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Table of Contents: August 2015

COVER

APLP2 regulates refractive error development in mice and humans.

Image Credit: Andrei V. Tkatchenko
Issue Image

Genetic factors are believed to play a key role in determining the impact of environmental factors such as reading and nearwork on refractive eye development and development of myopia; however, experimental proof of this gene-environment interaction has been missing. Analysis of genetic variation of the APLP2 gene revealed that a low-frequency variant of APLP2 is associated with myopia in children if they engage in above-average levels of reading. Furthermore, lack of APLP2 leads to a dose-dependent reduction in susceptibility to form-deprivation myopia in mice; thus, confirming interaction between APLP2 and visual input observed in humans. See Tkatchenko et al.

Perspective

Review

Research Articles

The Relationship between Gene Network Structure and Expression Variation among Individuals and Species

Karen E. Sears, Jennifer A. Maier, Marcelo Rivas-Astroza, Rachel Poe, Sheng Zhong, Kari Kosog, Jonathan D. Marcot, Richard R. Behringer, Chris J. Cretekos, John J. Rasweiler IV, Zoi Rapti

Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck

Daniel J. Balick, Ron Do, Christopher A. Cassa, David Reich, Shamil R. Sunyaev

Regulation of Mutagenic DNA Polymerase V Activation in Space and Time

Andrew Robinson, John P. McDonald, Victor E. A. Caldas, Meghna Patel, Elizabeth A. Wood, Christiaan M. Punter, Harshad Ghodke, Michael M. Cox, Roger Woodgate, Myron F. Goodman, Antoine M. van Oijen

APLP2 Regulates Refractive Error and Myopia Development in Mice and Humans

Andrei V. Tkatchenko, Tatiana V. Tkatchenko, Jeremy A. Guggenheim, Virginie J. M. Verhoeven, Pirro G. Hysi, Robert Wojciechowski, Pawan Kumar Singh, Ashok Kumar, Gopal Thinakaran, Cathy Williams , Consortium for Refractive Error and Myopia (CREAM)

SmD1 Modulates the miRNA Pathway Independently of Its Pre-mRNA Splicing Function

Xiao-Peng Xiong, Georg Vogler, Krishna Kurthkoti, Anastasia Samsonova, Rui Zhou

Genome-Wide Association and Trans-ethnic Meta-Analysis for Advanced Diabetic Kidney Disease: Family Investigation of Nephropathy and Diabetes (FIND)

Sudha K. Iyengar, John R. Sedor, Barry I. Freedman, W. H. Linda Kao, Matthias Kretzler, Benjamin J. Keller, Hanna E. Abboud, Sharon G. Adler, Lyle G. Best, Donald W. Bowden, Allison Burlock, Yii-Der Ida Chen, Shelley A. Cole, Mary E. Comeau, Jeffrey M. Curtis, Jasmin Divers, Christiane Drechsler, Ravi Duggirala, Robert C. Elston, Xiuqing Guo, Huateng Huang, Michael Marcus Hoffmann, Barbara V. Howard, Eli Ipp, Paul L. Kimmel, Michael J. Klag, William C. Knowler, Orly F. Kohn, Tennille S. Leak, David J. Leehey, Man Li, Alka Malhotra, Winfried März, Viji Nair, Robert G. Nelson, Susanne B. Nicholas, Stephen J. O’Brien, Madeleine V. Pahl, Rulan S. Parekh, Marcus G. Pezzolesi, Rebekah S. Rasooly, Charles N. Rotimi, Jerome I. Rotter, Jeffrey R. Schelling, Michael F. Seldin, Vallabh O. Shah, Adam M. Smiles, Michael W. Smith, Kent D. Taylor, Farook Thameem, Denyse P. Thornley-Brown, Barbara J. Truitt, Christoph Wanner, E. Jennifer Weil, Cheryl A. Winkler, Philip G. Zager, Robert P. Igo Jr, Robert L. Hanson, Carl D. Langefeld , Family Investigation of Nephropathy and Diabetes (FIND)

Non-synonymous FGD3 Variant as Positional Candidate for Disproportional Tall Stature Accounting for a Carcass Weight QTL (CW-3) and Skeletal Dysplasia in Japanese Black Cattle

Akiko Takasuga, Kunio Sato, Ryouichi Nakamura, Yosuke Saito, Shinji Sasaki, Takehito Tsuji, Akio Suzuki, Hiroshi Kobayashi, Tamako Matsuhashi, Koji Setoguchi, Hiroshi Okabe, Toshitake Ootsubo, Ichiro Tabuchi, Tatsuo Fujita, Naoto Watanabe, Takashi Hirano, Shota Nishimura, Toshio Watanabe, Makio Hayakawa, Yoshikazu Sugimoto, Takatoshi Kojima

Transient laminin beta 1a Induction Defines the Wound Epidermis during Zebrafish Fin Regeneration

Chen-Hui Chen, Alexander F. Merriman, Jeremiah Savage, Jason Willer, Taylor Wahlig, Nicholas Katsanis, Viravuth P. Yin, Kenneth D. Poss

Systems Genetics Reveals the Functional Context of PCOS Loci and Identifies Genetic and Molecular Mechanisms of Disease Heterogeneity

Michelle R. Jones, Meredith A. Brower, Ning Xu, Jinrui Cui, Emebet Mengesha, Yii-Der I. Chen, Kent D. Taylor, Ricardo Azziz, Mark O. Goodarzi

Rac1 Regulates Endometrial Secretory Function to Control Placental Development

Juanmahel Davila, Mary J. Laws, Athilakshmi Kannan, Quanxi Li, Robert N. Taylor, Milan K. Bagchi, Indrani C. Bagchi

The Homeodomain Iroquois Proteins Control Cell Cycle Progression and Regulate the Size of Developmental Fields

Natalia Barrios, Esther González-Pérez, Rosario Hernández, Sonsoles Campuzano

Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana

Christian Kappel, Gerda Trost, Hjördis Czesnick, Anna Ramming, Benjamin Kolbe, Son Lang Vi, Cláudia Bispo, Jörg D. Becker, Cornelia de Moor, Michael Lenhard

Evidence for Retromutagenesis as a Mechanism for Adaptive Mutation in Escherichia coli

Jordan Morreall, Alice Kim, Yuan Liu, Natalya Degtyareva, Bernard Weiss, Paul W. Doetsch

Reduced Crossover Interference and Increased ZMM-Independent Recombination in the Absence of Tel1/ATM

Carol M. Anderson, Ashwini Oke, Phoebe Yam, Tangna Zhuge, Jennifer C. Fung

The Evolutionarily Conserved LIM Homeodomain Protein LIM-4/LHX6 Specifies the Terminal Identity of a Cholinergic and Peptidergic C. elegans Sensory/Inter/Motor Neuron-Type

Jinmahn Kim, Jihye Yeon, Seong-Kyoon Choi, Yang Hoon Huh, Zi Fang, Seo Jin Park, Myoung Ok Kim, Zae Young Ryoo, Kyeongjin Kang, Hee-Seok Kweon, Won Bae Jeon, Chris Li, Kyuhyung Kim

CCNYL1, but Not CCNY, Cooperates with CDK16 to Regulate Spermatogenesis in Mouse

Zhenzhen Zi, Zhuzhen Zhang, Qingrun Li, Weiwei An, Liyong Zeng, Dayuan Gao, Ying Yang, Xueliang Zhu, Rong Zeng, Winnie Waichi Shum, Jiarui Wu

YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers

Claudia Stein, Anaïs Flore Bardet, Guglielmo Roma, Sebastian Bergling, Ieuan Clay, Alexandra Ruchti, Claudia Agarinis, Tobias Schmelzle, Tewis Bouwmeester, Dirk Schübeler, Andreas Bauer

Identification of Driving ALK Fusion Genes and Genomic Landscape of Medullary Thyroid Cancer

Jun Ho Ji, Young Lyun Oh, Mineui Hong, Jae Won Yun, Hyun-Woo Lee, DeokGeun Kim, Yongick Ji, Duk-Hwan Kim, Woong-Yang Park, Hyun-Tae Shin, Kyoung-Mee Kim, Myung-Ju Ahn, Keunchil Park, Jong-Mu Sun

Retinoic Acid Signaling Regulates Differential Expression of the Tandemly-Duplicated Long Wavelength-Sensitive Cone Opsin Genes in Zebrafish

Diana M. Mitchell, Craig B. Stevens, Ruth A. Frey, Samuel S. Hunter, Ryuichi Ashino, Shoji Kawamura, Deborah L. Stenkamp

Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference

Lucy van Dorp, David Balding, Simon Myers, Luca Pagani, Chris Tyler-Smith, Endashaw Bekele, Ayele Tarekegn, Mark G. Thomas, Neil Bradman, Garrett Hellenthal

Rhoptry Proteins ROP5 and ROP18 Are Major Murine Virulence Factors in Genetically Divergent South American Strains of Toxoplasma gondii

Michael S. Behnke, Asis Khan, Elvin J. Lauron, John R. Jimah, Qiuling Wang, Niraj H. Tolia, L. David Sibley

Loss and Gain of Natural Killer Cell Receptor Function in an African Hunter-Gatherer Population

Hugo G. Hilton, Paul J. Norman, Neda Nemat-Gorgani, Ana Goyos, Jill A. Hollenbach, Brenna M. Henn, Christopher R. Gignoux, Lisbeth A. Guethlein, Peter Parham

Trans-Reactivation: A New Epigenetic Phenomenon Underlying Transcriptional Reactivation of Silenced Genes

Maria Cristina Onorati, Walter Arancio, Vincenzo Cavalieri, Antonia M. R. Ingrassia, Giulio Pavesi, Davide F. V. Corona

Evolution and Design Governing Signal Precision and Amplification in a Bacterial Chemosensory Pathway

Mathilde Guzzo, Rym Agrebi, Leon Espinosa, Grégory Baronian, Virginie Molle, Emilia M. F. Mauriello, Céline Brochier-Armanet, Tâm Mignot

Functional Divergence in the Role of N-Linked Glycosylation in Smoothened Signaling

Suresh Marada, Gemma Navarro, Ashley Truong, Daniel P. Stewart, Angela M. Arensdorf, Sigrid Nachtergaele, Edgar Angelats, Joseph T. Opferman, Rajat Rohatgi, Peter J. McCormick, Stacey K. Ogden

Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development

Yu Hasegawa, Deanne Taylor, Dmitry A. Ovchinnikov, Ernst J. Wolvetang, Laurence de Torrenté, Jessica C. Mar

In Vivo Evidence for Lysosome Depletion and Impaired Autophagic Clearance in Hereditary Spastic Paraplegia Type SPG11

Rita-Eva Varga, Mukhran Khundadze, Markus Damme, Sandor Nietzsche, Birgit Hoffmann, Tobias Stauber, Nicole Koch, J. Christopher Hennings, Patricia Franzka, Antje K. Huebner, Michael M. Kessels, Christoph Biskup, Thomas J. Jentsch, Britta Qualmann, Thomas Braulke, Ingo Kurth, Christian Beetz, Christian A. Hübner

Cyclin G Functions as a Positive Regulator of Growth and Metabolism in Drosophila

Patrick Fischer, Martina K. La Rosa, Adriana Schulz, Anette Preiss, Anja C. Nagel

Hypoxia and Temperature Regulated Morphogenesis in Candida albicans

Prashant R. Desai, Lasse van Wijlick, Dagmar Kurtz, Mateusz Juchimiuk, Joachim F. Ernst

Regulation of Gene Expression Patterns in Mosquito Reproduction

Sourav Roy, Tusar T. Saha, Lisa Johnson, Bo Zhao, Jisu Ha, Kevin P. White, Thomas Girke, Zhen Zou, Alexander S. Raikhel

Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence

Julien Y. Dutheil, Kasper Munch, Kiwoong Nam, Thomas Mailund, Mikkel H. Schierup

Runx1 Transcription Factor Is Required for Myoblasts Proliferation during Muscle Regeneration

Kfir Baruch Umansky, Yael Gruenbaum-Cohen, Michael Tsoory, Ester Feldmesser, Dalia Goldenberg, Ori Brenner, Yoram Groner

SHOEBOX Modulates Root Meristem Size in Rice through Dose-Dependent Effects of Gibberellins on Cell Elongation and Proliferation

Jintao Li, Yu Zhao, Huangwei Chu, Likai Wang, Yanru Fu, Ping Liu, Narayana Upadhyaya, Chunli Chen, Tongmin Mou, Yuqi Feng, Prakash Kumar, Jian Xu

Molecular Basis of Gene-Gene Interaction: Cyclic Cross-Regulation of Gene Expression and Post-GWAS Gene-Gene Interaction Involved in Atrial Fibrillation

Yufeng Huang, Chuchu Wang, Yufeng Yao, Xiaoyu Zuo, Shanshan Chen, Chengqi Xu, Hongfu Zhang, Qiulun Lu, Le Chang, Fan Wang, Pengxia Wang, Rongfeng Zhang, Zhenkun Hu, Qixue Song, Xiaowei Yang, Cong Li, Sisi Li, Yuanyuan Zhao, Qin Yang, Dan Yin, Xiaojing Wang, Wenxia Si, Xiuchun Li, Xin Xiong, Dan Wang, Yuan Huang, Chunyan Luo, Jia Li, Jingjing Wang, Jing Chen, Longfei Wang, Li Wang, Meng Han, Jian Ye, Feifei Chen, Jingqiu Liu, Ying Liu, Gang Wu, Bo Yang, Xiang Cheng, Yuhua Liao, Yanxia Wu, Tie Ke, Qiuyun Chen, Xin Tu, Robert Elston, Shaoqi Rao, Yanzong Yang, Yunlong Xia, Qing K. Wang

New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

Nicola De Maio, Chieh-Hsi Wu, Kathleen M O’Reilly, Daniel Wilson

Binding of Multiple Rap1 Proteins Stimulates Chromosome Breakage Induction during DNA Replication

Greicy H. Goto, Sevil Zencir, Yukinori Hirano, Hiroo Ogi, Andreas Ivessa, Katsunori Sugimoto

Nbs1 ChIP-Seq Identifies Off-Target DNA Double-Strand Breaks Induced by AID in Activated Splenic B Cells

Lyne Khair, Richard E. Baker, Erin K. Linehan, Carol E. Schrader, Janet Stavnezer

Suppression of Somatic Expansion Delays the Onset of Pathophysiology in a Mouse Model of Huntington’s Disease

Helen Budworth, Faye R. Harris, Paul Williams, Do Yup Lee, Amy Holt, Jens Pahnke, Bartosz Szczesny, Karina Acevedo-Torres, Sylvette Ayala-Peña, Cynthia T. McMurray

Calmodulin Methyltransferase Is Required for Growth, Muscle Strength, Somatosensory Development and Brain Function

Sitvanit Haziza, Roberta Magnani, Dima Lan, Omer Keinan, Ann Saada, Eli Hershkovitz, Nurit Yanay, Yoram Cohen, Yoram Nevo, Robert L. Houtz, Val C. Sheffield, Hava Golan, Ruti Parvari

Coordinated Evolution of Influenza A Surface Proteins

Alexey D. Neverov, Sergey Kryazhimskiy, Joshua B. Plotkin, Georgii A. Bazykin

SLIRP Regulates the Rate of Mitochondrial Protein Synthesis and Protects LRPPRC from Degradation

Marie Lagouge, Arnaud Mourier, Hyun Ju Lee, Henrik Spåhr, Timothy Wai, Christian Kukat, Eduardo Silva Ramos, Elisa Motori, Jakob D. Busch, Stefan Siira, Elisabeth Kremmer, Aleksandra Filipovska, Nils-Göran Larsson , German Mouse Clinic Consortium

A Genome Scale Screen for Mutants with Delayed Exit from Mitosis: Ire1-Independent Induction of Autophagy Integrates ER Homeostasis into Mitotic Lifespan

Ata Ghavidel, Kunal Baxi, Vladimir Ignatchenko, Martin Prusinkiewicz, Terra G. Arnason, Thomas Kislinger, Carlos E. Carvalho, Troy A. A. Harkness

Let-7 Represses Carcinogenesis and a Stem Cell Phenotype in the Intestine via Regulation of Hmga2

Blair B. Madison, Arjun N. Jeganathan, Rei Mizuno, Monte M. Winslow, Antoni Castells, Miriam Cuatrecasas, Anil K. Rustgi

Xist Exon 7 Contributes to the Stable Localization of Xist RNA on the Inactive X-Chromosome

Norishige Yamada, Yuko Hasegawa, Minghui Yue, Tomofumi Hamada, Shinichi Nakagawa, Yuya Ogawa

Functional Activation of the Flagellar Type III Secretion Export Apparatus

Andrew M. Phillips, Rebecca A. Calvo, Daniel B. Kearns

The Evolutionary Potential of Phenotypic Mutations

Hayato Yanagida, Ariel Gispan, Noam Kadouri, Shelly Rozen, Michal Sharon, Naama Barkai, Dan S. Tawfik

piRNAs Are Associated with Diverse Transgenerational Effects on Gene and Transposon Expression in a Hybrid Dysgenic Syndrome of D. virilis

Alexandra A. Erwin, Mauricio A. Galdos, Michelle L. Wickersheim, Chris C. Harrison, Kendra D. Marr, Jack M. Colicchio, Justin P. Blumenstiel

TSPO, a Mitochondrial Outer Membrane Protein, Controls Ethanol-Related Behaviors in Drosophila

Ran Lin, Danielle Rittenhouse, Katelyn Sweeney, Prasanth Potluri, Douglas C. Wallace

The Spalt Transcription Factors Generate the Transcriptional Landscape of the Drosophila melanogaster Wing Pouch Central Region

María F. Organista, Mercedes Martín, Jesus M. de Celis, Rosa Barrio, Ana López-Varea, Nuria Esteban, Mar Casado, Jose F. de Celis

Retrohoming of a Mobile Group II Intron in Human Cells Suggests How Eukaryotes Limit Group II Intron Proliferation

David M. Truong, F. Curtis Hewitt, Joseph H. Hanson, Xiaoxia Cui, Alan M. Lambowitz

mTORC1 Prevents Preosteoblast Differentiation through the Notch Signaling Pathway

Bin Huang, Yongkui Wang, Wenhao Wang, Juan Chen, Pinglin Lai, Zhongyu Liu, Bo Yan, Song Xu, Zhongmin Zhang, Chun Zeng, Limin Rong, Bin Liu, Daozhang Cai, Dadi Jin, Xiaochun Bai

Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas

Diane I. Schroeder, Kartika Jayashankar, Kory C. Douglas, Twanda L. Thirkill, Daniel York, Pete J. Dickinson, Lawrence E. Williams, Paul B. Samollow, Pablo J. Ross, Danika L. Bannasch, Gordon C. Douglas, Janine M. LaSalle