. Seth Childers, Brandon Williams, Tao Long, Sean Crosson, Harley H. McAdams, Jonathan S. Weissman, Lucy Shapiro

Hypoxia Adaptations in the Grey Wolf (Canis lupus chanco) from Qinghai-Tibet Plateau

Wenping Zhang, Zhenxin Fan, Eunjung Han, Rong Hou, Liang Zhang, Marco Galaverni, Jie Huang, Hong Liu, Pedro Silva, Peng Li, John P. Pollinger, Lianming Du, XiuyYue Zhang, Bisong Yue, Robert K. Wayne, Zhihe Zhang

A Novel MMP12 Locus Is Associated with Large Artery Atherosclerotic Stroke Using a Genome-Wide Age-at-Onset Informed Approach

Matthew Traylor, Kari-Matti Mäkelä, Laura L. Kilarski, Elizabeth G. Holliday, William J. Devan, Mike A. Nalls, Kerri L. Wiggins, Wei Zhao, Yu-Ching Cheng, Sefanja Achterberg, Rainer Malik, Cathie Sudlow, Steve Bevan, Emma Raitoharju, Niku Oksala, Vincent Thijs, Robin Lemmens, Arne Lindgren, Agnieszka Slowik, Jane M. Maguire, Matthew Walters, Ale Algra, Pankaj Sharma, John R. Attia, Giorgio B. Boncoraglio, Peter M. Rothwell, Paul I. W. de Bakker, Joshua C. Bis, Danish Saleheen, Steven J. Kittner, Braxton D. Mitchell, Jonathan Rosand, James F. Meschia, Christopher Levi, Martin Dichgans, Terho Lehtimäki, Cathryn M. Lewis, Hugh S. Markus , METASTROKE, International Stroke Genetics Consortium, Wellcome Trust Case Consortium 2 (WTCCC2)

Distribution and Medical Impact of Loss-of-Function Variants in the Finnish Founder Population

Elaine T. Lim, Peter Würtz, Aki S. Havulinna, Priit Palta, Taru Tukiainen, Karola Rehnström, Tõnu Esko, Reedik Mägi, Michael Inouye, Tuuli Lappalainen, Yingleong Chan, Rany M. Salem, Monkol Lek, Jason Flannick, Xueling Sim, Alisa Manning, Claes Ladenvall, Suzannah Bumpstead, Eija Hämäläinen, Kristiina Aalto, Mikael Maksimow, Marko Salmi, Stefan Blankenberg, Diego Ardissino, Svati Shah, Benjamin Horne, Ruth McPherson, Gerald K. Hovingh, Muredach P. Reilly, Hugh Watkins, Anuj Goel, Martin Farrall, Domenico Girelli, Alex P. Reiner, Nathan O. Stitziel, Sekar Kathiresan, Stacey Gabriel, Jeffrey C. Barrett, Terho Lehtimäki, Markku Laakso, Leif Groop, Jaakko Kaprio, Markus Perola, Mark I. McCarthy, Michael Boehnke, David M. Altshuler, Cecilia M. Lindgren, Joel N. Hirschhorn, Andres Metspalu, Nelson B. Freimer, Tanja Zeller, Sirpa Jalkanen, Seppo Koskinen, Olli Raitakari, Richard Durbin, Daniel G. MacArthur, Veikko Salomaa, Samuli Ripatti, Mark J. Daly, Aarno Palotie , for the Sequencing Initiative Suomi (SISu) Project

Novel Approach Identifies SNPs in SLC2A10 and KCNK9 with Evidence for Parent-of-Origin Effect on Body Mass Index

Clive J. Hoggart, Giulia Venturini, Massimo Mangino, Felicia Gomez, Giulia Ascari, Jing Hua Zhao, Alexander Teumer, Thomas W. Winkler, Natalia Tšernikova, Jian'an Luan, Evelin Mihailov, Georg B. Ehret, Weihua Zhang, David Lamparter, Tõnu Esko, Aurelien Macé, Sina Rüeger, Pierre-Yves Bochud, Matteo Barcella, Yves Dauvilliers, Beben Benyamin, David M. Evans, Caroline Hayward, Mary F. Lopez, Lude Franke, Alessia Russo, Iris M. Heid, Erika Salvi, Sailaja Vendantam, Dan E. Arking, Eric Boerwinkle, John C. Chambers, Giovanni Fiorito, Harald Grallert, Simonetta Guarrera, Georg Homuth, Jennifer E. Huffman, David Porteous, Darius Moradpour, Alex Iranzo, Johannes Hebebrand, John P. Kemp, Gert J. Lammers, Vincent Aubert, Markus H. Heim, Nicholas G. Martin, Grant W. Montgomery, Rosa Peraita-Adrados, Joan Santamaria, Francesco Negro, Carsten O. Schmidt, Robert A. Scott, Tim D. Spector, Konstantin Strauch, Henry Völzke, Nicholas J. Wareham, Wei Yuan, Jordana T. Bell, Aravinda Chakravarti, Jaspal S. Kooner, Annette Peters, Giuseppe Matullo, Henri Wallaschofski, John B. Whitfield, Fred Paccaud, Peter Vollenweider, Sven Bergmann, Jacques S. Beckmann, Mehdi Tafti, Nicholas D. Hastie, Daniele Cusi, Murielle Bochud, Timothy M. Frayling, Andres Metspalu, Marjo-Riitta Jarvelin, André Scherag, George Davey Smith, Ingrid B. Borecki, Valentin Rousson, Joel N. Hirschhorn, Carlo Rivolta, Ruth J. F. Loos, Zoltán Kutalik , Generation Scotland Consortium, The LifeLines Cohort study, The GIANT Consortium

The Co-factor of LIM Domains (CLIM/LDB/NLI) Maintains Basal Mammary Epithelial Stem Cells and Promotes Breast Tumorigenesis

Michael L. Salmans, Zhengquan Yu, Kazuhide Watanabe, Eric Cam, Peng Sun, Padhraic Smyth, Xing Dai, Bogi Andersen

Stage-Dependent and Locus-Specific Role of Histone Demethylase Jumonji D3 (JMJD3) in the Embryonic Stages of Lung Development

Qingtian Li, Helen Y. Wang, Iouri Chepelev, Qingyuan Zhu, Gang Wei, Keji Zhao, Rong-Fu Wang

Essential Genetic Interactors of SIR2 Required for Spatial Sequestration and Asymmetrical Inheritance of Protein Aggregates

Jia Song, Qian Yang, Junsheng Yang, Lisa Larsson, Xinxin Hao, Xuefeng Zhu, Sandra Malmgren-Hill, Marija Cvijovic, Julia Fernandez-Rodriguez, Julie Grantham, Claes M. Gustafsson, Beidong Liu, Thomas Nyström

Silencing Is Noisy: Population and Cell Level Noise in Telomere-Adjacent Genes Is Dependent on Telomere Position and Sir2

Matthew Z. Anderson, Aleeza C. Gerstein, Lauren Wigen, Joshua A. Baller, Judith Berman

MDRL lncRNA Regulates the Processing of miR-484 Primary Transcript by Targeting miR-361

Kun Wang, Teng Sun, Na Li, Yin Wang, Jian-Xun Wang, Lu-Yu Zhou, Bo Long, Cui-Yun Liu, Fang Liu, Pei-Feng Li

Cuba: Exploring the History of Admixture and the Genetic Basis of Pigmentation Using Autosomal and Uniparental Markers

Beatriz Marcheco-Teruel, Esteban J. Parra, Evelyn Fuentes-Smith, Antonio Salas, Henriette N. Buttenschøn, Ditte Demontis, María Torres-Español, Lilia C. Marín-Padrón, Enrique J. Gómez-Cabezas, Vanesa Álvarez-Iglesias, Ana Mosquera-Miguel, Antonio Martínez-Fuentes, Ángel Carracedo, Anders D. Børglum, Ole Mors

An Intronic microRNA Links Rb/E2F and EGFR Signaling

Mary Truscott, Abul B. M. M. K. Islam, James Lightfoot, Núria López-Bigas, Maxim V. Frolov

Determinative Developmental Cell Lineages Are Robust to Cell Deaths

Jian-Rong Yang, Shuxiang Ruan, Jianzhi Zhang

Requirements for Pseudomonas aeruginosa Acute Burn and Chronic Surgical Wound Infection

Keith H. Turner, Jake Everett, Urvish Trivedi, Kendra P. Rumbaugh, Marvin Whiteley

Intrapopulation Genome Size Variation in D. melanogaster Reflects Life History Variation and Plasticity

Lisa L. Ellis, Wen Huang, Andrew M. Quinn, Astha Ahuja, Ben Alfrejd, Francisco E. Gomez, Carl E. Hjelmen, Kristi L. Moore, Trudy F. C. Mackay, J. Spencer Johnston, Aaron M. Tarone

Mechanisms of CFTR Functional Variants That Impair Regulated Bicarbonate Permeation and Increase Risk for Pancreatitis but Not for Cystic Fibrosis

Jessica LaRusch, Jinsei Jung, Ignacio J. General, Michele D. Lewis, Hyun Woo Park, Randall E. Brand, Andres Gelrud, Michelle A. Anderson, Peter A. Banks, Darwin Conwell, Christopher Lawrence, Joseph Romagnuolo, John Baillie, Samer Alkaade, Gregory Cote, Timothy B. Gardner, Stephen T. Amann, Adam Slivka, Bimaljit Sandhu, Amy Aloe, Michelle L. Kienholz, Dhiraj Yadav, M. Michael Barmada, Ivet Bahar, Min Goo Lee, David C. Whitcomb , the North American Pancreatitis Study Group

Comparison of Methods to Account for Relatedness in Genome-Wide Association Studies with Family-Based Data

Jakris Eu-ahsunthornwattana, E. Nancy Miller, Michaela Fakiola, Selma M. B. Jeronimo, Jenefer M. Blackwell, Heather J. Cordell , Wellcome Trust Case Control Consortium 2

LIN-42, the Caenorhabditis elegans PERIOD homolog, Negatively Regulates MicroRNA Transcription

Roberto Perales, Dana M. King, Cristina Aguirre-Chen, Christopher M. Hammell

Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution

Pierre-Marc Delaux, Kranthi Varala, Patrick P. Edger, Gloria M. Coruzzi, J. Chris Pires, Jean-Michel Ané

Muscle-Specific SIRT1 Gain-of-Function Increases Slow-Twitch Fibers and Ameliorates Pathophysiology in a Mouse Model of Duchenne Muscular Dystrophy

Angeliki Chalkiadaki, Masaki Igarashi, Armiyaw Sebastian Nasamu, Jovana Knezevic, Leonard Guarente

Arabidopsis thaliana WAPL Is Essential for the Prophase Removal of Cohesin during Meiosis

Kuntal De, Lauren Sterle, Laura Krueger, Xiaohui Yang, Christopher A. Makaroff

Microsatellite Interruptions Stabilize Primate Genomes and Exist as Population-Specific Single Nucleotide Polymorphisms within Individual Human Genomes

Guruprasad Ananda, Suzanne E. Hile, Amanda Breski, Yanli Wang, Yogeshwar Kelkar, Kateryna D. Makova, Kristin A. Eckert

Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease

Ville-Petteri Mäkinen, Mete Civelek, Qingying Meng, Bin Zhang, Jun Zhu, Candace Levian, Tianxiao Huan, Ayellet V. Segrè, Sujoy Ghosh, Juan Vivar, Majid Nikpay, Alexandre F. R. Stewart, Christopher P. Nelson, Christina Willenborg, Jeanette Erdmann, Stefan Blakenberg, Christopher J. O'Donnell, Winfried März, Reijo Laaksonen, Stephen E. Epstein, Sekar Kathiresan, Svati H. Shah, Stanley L. Hazen, Muredach P. Reilly, Aldons J. Lusis, Nilesh J. Samani, Heribert Schunkert, Thomas Quertermous, Ruth McPherson, Xia Yang, Themistocles L. Assimes , the Coronary ARtery DIsease Genome-Wide Replication And Meta-Analysis (CARDIoGRAM) Consortium

Recombination in the Human Pseudoautosomal Region PAR1

Anjali G. Hinch, Nicolas Altemose, Nudrat Noor, Peter Donnelly, Simon R. Myers

Knock-In Reporter Mice Demonstrate that DNA Repair by Non-homologous End Joining Declines with Age

Amita Vaidya, Zhiyong Mao, Xiao Tian, Brianna Spencer, Andrei Seluanov, Vera Gorbunova

The PTK7-Related Transmembrane Proteins Off-track and Off-track 2 Are Co-receptors for Drosophila Wnt2 Required for Male Fertility

Karen Linnemannstöns, Caroline Ripp, Mona Honemann-Capito, Katja Brechtel-Curth, Marie Hedderich, Andreas Wodarz

The Two Cis-Acting Sites, parS1 and oriC1, Contribute to the Longitudinal Organisation of Vibrio cholerae Chromosome I

Ariane David, Gaëlle Demarre, Leila Muresan, Evelyne Paly, François-Xavier Barre, Christophe Possoz

A Loss of Function Screen of Identified Genome-Wide Association Study Loci Reveals New Genes Controlling Hematopoiesis

Ewa Bielczyk-Maczyńska, Jovana Serbanovic-Canic, Lauren Ferreira, Nicole Soranzo, Derek L. Stemple, Willem H. Ouwehand, Ana Cvejic

Brg1 Loss Attenuates Aberrant Wnt-Signalling and Prevents Wnt-Dependent Tumourigenesis in the Murine Small Intestine

Aliaksei Z. Holik, Madeleine Young, Joanna Krzystyniak, Geraint T. Williams, Daniel Metzger, Boris Y. Shorning, Alan R. Clarke

Unraveling Genetic Modifiers in the Gria4 Mouse Model of Absence Epilepsy

Wayne N. Frankel, Connie L. Mahaffey, Tracy C. McGarr, Barbara J. Beyer, Verity A. Letts

Age-Associated Sperm DNA Methylation Alterations: Possible Implications in Offspring Disease Susceptibility

Timothy G. Jenkins, Kenneth I. Aston, Christian Pflueger, Bradley R. Cairns, Douglas T. Carrell

Activation of the Arabidopsis thaliana Immune System by Combinations of Common ACD6 Alleles

Marco Todesco, Sang-Tae Kim, Eunyoung Chae, Kirsten Bomblies, Maricris Zaidem, Lisa M. Smith, Detlef Weigel, Roosa A. E. Laitinen

Cis and Trans Effects of Human Genomic Variants on Gene Expression

Julien Bryois, Alfonso Buil, David M. Evans, John P. Kemp, Stephen B. Montgomery, Donald F. Conrad, Karen M. Ho, Susan Ring, Matthew Hurles, Panos Deloukas, George Davey Smith, Emmanouil T. Dermitzakis

Clonal Architecture of Secondary Acute Myeloid Leukemia Defined by Single-Cell Sequencing

Andrew E. O. Hughes, Vincent Magrini, Ryan Demeter, Christopher A. Miller, Robert Fulton, Lucinda L. Fulton, William C. Eades, Kevin Elliott, Sharon Heath, Peter Westervelt, Li Ding, Donald F. Conrad, Brian S. White, Jin Shao, Daniel C. Link, John F. DiPersio, Elaine R. Mardis, Richard K. Wilson, Timothy J. Ley, Matthew J. Walter, Timothy A. Graubert

Arabidopsis DELLA Protein Degradation Is Controlled by a Type-One Protein Phosphatase, TOPP4

Qianqian Qin, Wei Wang, Xiaola Guo, Jing Yue, Yan Huang, Xiufei Xu, Jia Li, Suiwen Hou

Hypersensitivity of Primordial Germ Cells to Compromised Replication-Associated DNA Repair Involves ATM-p53-p21 Signaling

Yunhai Luo, Suzanne A. Hartford, Ruizhu Zeng, Teresa L. Southard, Naoko Shima, John C. Schimenti

Genome Wide Association Identifies Common Variants at the SERPINA6/SERPINA1 Locus Influencing Plasma Cortisol and Corticosteroid Binding Globulin

Jennifer L. Bolton, Caroline Hayward, Nese Direk, John G. Lewis, Geoffrey L. Hammond, Lesley A. Hill, Anna Anderson, Jennifer Huffman, James F. Wilson, Harry Campbell, Igor Rudan, Alan Wright, Nicholas Hastie, Sarah H. Wild, Fleur P. Velders, Albert Hofman, Andre G. Uitterlinden, Jari Lahti, Katri Räikkönen, Eero Kajantie, Elisabeth Widen, Aarno Palotie, Johan G. Eriksson, Marika Kaakinen, Marjo-Riitta Järvelin, Nicholas J. Timpson, George Davey Smith, Susan M. Ring, David M. Evans, Beate St Pourcain, Toshiko Tanaka, Yuri Milaneschi, Stefania Bandinelli, Luigi Ferrucci, Pim van der Harst, Judith G. M. Rosmalen, Stephen J. L. Bakker, Niek Verweij, Robin P. F. Dullaart, Anubha Mahajan, Cecilia M. Lindgren, Andrew Morris, Lars Lind, Erik Ingelsson, Laura N. Anderson, Craig E. Pennell, Stephen J. Lye, Stephen G. Matthews, Joel Eriksson, Dan Mellstrom, Claes Ohlsson, Jackie F. Price, Mark W. J. Strachan, Rebecca M. Reynolds, Henning Tiemeier, Brian R. Walker , on behalf of the CORtisol NETwork (CORNET) Consortium

The Genomic Landscape of the Ewing Sarcoma Family of Tumors Reveals Recurrent STAG2 Mutation

Andrew S. Brohl, David A. Solomon, Wendy Chang, Jianjun Wang, Young Song, Sivasish Sindiri, Rajesh Patidar, Laura Hurd, Li Chen, Jack F. Shern, Hongling Liao, Xinyu Wen, Julia Gerard, Jung-Sik Kim, Jose Antonio Lopez Guerrero, Isidro Machado, Daniel H. Wai, Piero Picci, Timothy Triche, Andrew E. Horvai, Markku Miettinen, Jun S. Wei, Daniel Catchpool, Antonio Llombart-Bosch, Todd Waldman, Javed Khan

Apomictic and Sexual Germline Development Differ with Respect to Cell Cycle, Transcriptional, Hormonal and Epigenetic Regulation

Anja Schmidt, Marc W. Schmid, Ulrich C. Klostermeier, Weihong Qi, Daniela Guthörl, Christian Sailer, Manuel Waller, Philip Rosenstiel, Ueli Grossniklaus

Sox11 Is Required to Maintain Proper Levels of Hedgehog Signaling during Vertebrate Ocular Morphogenesis

Lakshmi Pillai-Kastoori, Wen Wen, Stephen G. Wilson, Erin Strachan, Adriana Lo-Castro, Marco Fichera, Sebastiano A. Musumeci, Ordan J. Lehmann, Ann C. Morris

Meiosis-Specific Cohesin Component, Stag3 Is Essential for Maintaining Centromere Chromatid Cohesion, and Required for DNA Repair and Synapsis between Homologous Chromosomes

Jessica Hopkins, Grace Hwang, Justin Jacob, Nicklas Sapp, Rick Bedigian, Kazuhiro Oka, Paul Overbeek, Steve Murray, Philip W. Jordan

DNA Topoisomerase 1α Promotes Transcriptional Silencing of Transposable Elements through DNA Methylation and Histone Lysine 9 Dimethylation in Arabidopsis

Thanh Theresa Dinh, Lei Gao, Xigang Liu, Dongming Li, Shengben Li, Yuanyuan Zhao, Michael O'Leary, Brandon Le, Robert J. Schmitz, Pablo Manavella, Shaofang Li, Detlef Weigel, Olga Pontes, Joseph R. Ecker, Xuemei Chen

Nucleosomes Shape DNA Polymorphism and Divergence

Sasha A. Langley, Gary H. Karpen, Charles H. Langley

Common Transcriptional Mechanisms for Visual Photoreceptor Cell Differentiation among Pancrustaceans

Simpla Mahato, Shinichi Morita, Abraham E. Tucker, Xulong Liang, Magdalena Jackowska, Markus Friedrich, Yasuhiro Shiga, Andrew C. Zelhof