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Table of Contents: February 2015

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Dogs are not only “man's best friend” for their loyalty, they are also the geneticist’s best friend. The artificial breed structure has created genetically isolated groups of dogs, with differential predisposition to diseases they share with us. This facilitates mapping of diseases relevant also to humans. Golden retrievers are predisposed to various cancers, including B-cell lymphoma and hemangiosarcoma. The genetic risk factors for these diseases in humans are still being elucidated. Surprisingly, golden retrievers have two nearby genetic loci with haplotypes predisposing to both diseases. See Tonomura et al.

Editorial

Perspective

R2d2 and Hyperdrive Mechanisms (in Mouse Meiosis)

Sarah E. Zanders, Harmit S. Malik

Review

Research Articles

Proteotoxic Stress Induces Phosphorylation of p62/SQSTM1 by ULK1 to Regulate Selective Autophagic Clearance of Protein Aggregates

Junghyun Lim, M. Lenard Lachenmayer, Shuai Wu, Wenchao Liu, Mondira Kundu, Rong Wang, Masaaki Komatsu, Young J. Oh, Yanxiang Zhao, Zhenyu Yue

Prodomain Removal Enables Neto to Stabilize Glutamate Receptors at the Drosophila Neuromuscular Junction

Young-Jun Kim, Oghomwen Igiesuorobo, Cathy I. Ramos, Hong Bao, Bing Zhang, Mihaela Serpe

Region-Specific Activation of oskar mRNA Translation by Inhibition of Bruno-Mediated Repression

Goheun Kim, Chin-I Pai, Keiji Sato, Maria D. Person, Akira Nakamura, Paul M. Macdonald

Mutations in MAB21L2 Result in Ocular Coloboma, Microcornea and Cataracts

Brett Deml, Ariana Kariminejad, Razieh H. R. Borujerdi, Sanaa Muheisen, Linda M. Reis, Elena V. Semina

An Essential Role of the Arginine Vasotocin System in Mate-Guarding Behaviors in Triadic Relationships of Medaka Fish (Oryzias latipes)

Saori Yokoi, Teruhiro Okuyama, Yasuhiro Kamei, Kiyoshi Naruse, Yoshihito Taniguchi, Satoshi Ansai, Masato Kinoshita, Larry J. Young, Nobuaki Takemori, Takeo Kubo, Hideaki Takeuchi

microRNAs Regulate Cell-to-Cell Variability of Endogenous Target Gene Expression in Developing Mouse Thymocytes

Rory Blevins, Ludovica Bruno, Thomas Carroll, James Elliott, Antoine Marcais, Christina Loh, Arnulf Hertweck, Azra Krek, Nikolaus Rajewsky, Chang-Zheng Chen, Amanda G. Fisher, Matthias Merkenschlager

acal is a Long Non-coding RNA in JNK Signaling in Epithelial Shape Changes during Drosophila Dorsal Closure

Luis Daniel Ríos-Barrera, Irene Gutiérrez-Pérez, María Domínguez, Juan Rafael Riesgo-Escovar

Hyper-Acetylation of Histone H3K56 Limits Break-Induced Replication by Inhibiting Extensive Repair Synthesis

Jun Che, Stephanie Smith, Yoo Jung Kim, Eun Yong Shim, Kyungjae Myung, Sang Eun Lee

Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

Nandita R. Garud, Philipp W. Messer, Erkan O. Buzbas, Dmitri A. Petrov

Recurrent Evolution of Melanism in South American Felids

Alexsandra Schneider, Corneliu Henegar, Kenneth Day, Devin Absher, Constanza Napolitano, Leandro Silveira, Victor A. David, Stephen J. O’Brien, Marilyn Menotti-Raymond, Gregory S. Barsh, Eduardo Eizirik

Matrix Metalloproteinase 2 Is Required for Ovulation and Corpus Luteum Formation in Drosophila

Lylah D. Deady, Wei Shen, Sarah A. Mosure, Allan C. Spradling, Jianjun Sun

Essential Role for Endogenous siRNAs during Meiosis in Mouse Oocytes

Paula Stein, Nikolay V. Rozhkov, Fan Li, Fabián L. Cárdenas, Olga Davydenk, Lee E. Vandivier, Brian D. Gregory, Gregory J. Hannon, Richard M. Schultz

Systemic Delivery of MicroRNA-101 Potently Inhibits Hepatocellular Carcinoma In Vivo by Repressing Multiple Targets

Fang Zheng, Yi-Ji Liao, Mu-Yan Cai, Tian-Hao Liu, Shu-Peng Chen, Pei-Hong Wu, Long Wu, Xiu-Wu Bian, Xin-Yuan Guan, Yi-Xin Zeng, Yun-Fei Yuan, Hsiang-Fu Kung, Dan Xie

The Arabidopsis DNA Polymerase δ Has a Role in the Deposition of Transcriptionally Active Epigenetic Marks, Development and Flowering

Francisco M. Iglesias, Natalia A. Bruera, Sebastián Dergan-Dylon, Cristina Marino-Buslje, Hernán Lorenzi, Julieta L. Mateos, Franziska Turck, George Coupland, Pablo D. Cerdán

A Rolling Circle Replication Mechanism Produces Multimeric Lariats of Mitochondrial DNA in Caenorhabditis elegans

Samantha C. Lewis, Priit Joers, Smaranda Willcox, Jack D. Griffith, Howard T. Jacobs, Bradley C. Hyman

A Genome-Wide Hybrid Incompatibility Landscape between Caenorhabditis briggsae and C. nigoni

Yu Bi, Xiaoliang Ren, Cheung Yan, Jiaofang Shao, Dongying Xie, Zhongying Zhao

Fatty Acid Synthase Cooperates with Glyoxalase 1 to Protect against Sugar Toxicity

Damien Garrido, Thomas Rubin, Mickael Poidevin, Brigitte Maroni, Arnaud Le Rouzic, Jean-Philippe Parvy, Jacques Montagne

An Integrative Multi-scale Analysis of the Dynamic DNA Methylation Landscape in Aging

Tian Yuan, Yinming Jiao, Simone de Jong, Roel A. Ophoff, Stephan Beck, Andrew E. Teschendorff

Regulators of Autophagosome Formation in Drosophila Muscles

Jonathan Zirin, Joppe Nieuwenhuis, Anastasia Samsonova, Rong Tao, Norbert Perrimon

A Multi-Megabase Copy Number Gain Causes Maternal Transmission Ratio Distortion on Mouse Chromosome 2

John P. Didion, Andrew P. Morgan, Amelia M.-F. Clayshulte, Rachel C. Mcmullan, Liran Yadgary, Petko M. Petkov, Timothy A. Bell, Daniel M. Gatti, James J. Crowley, Kunjie Hua, David L. Aylor, Ling Bai, Mark Calaway, Elissa J. Chesler, John E. French, Thomas R. Geiger, Terry J. Gooch, Theodore Garland Jr., Alison H. Harrill, Kent Hunter, Leonard McMillan, Matt Holt, Darla R. Miller, Deborah A. O'Brien, Kenneth Paigen, Wenqi Pan, Lucy B. Rowe, Ginger D. Shaw, Petr Simecek, Patrick F. Sullivan, Karen L Svenson, George M. Weinstock, David W. Threadgill, Daniel Pomp, Gary A. Churchill, Fernando Pardo-Manuel de Villena

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

Philine G. D. Feulner, Frédéric J. J. Chain, Mahesh Panchal, Yun Huang, Christophe Eizaguirre, Martin Kalbe, Tobias L. Lenz, Irene E. Samonte, Monika Stoll, Erich Bornberg-Bauer, Thorsten B. H. Reusch, Manfred Milinski

Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling

Kristofer Davie, Jelle Jacobs, Mardelle Atkins, Delphine Potier, Valerie Christiaens, Georg Halder, Stein Aerts

The Exosome Component Rrp6 Is Required for RNA Polymerase II Termination at Specific Targets of the Nrd1-Nab3 Pathway

Melanie J. Fox, Hongyu Gao, Whitney R. Smith-Kinnaman, Yunlong Liu, Amber L. Mosley

Transcriptome Wide Annotation of Eukaryotic RNase III Reactivity and Degradation Signals

Jules Gagnon, Mathieu Lavoie, Mathieu Catala, Francis Malenfant, Sherif Abou Elela

Elevated In Vivo Levels of a Single Transcription Factor Directly Convert Satellite Glia into Oligodendrocyte-like Cells

Matthias Weider, Amélie Wegener, Christian Schmitt, Melanie Küspert, Simone Hillgärtner, Michael R. Bösl, Irm Hermans-Borgmeyer, Brahim Nait-Oumesmar, Michael Wegner

Sex-specific Trans-regulatory Variation on the Drosophila melanogaster X Chromosome

Michael Stocks, Rebecca Dean, Björn Rogell, Urban Friberg

Contribution of the Two Genes Encoding Histone Variant H3.3 to Viability and Fertility in Mice

Michelle C. W. Tang, Shelley A. Jacobs, Deidre M. Mattiske, Yu May Soh, Alison N. Graham, An Tran, Shu Ly Lim, Damien F. Hudson, Paul Kalitsis, Moira K. O’Bryan, Lee H. Wong, Jeffrey R. Mann

Drosophila TIM Binds Importin α1, and Acts as an Adapter to Transport PER to the Nucleus

A. Reum Jang, Katarina Moravcevic, Lino Saez, Michael W. Young, Amita Sehgal

Partially Redundant Enhancers Cooperatively Maintain Mammalian Pomc Expression Above a Critical Functional Threshold

Daniel D. Lam, Flavio S. J. de Souza, Sofia Nasif, Miho Yamashita, Rodrigo López-Leal, Veronica Otero-Corchon, Kana Meece, Harini Sampath, Aaron J. Mercer, Sharon L. Wardlaw, Marcelo Rubinstein, Malcolm J. Low

Pooled Sequencing of 531 Genes in Inflammatory Bowel Disease Identifies an Associated Rare Variant in BTNL2 and Implicates Other Immune Related Genes

Natalie J. Prescott, Benjamin Lehne, Kristina Stone, James C. Lee, Kirstin Taylor, Jo Knight, Efterpi Papouli, Muddassar M. Mirza, Michael A. Simpson, Sarah L. Spain, Grace Lu, Franca Fraternali, Suzannah J. Bumpstead, Emma Gray, Ariella Amar, Hannah Bye, Peter Green, Guy Chung-Faye, Bu’Hussain Hayee, Richard Pollok, Jack Satsangi, Miles Parkes, Jeffrey C. Barrett, John C. Mansfield, Jeremy Sanderson, Cathryn M. Lewis, Michael E. Weale, Thomas Schlitt, Christopher G. Mathew , UK IBD Genetics Consortium

African Glucose-6-Phosphate Dehydrogenase Alleles Associated with Protection from Severe Malaria in Heterozygous Females in Tanzania

Alphaxard Manjurano, Nuno Sepulveda, Behzad Nadjm, George Mtove, Hannah Wangai, Caroline Maxwell, Raimos Olomi, Hugh Reyburn, Eleanor M. Riley, Christopher J. Drakeley, Taane G. Clark , MalariaGEN Consortium

Mitochondrial and Cytoplasmic ROS Have Opposing Effects on Lifespan

Claire E. Schaar, Dylan J. Dues, Katie K. Spielbauer, Emily Machiela, Jason F. Cooper, Megan Senchuk, Siegfried Hekimi, Jeremy M. Van Raamsdonk

Tribolium castaneum RR-1 Cuticular Protein TcCPR4 Is Required for Formation of Pore Canals in Rigid Cuticle

Mi Young Noh, Subbaratnam Muthukrishnan, Karl J. Kramer, Yasuyuki Arakane

Regulation of Toll-like Receptor Signaling by the SF3a mRNA Splicing Complex

Brian P. O’Connor, Thomas Danhorn, Lesly De Arras, Brenna R. Flatley, Roland A. Marcus, Eveline Farias-Hesson, Sonia M. Leach, Scott Alper

Asymmetry of the Budding Yeast Tem1 GTPase at Spindle Poles Is Required for Spindle Positioning But Not for Mitotic Exit

Ilaria Scarfone, Marianna Venturetti, Manuel Hotz, Jette Lengefeld, Yves Barral, Simonetta Piatti

GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands

Florent Lassalle, Séverine Périan, Thomas Bataillon, Xavier Nesme, Laurent Duret, Vincent Daubin

Modeling of the Human Alveolar Rhabdomyosarcoma Pax3-Foxo1 Chromosome Translocation in Mouse Myoblasts Using CRISPR-Cas9 Nuclease

Irina V. Lagutina, Virginia Valentine, Fabrizio Picchione, Frank Harwood, Marcus B. Valentine, Barbara Villarejo-Balcells, Jaime J. Carvajal, Gerard C. Grosveld

K-homology Nuclear Ribonucleoproteins Regulate Floral Organ Identity and Determinacy in Arabidopsis

Encarnación Rodríguez-Cazorla, Juan José Ripoll, Alfonso Andújar, Lindsay J. Bailey, Antonio Martínez-Laborda, Martin F. Yanofsky, Antonio Vera

Discovery of CTCF-Sensitive Cis-Spliced Fusion RNAs between Adjacent Genes in Human Prostate Cells

Fujun Qin, Zhenguo Song, Mihaela Babiceanu, Yansu Song, Loryn Facemire, Ritambhara Singh, Mazhar Adli, Hui Li

The Genetic Architecture of the Genome-Wide Transcriptional Response to ER Stress in the Mouse

Clement Y Chow, Xu Wang, David Riccardi, Mariana F. Wolfner, Andrew G. Clark

Systematic Cell-Based Phenotyping of Missense Alleles Empowers Rare Variant Association Studies: A Case for LDLR and Myocardial Infarction

Aenne S. Thormaehlen, Christian Schuberth, Hong-Hee Won, Peter Blattmann, Brigitte Joggerst-Thomalla, Susanne Theiss, Rosanna Asselta, Stefano Duga, Pier Angelica Merlini, Diego Ardissino, Eric S. Lander, Stacey Gabriel, Daniel J. Rader, Gina M. Peloso, Rainer Pepperkok, Sekar Kathiresan, Heiko Runz

Inflammation-Induced Cell Proliferation Potentiates DNA Damage-Induced Mutations In Vivo

Orsolya Kiraly, Guanyu Gong, Werner Olipitz, Sureshkumar Muthupalani, Bevin P. Engelward

Membrane Recognition and Dynamics of the RNA Degradosome

Henrik Strahl, Catherine Turlan, Syma Khalid, Peter J. Bond, Jean-Marie Kebalo, Pascale Peyron, Leonora Poljak, Marie Bouvier, Leendert Hamoen, Ben F. Luisi, Agamemnon J. Carpousis

Identification and Functional Analysis of Healing Regulators in Drosophila

Carmen Álvarez-Fernández, Srividya Tamirisa, Federico Prada, Ariel Chernomoretz, Osvaldo Podhajcer, Enrique Blanco, Enrique Martín-Blanco

Structured Observations Reveal Slow HIV-1 CTL Escape

Hannah E. Roberts, Jacob Hurst, Nicola Robinson, Helen Brown, Peter Flanagan, Laura Vass, Sarah Fidler, Jonathan Weber, Abdel Babiker, Rodney E. Phillips, Angela R. McLean, John Frater , SPARTAC trial investigators

Genome-wide Association Study Identifies Shared Risk Loci Common to Two Malignancies in Golden Retrievers

Noriko Tonomura, Ingegerd Elvers, Rachael Thomas, Kate Megquier, Jason Turner-Maier, Cedric Howald, Aaron L. Sarver, Ross Swofford, Aric M. Frantz, Daisuke Ito, Evan Mauceli, Maja Arendt, Hyun Ji Noh, Michele Koltookian, Tara Biagi, Sarah Fryc, Christina Williams, Anne C. Avery, Jong-Hyuk Kim, Lisa Barber, Kristine Burgess, Eric S. Lander, Elinor K. Karlsson, Chieko Azuma, Jaime F. Modiano, Matthew Breen, Kerstin Lindblad-Toh

A Nitric Oxide Regulated Small RNA Controls Expression of Genes Involved in Redox Homeostasis in Bacillus subtilis

Sylvain Durand, Frédérique Braun, Efthimia Lioliou, Cédric Romilly, Anne-Catherine Helfer, Laurianne Kuhn, Noé Quittot, Pierre Nicolas, Pascale Romby, Ciarán Condon