November 2014

Recombination hotspots are subject to an evolutionary process, called biased gene conversion (BGC), which favors mutations suppressing their recombination activity. The analysis of an archaic human genome (Denisovan) showed that this self-destructive process is extremely fast, as the life expectancy of most active hotspots is less than 100,000 generations. This suggests that the turnover of recombination hotspots might be the consequence of a Red Queen process: the activity of recombination hotspots leads to their rapid loss by BGC, and the genes that determine the location of hotspots are therefore regularly under selective pressure to switch to new targets. See Lesecque et al.

Image Credit: Pauline Sémon

Interview

The Ethics of Our Inquiry: An Interview with Hank Greely

Jane Gitschier

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004780

Review

Regularized Machine Learning in the Genetic Prediction of Complex Traits

Sebastian Okser, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Samuli Ripatti, Tero Aittokallio

PLOS Genetics: published November 13, 2014 | https://doi.org/10.1371/journal.pgen.1004754

Research Articles

The CSN/COP9 Signalosome Regulates Synaptonemal Complex Assembly during Meiotic Prophase I of Caenorhabditis elegans

Heather Brockway, Nathan Balukoff, Martha Dean, Benjamin Alleva, Sarit Smolikove

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004757

The Role of cis Regulatory Evolution in Maize Domestication

Zachary H. Lemmon, Robert Bukowski, Qi Sun, John F. Doebley

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004745

Systematic Analysis of the Role of RNA-Binding Proteins in the Regulation of RNA Stability

Ayesha Hasan, Cristina Cotobal, Caia D. S. Duncan, Juan Mata

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004684

ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing

Justin R. Pritchard, Michael C. Chao, Sören Abel, Brigid M. Davis, Catherine Baranowski, Yanjia J. Zhang, Eric J. Rubin, Matthew K. Waldor

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004782

Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila

Alan O. Bergland, Emily L. Behrman, Katherine R. O'Brien, Paul S. Schmidt, Dmitri A. Petrov

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004775

Natural Polymorphisms in Human APOBEC3H and HIV-1 Vif Combine in Primary T Lymphocytes to Affect Viral G-to-A Mutation Levels and Infectivity

Eric W. Refsland, Judd F. Hultquist, Elizabeth M. Luengas, Terumasa Ikeda, Nadine M. Shaban, Emily K. Law, William L. Brown, Cavan Reilly, Michael Emerman, Reuben S. Harris

PLOS Genetics: published November 20, 2014 | https://doi.org/10.1371/journal.pgen.1004761

Regulation of mRNA Abundance by Polypyrimidine Tract-Binding Protein-Controlled Alternate 5′ Splice Site Choice

Fursham M. Hamid, Eugene V. Makeyev

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004771

Genome-Wide Associations between Genetic and Epigenetic Variation Influence mRNA Expression and Insulin Secretion in Human Pancreatic Islets

Anders H. Olsson, Petr Volkov, Karl Bacos, Tasnim Dayeh, Elin Hall, Emma A. Nilsson, Claes Ladenvall, Tina Rönn, Charlotte Ling

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004735

Coordinate Regulation of Stem Cell Competition by Slit-Robo and JAK-STAT Signaling in the Drosophila Testis

Rachel R. Stine, Leah J. Greenspan, Kapil V. Ramachandran, Erika L. Matunis

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004713

A Germline Polymorphism of Thymine DNA Glycosylase Induces Genomic Instability and Cellular Transformation

Ashley Sjolund, Antonia A. Nemec, Nicolas Paquet, Aishwarya Prakash, Patrick Sung, Sylvie Doublié, Joann B. Sweasy

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004753

Stress Granule-Defective Mutants Deregulate Stress Responsive Transcripts

Xiaoxue Yang, Yi Shen, Elena Garre, Xinxin Hao, Daniel Krumlinde, Marija Cvijović, Christina Arens, Thomas Nyström, Beidong Liu, Per Sunnerhagen

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004763

24-Hour Rhythms of DNA Methylation and Their Relation with Rhythms of RNA Expression in the Human Dorsolateral Prefrontal Cortex

Andrew S. P. Lim, Gyan P. Srivastava, Lei Yu, Lori B. Chibnik, Jishu Xu, Aron S. Buchman, Julie A. Schneider, Amanda J. Myers, David A. Bennett, Philip L. De Jager

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004792

A Functional Portrait of Med7 and the Mediator Complex in Candida albicans

Faiza Tebbji, Yaolin Chen, Julien Richard Albert, Kearney T. W. Gunsalus, Carol A. Kumamoto, André Nantel, Adnane Sellam, Malcolm Whiteway

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004770

Pseudoautosomal Region 1 Length Polymorphism in the Human Population

Martin A. Mensah, Matthew S. Hestand, Maarten H. D. Larmuseau, Mala Isrie, Nancy Vanderheyden, Matthias Declercq, Erika L. Souche, Jeroen Van Houdt, Radka Stoeva, Hilde Van Esch, Koen Devriendt, Thierry Voet, Ronny Decorte, Peter N. Robinson, Joris R. Vermeesch

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004578

Evolution of DNA Methylation Patterns in the Brassicaceae is Driven by Differences in Genome Organization

Danelle K. Seymour, Daniel Koenig, Jörg Hagmann, Claude Becker, Detlef Weigel

PLOS Genetics: published November 13, 2014 | https://doi.org/10.1371/journal.pgen.1004785

ATPase-Independent Type-III Protein Secretion in Salmonella enterica

Marc Erhardt, Max E. Mertens, Florian D. Fabiani, Kelly T. Hughes

PLOS Genetics: published November 13, 2014 | https://doi.org/10.1371/journal.pgen.1004800

Functional Diversity of Carbohydrate-Active Enzymes Enabling a Bacterium to Ferment Plant Biomass

Magali Boutard, Tristan Cerisy, Pierre-Yves Nogue, Adriana Alberti, Jean Weissenbach, Marcel Salanoubat, Andrew C. Tolonen

PLOS Genetics: published November 13, 2014 | https://doi.org/10.1371/journal.pgen.1004773

Approximation to the Distribution of Fitness Effects across Functional Categories in Human Segregating Polymorphisms

Fernando Racimo, Joshua G. Schraiber

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004697

p53- and ERK7-Dependent Ribosome Surveillance Response Regulates Drosophila Insulin-Like Peptide Secretion

Kiran Hasygar, Ville Hietakangas

PLOS Genetics: published November 13, 2014 | https://doi.org/10.1371/journal.pgen.1004764

The COP9 Signalosome Converts Temporal Hormone Signaling to Spatial Restriction on Neural Competence

Yi-Chun Huang, Yu-Nung Lu, June-Tai Wu, Cheng-Ting Chien, Haiwei Pi

PLOS Genetics: published November 13, 2014 | https://doi.org/10.1371/journal.pgen.1004760

A Thermolabile Aldolase A Mutant Causes Fever-Induced Recurrent Rhabdomyolysis without Hemolytic Anemia

Asmaa Mamoune, Michel Bahuau, Yamina Hamel, Valérie Serre, Michele Pelosi, Florence Habarou, Marie-Ange Nguyen Morel, Bertrand Boisson, Sabrina Vergnaud, Mai Thao Viou, Luc Nonnenmacher, Monique Piraud, Patrick Nusbaum, Joseph Vamecq, Norma Romero, Chris Ottolenghi, Jean-Laurent Casanova, Pascale de Lonlay

PLOS Genetics: published November 13, 2014 | https://doi.org/10.1371/journal.pgen.1004711

Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response

Erin A. Becker, Phillip M. Seitzer, Andrew Tritt, David Larsen, Megan Krusor, Andrew I. Yao, Dongying Wu, Dominique Madern, Jonathan A. Eisen, Aaron E. Darling, Marc T. Facciotti

PLOS Genetics: published November 13, 2014 | https://doi.org/10.1371/journal.pgen.1004784

Rad59-Facilitated Acquisition of Y′ Elements by Short Telomeres Delays the Onset of Senescence

Dmitri Churikov, Ferose Charifi, Marie-Noëlle Simon, Vincent Géli

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004736

GPA: A Statistical Approach to Prioritizing GWAS Results by Integrating Pleiotropy and Annotation

Dongjun Chung, Can Yang, Cong Li, Joel Gelernter, Hongyu Zhao

PLOS Genetics: published November 13, 2014 | https://doi.org/10.1371/journal.pgen.1004787

RNA Processing Factors Swd2.2 and Sen1 Antagonize RNA Pol III-Dependent Transcription and the Localization of Condensin at Pol III Genes

Pénélope Legros, Amélie Malapert, Sho Niinuma, Pascal Bernard, Vincent Vanoosthuyse

PLOS Genetics: published November 13, 2014 | https://doi.org/10.1371/journal.pgen.1004794

Genetic Analysis of a Novel Tubulin Mutation That Redirects Synaptic Vesicle Targeting and Causes Neurite Degeneration in C. elegans

Jiun-Min Hsu, Chun-Hao Chen, Yen-Chih Chen, Kent L. McDonald, Mark Gurling, Albert Lee, Gian Garriga, Chun-Liang Pan

PLOS Genetics: published November 13, 2014 | https://doi.org/10.1371/journal.pgen.1004715

Systematic Comparison of the Effects of Alpha-synuclein Mutations on Its Oligomerization and Aggregation

Diana F. Lázaro, Eva F. Rodrigues, Ramona Langohr, Hedieh Shahpasandzadeh, Thales Ribeiro, Patrícia Guerreiro, Ellen Gerhardt, Katharina Kröhnert, Jochen Klucken, Marcos D. Pereira, Blagovesta Popova, Niels Kruse, Brit Mollenhauer, Silvio O. Rizzoli, Gerhard H. Braus, Karin M. Danzer, Tiago F. Outeiro

PLOS Genetics: published November 13, 2014 | https://doi.org/10.1371/journal.pgen.1004741

The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes

Yann Lesecque, Sylvain Glémin, Nicolas Lartillot, Dominique Mouchiroud, Laurent Duret

PLOS Genetics: published November 13, 2014 | https://doi.org/10.1371/journal.pgen.1004790

The Protein O-glucosyltransferase Rumi Modifies Eyes Shut to Promote Rhabdomere Separation in Drosophila

Amanda R. Haltom, Tom V. Lee, Beth M. Harvey, Jessica Leonardi, Yi-Jiun Chen, Yang Hong, Robert S. Haltiwanger, Hamed Jafar-Nejad

PLOS Genetics: published November 20, 2014 | https://doi.org/10.1371/journal.pgen.1004795

The Talin Head Domain Reinforces Integrin-Mediated Adhesion by Promoting Adhesion Complex Stability and Clustering

Stephanie J. Ellis, Emily Lostchuck, Benjamin T. Goult, Mohamed Bouaouina, Michael J. Fairchild, Pablo López-Ceballos, David A. Calderwood, Guy Tanentzapf

PLOS Genetics: published November 13, 2014 | https://doi.org/10.1371/journal.pgen.1004756

Three RNA Binding Proteins Form a Complex to Promote Differentiation of Germline Stem Cell Lineage in Drosophila

Di Chen, Chan Wu, Shaowei Zhao, Qing Geng, Yu Gao, Xin Li, Yang Zhang, Zhaohui Wang

PLOS Genetics: published November 20, 2014 | https://doi.org/10.1371/journal.pgen.1004797

Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association

Zhihao Ding, Yunyun Ni, Sander W. Timmer, Bum-Kyu Lee, Anna Battenhouse, Sandra Louzada, Fengtang Yang, Ian Dunham, Gregory E. Crawford, Jason D. Lieb, Richard Durbin, Vishwanath R. Iyer, Ewan Birney

PLOS Genetics: published November 20, 2014 | https://doi.org/10.1371/journal.pgen.1004798

HAM-5 Functions As a MAP Kinase Scaffold during Cell Fusion in Neurospora crassa

Wilfried Jonkers, Abigail C. Leeder, Charles Ansong, Yuexi Wang, Feng Yang, Trevor L. Starr, David G. Camp II, Richard D. Smith, N. Louise Glass

PLOS Genetics: published November 20, 2014 | https://doi.org/10.1371/journal.pgen.1004783

Inversion of the Chromosomal Region between Two Mating Type Loci Switches the Mating Type in Hansenula polymorpha

Hiromi Maekawa, Yoshinobu Kaneko

PLOS Genetics: published November 20, 2014 | https://doi.org/10.1371/journal.pgen.1004796

A Systems Genetics Approach Identifies CXCL14, ITGAX, and LPCAT2 as Novel Aggressive Prostate Cancer Susceptibility Genes

Kendra A. Williams, Minnkyong Lee, Ying Hu, Jonathan Andreas, Shashank J. Patel, Suiyuan Zhang, Peter Chines, Abdel Elkahloun, Settara Chandrasekharappa, J. Silvio Gutkind, Alfredo A. Molinolo, Nigel P. S. Crawford

PLOS Genetics: published November 20, 2014 | https://doi.org/10.1371/journal.pgen.1004809

An RNA-Seq Screen of the Drosophila Antenna Identifies a Transporter Necessary for Ammonia Detection

Karen Menuz, Nikki K. Larter, Joori Park, John R. Carlson

PLOS Genetics: published November 20, 2014 | https://doi.org/10.1371/journal.pgen.1004810

Fungal Communication Requires the MAK-2 Pathway Elements STE-20 and RAS-2, the NRC-1 Adapter STE-50 and the MAP Kinase Scaffold HAM-5

Anne Dettmann, Yvonne Heilig, Oliver Valerius, Sarah Ludwig, Stephan Seiler

PLOS Genetics: published November 20, 2014 | https://doi.org/10.1371/journal.pgen.1004762

The Complex I Subunit NDUFA10 Selectively Rescues Drosophila pink1 Mutants through a Mechanism Independent of Mitophagy

Joe H. Pogson, Rachael M. Ivatt, Alvaro Sanchez-Martinez, Roberta Tufi, Emma Wilson, Heather Mortiboys, Alexander J. Whitworth

PLOS Genetics: published November 20, 2014 | https://doi.org/10.1371/journal.pgen.1004815

SAS-1 Is a C2 Domain Protein Critical for Centriole Integrity in C. elegans

Lukas von Tobel, Tamara Mikeladze-Dvali, Marie Delattre, Fernando R. Balestra, Simon Blanchoud, Susanne Finger, Graham Knott, Thomas Müller-Reichert, Pierre Gönczy

PLOS Genetics: published November 20, 2014 | https://doi.org/10.1371/journal.pgen.1004777

Heat-Induced Release of Epigenetic Silencing Reveals the Concealed Role of an Imprinted Plant Gene

Diego H. Sanchez, Jerzy Paszkowski

PLOS Genetics: published November 20, 2014 | https://doi.org/10.1371/journal.pgen.1004806

Corrections

Correction: Genome-Wide Association Meta-analysis of Neuropathologic Features of Alzheimer’s Disease and Related Dementias

The PLOS Genetics Staff

PLOS Genetics: published November 12, 2014 | https://doi.org/10.1371/journal.pgen.1004867

Correction: Controlling Meiotic Recombinational Repair – Specifying the Roles of ZMMs, Sgs1 and Mus81/Mms4 in Crossover Formation

The PLOS Genetics Staff

PLOS Genetics: published November 12, 2014 | https://doi.org/10.1371/journal.pgen.1004870

Correction: Selection on a Variant Associated with Improved Viral Clearance Drives Local, Adaptive Pseudogenization of Interferon Lambda 4 (IFNL4)

The PLOS Genetics Staff

PLOS Genetics: published November 19, 2014 | https://doi.org/10.1371/journal.pgen.1004882

Formal Comments

Establishing a Multidisciplinary Context for Modeling 3D Facial Shape from DNA

Peter Claes, Mark D. Shriver

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004725

Let's Face It—Complex Traits Are Just Not That Simple

Benedikt Hallgrimsson, Washington Mio, Ralph S. Marcucio, Richard Spritz

PLOS Genetics: published November 6, 2014 | https://doi.org/10.1371/journal.pgen.1004724

Glutamate Receptor Gene GRIN2A, Coffee, and Parkinson Disease

Taye H. Hamza, Erin M. Hill-Burns, William K. Scott, Jeffrey M. Vance, Stewart A. Factor, Cyrus P. Zabetian, Haydeh Payami

PLOS Genetics: published November 20, 2014 | https://doi.org/10.1371/journal.pgen.1004774

Lack of Replication of the GRIN2A-by-Coffee Interaction in Parkinson Disease

Ismaïl Ahmed, Pei-Chen Lee, Christina M. Lill, Susan Searles Nielsen, Fanny Artaud, Lisa G. Gallagher, Marie-Anne Loriot, Claire Mulot, Magali Nacfer, Tian Liu, Joanna M. Biernacka, Sebastian Armasu, Kari Anderson, Federico M. Farin, Christina Funch Lassen, Johnni Hansen, Jørgen H. Olsen, Lars Bertram, Demetrius M. Maraganore, Harvey Checkoway, Beate Ritz, Alexis Elbaz

PLOS Genetics: published November 20, 2014 | https://doi.org/10.1371/journal.pgen.1004788

Cover

Rapid turnover of recombination hotspots: the comparative analysis of modern and archaic human genomes supports a model of Red Queen evolution.

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