March 2017

By comparing phenotypic and genetic differentiation across populations, Zaidi et al. show that while most aspects of nose shape seem to be evolving neutrally, the width of the nares shows signals of adaptation to climate. The featured image is an artistic representation of this finding. The network represents evolutionary processes underlying population-differentiation in nares width. Blue boxes represent alleles for narrower nares while red boxes represent alleles for wider nares. Colors in between represent intermediate phenotypes. This color scale serves to highlight the association between nares' width and climate, suggesting that narrow nares might have been favored in cold-dry climates while wider nares were favored in warm-humid climates. See Zaidi et al.

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Image Credit: Arslan A. Zaidi

Editorial

PLOS Genetics 2016 Reviewer and Editorial Board Thank You

PLOS Genetics: published March 20, 2017 | https://doi.org/10.1371/journal.pgen.1006671

Perspectives

Fishing for adaptive epistasis using mitonuclear interactions

David M. Rand

PLOS Genetics: published March 31, 2017 | https://doi.org/10.1371/journal.pgen.1006662

The social genome: Current findings and implications for the study of human genetics

Benjamin W. Domingue, Daniel W. Belsky

PLOS Genetics: published March 16, 2017 | https://doi.org/10.1371/journal.pgen.1006615

Research Articles

Cis-eQTL-based trans-ethnic meta-analysis reveals novel genes associated with breast cancer risk

Joshua D. Hoffman, Rebecca E. Graff, Nima C. Emami, Caroline G. Tai, Michael N. Passarelli, Donglei Hu, Scott Huntsman, Dexter Hadley, Lancelote Leong, Arunabha Majumdar, Noah Zaitlen, Elad Ziv, John S. Witte

PLOS Genetics: published March 31, 2017 | https://doi.org/10.1371/journal.pgen.1006690

Comparison of independent screens on differentially vulnerable motor neurons reveals alpha-synuclein as a common modifier in motor neuron diseases

Rachel A. Kline, Kevin A. Kaifer, Erkan Y. Osman, Francesco Carella, Ariana Tiberi, Jolill Ross, Giuseppa Pennetta, Christian L. Lorson, Lyndsay M. Murray

PLOS Genetics: published March 31, 2017 | https://doi.org/10.1371/journal.pgen.1006680

Evolved genetic and phenotypic differences due to mitochondrial-nuclear interactions

Tara Z. Baris, Dominique N. Wagner, David I. Dayan, Xiao Du, Pierre U. Blier, Nicolas Pichaud, Marjorie F. Oleksiak, Douglas L. Crawford

PLOS Genetics: published March 31, 2017 | https://doi.org/10.1371/journal.pgen.1006517

Fast growth conditions uncouple the final stages of chromosome segregation and cell division in Escherichia coli

Elisa Galli, Caroline Midonet, Evelyne Paly, François-Xavier Barre

PLOS Genetics: published March 30, 2017 | https://doi.org/10.1371/journal.pgen.1006702

Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations

Shantao Li, Brian M. Shuch, Mark B. Gerstein

PLOS Genetics: published March 30, 2017 | https://doi.org/10.1371/journal.pgen.1006685

Salmonella genomic island 1 (SGI1) reshapes the mating apparatus of IncC conjugative plasmids to promote self-propagation

Nicolas Carraro, Romain Durand, Nicolas Rivard, Charley Anquetil, Catherine Barrette, Malika Humbert, Vincent Burrus

PLOS Genetics: published March 29, 2017 | https://doi.org/10.1371/journal.pgen.1006705

Transcriptome-wide analysis of alternative routes for RNA substrates into the exosome complex

Clémentine Delan-Forino, Claudia Schneider, David Tollervey

PLOS Genetics: published March 29, 2017 | https://doi.org/10.1371/journal.pgen.1006699

Transaldolase inhibition impairs mitochondrial respiration and induces a starvation-like longevity response in Caenorhabditis elegans

Christopher F. Bennett, Jane J. Kwon, Christine Chen, Joshua Russell, Kathlyn Acosta, Nikolay Burnaevskiy, Matthew M. Crane, Alessandro Bitto, Helen Vander Wende, Marissa Simko, Victor Pineda, Ryan Rossner, Brian M. Wasko, Haeri Choi, Shiwen Chen, Shirley Park, Gholamali Jafari, Bryan Sands, Carissa Perez Olsen, Alexander R. Mendenhall, Philip G. Morgan, Matt Kaeberlein

PLOS Genetics: published March 29, 2017 | https://doi.org/10.1371/journal.pgen.1006695

CLAVATA1 controls distinct signaling outputs that buffer shoot stem cell proliferation through a two-step transcriptional compensation loop

Zachary L. Nimchuk

PLOS Genetics: published March 29, 2017 | https://doi.org/10.1371/journal.pgen.1006681

A genetic switch controls the production of flagella and toxins in Clostridium difficile

Brandon R. Anjuwon-Foster, Rita Tamayo

PLOS Genetics: published March 27, 2017 | https://doi.org/10.1371/journal.pgen.1006701

Disruption of SorCS2 reveals differences in the regulation of stereociliary bundle formation between hair cell types in the inner ear

Andrew Forge, Ruth R. Taylor, Sally J. Dawson, Michael Lovett, Daniel J. Jagger

PLOS Genetics: published March 27, 2017 | https://doi.org/10.1371/journal.pgen.1006692

Reduced dosage of β-catenin provides significant rescue of cardiac outflow tract anomalies in a Tbx1 conditional null mouse model of 22q11.2 deletion syndrome

Silvia E. Racedo, Erica Hasten, Mingyan Lin, Gnanapackiam Sheela Devakanmalai, Tingwei Guo, Ertugrul M. Ozbudak, Chen-Leng Cai, Deyou Zheng, Bernice E. Morrow

PLOS Genetics: published March 27, 2017 | https://doi.org/10.1371/journal.pgen.1006687

Aberrant neuronal activity-induced signaling and gene expression in a mouse model of RASopathy

Franziska Altmüller, Santosh Pothula, Anil Annamneedi, Saeideh Nakhaei-Rad, Carolina Montenegro-Venegas, Eneko Pina-Fernández, Claudia Marini, Monica Santos, Denny Schanze, Dirk Montag, Mohammad R. Ahmadian, Oliver Stork, Martin Zenker, Anna Fejtova

PLOS Genetics: published March 27, 2017 | https://doi.org/10.1371/journal.pgen.1006684

Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies

Rocio Acuna-Hidalgo, Pelagia Deriziotis, Marloes Steehouwer, Christian Gilissen, Sarah A. Graham, Sipko van Dam, Julie Hoover-Fong, Aida B. Telegrafi, Anne Destree, Robert Smigiel, Lindsday A. Lambie, Hülya Kayserili, Umut Altunoglu, Elisabetta Lapi, Maria Luisa Uzielli, Mariana Aracena, Banu G. Nur, Ercan Mihci, Lilia M. A. Moreira, Viviane Borges Ferreira, Dafne D. G. Horovitz, Katia M. da Rocha, Aleksandra Jezela-Stanek, Alice S. Brooks, Heiko Reutter, Julie S. Cohen, Ali Fatemi, Martin Smitka, Theresa A. Grebe, Nataliya Di Donato, Charu Deshpande, Anthony Vandersteen, Charles Marques Lourenço, Andreas Dufke, Eva Rossier, Gwenaelle Andre, Alessandra Baumer, Careni Spencer, Julie McGaughran, Lude Franke, Joris A. Veltman, Bert B. A. De Vries, Albert Schinzel, Simon E. Fisher, Alexander Hoischen, Bregje W. van Bon

PLOS Genetics: published March 27, 2017 | https://doi.org/10.1371/journal.pgen.1006683

Wnt/Tcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4/Arf locus

Anchel De Jaime-Soguero, Francesco Aulicino, Gokhan Ertaylan, Anna Griego, Aniello Cerrato, Aravind Tallam, Antonio del Sol, Maria Pia Cosma, Frederic Lluis

PLOS Genetics: published March 27, 2017 | https://doi.org/10.1371/journal.pgen.1006682

Rare variants in fox-1 homolog A (RBFOX1) are associated with lower blood pressure

Karen Y. He, Heming Wang, Brian E. Cade, Priyanka Nandakumar, Ayush Giri, Erin B. Ware, Jeffrey Haessler, Jingjing Liang, Jennifer A. Smith, Nora Franceschini, Thu H. Le, Charles Kooperberg, Todd L. Edwards, Sharon L. R. Kardia, Xihong Lin, Aravinda Chakravarti, Susan Redline, Xiaofeng Zhu

PLOS Genetics: published March 27, 2017 | https://doi.org/10.1371/journal.pgen.1006678

SEPT12 phosphorylation results in loss of the septin ring/sperm annulus, defective sperm motility and poor male fertility

Yi-Ru Shen, Han-Yu Wang, Yung-Che Kuo, Shih-Chuan Shih, Chun-Hua Hsu, Yet-Ran Chen, Shang-Rung Wu, Chia-Yih Wang, Pao-Lin Kuo

PLOS Genetics: published March 27, 2017 | https://doi.org/10.1371/journal.pgen.1006631

Functional classification of DNA variants by hybrid minigenes: Identification of 30 spliceogenic variants of BRCA2 exons 17 and 18

Eugenia Fraile-Bethencourt, Beatriz Díez-Gómez, Valeria Velásquez-Zapata, Alberto Acedo, David J. Sanz, Eladio A. Velasco

PLOS Genetics: published March 24, 2017 | https://doi.org/10.1371/journal.pgen.1006691

A non-canonical RNA degradation pathway suppresses RNAi-dependent epimutations in the human fungal pathogen Mucor circinelloides

Silvia Calo, Francisco E. Nicolás, Soo Chan Lee, Ana Vila, Maria Cervantes, Santiago Torres-Martinez, Rosa M. Ruiz-Vazquez, Maria E. Cardenas, Joseph Heitman

PLOS Genetics: published March 24, 2017 | https://doi.org/10.1371/journal.pgen.1006686

Meiotic recombination modulates the structure and dynamics of the synaptonemal complex during C. elegans meiosis

Divya Pattabiraman, Baptiste Roelens, Alexander Woglar, Anne M. Villeneuve

PLOS Genetics: published March 24, 2017 | https://doi.org/10.1371/journal.pgen.1006670

CSL encodes a leucine-rich-repeat protein implicated in red/violet light signaling to the circadian clock in Chlamydomonas

Ayumi Kinoshita, Yoshimi Niwa, Kiyoshi Onai, Takashi Yamano, Hideya Fukuzawa, Masahiro Ishiura, Takuya Matsuo

PLOS Genetics: published March 23, 2017 | https://doi.org/10.1371/journal.pgen.1006645

Visualizing the structure of RNA-seq expression data using grade of membership models

Kushal K. Dey, Chiaowen Joyce Hsiao, Matthew Stephens

PLOS Genetics: published March 23, 2017 | https://doi.org/10.1371/journal.pgen.1006599

COLEC10 is mutated in 3MC patients and regulates early craniofacial development

Mustafa M. Munye, Anna Diaz-Font, Louise Ocaka, Maiken L. Henriksen, Melissa Lees, Angela Brady, Dagan Jenkins, Jenny Morton, Soren W. Hansen, Chiara Bacchelli, Philip L. Beales, Victor Hernandez-Hernandez

PLOS Genetics: published March 16, 2017 | https://doi.org/10.1371/journal.pgen.1006679

Global analysis of translation termination in E. coli

Natalie E. Baggett, Yan Zhang, Carol A. Gross

PLOS Genetics: published March 16, 2017 | https://doi.org/10.1371/journal.pgen.1006676

Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts

Jean-Tristan Brandenburg, Tristan Mary-Huard, Guillem Rigaill, Sarah J. Hearne, Hélène Corti, Johann Joets, Clémentine Vitte, Alain Charcosset, Stéphane D. Nicolas, Maud I. Tenaillon

PLOS Genetics: published March 16, 2017 | https://doi.org/10.1371/journal.pgen.1006666

Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS

Lisa Krug, Nabanita Chatterjee, Rebeca Borges-Monroy, Stephen Hearn, Wen-Wei Liao, Kathleen Morrill, Lisa Prazak, Nikolay Rozhkov, Delphine Theodorou, Molly Hammell, Josh Dubnau

PLOS Genetics: published March 16, 2017 | https://doi.org/10.1371/journal.pgen.1006635

Investigating the case of human nose shape and climate adaptation

Arslan A. Zaidi, Brooke C. Mattern, Peter Claes, Brian McEcoy, Cris Hughes, Mark D. Shriver

PLOS Genetics: published March 16, 2017 | https://doi.org/10.1371/journal.pgen.1006616

An SMC-like protein binds and regulates Caenorhabditis elegans condensins

Lucy Fang-I Chao, Meha Singh, James Thompson, John R. Yates III, Kirsten A. Hagstrom

PLOS Genetics: published March 16, 2017 | https://doi.org/10.1371/journal.pgen.1006614

hnRNP I regulates neonatal immune adaptation and prevents colitis and colorectal cancer

Zhigang Jin, Feng Liang, Jing Yang, Wenyan Mei

PLOS Genetics: published March 15, 2017 | https://doi.org/10.1371/journal.pgen.1006672

Shared regulatory sites are abundant in the human genome and shed light on genome evolution and disease pleiotropy

Pin Tong, Jack Monahan, James G. D. Prendergast

PLOS Genetics: published March 10, 2017 | https://doi.org/10.1371/journal.pgen.1006673

The transjugation machinery of Thermus thermophilus: Identification of TdtA, an ATPase involved in DNA donation

Alba Blesa, Ignacio Baquedano, Nieves G. Quintáns, Carlos P. Mata, José R. Castón, José Berenguer

PLOS Genetics: published March 10, 2017 | https://doi.org/10.1371/journal.pgen.1006669

Adaptation of A-to-I RNA editing in Drosophila

Yuange Duan, Shengqian Dou, Shiqi Luo, Hong Zhang, Jian Lu

PLOS Genetics: published March 10, 2017 | https://doi.org/10.1371/journal.pgen.1006648

Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans

Kimberly F. McManus, Angela M. Taravella, Brenna M. Henn, Carlos D. Bustamante, Martin Sikora, Omar E. Cornejo

PLOS Genetics: published March 10, 2017 | https://doi.org/10.1371/journal.pgen.1006560

CUZD1 is a critical mediator of the JAK/STAT5 signaling pathway that controls mammary gland development during pregnancy

Janelle Mapes, Quanxi Li, Athilakshmi Kannan, Lavanya Anandan, Mary Laws, John P. Lydon, Indrani C. Bagchi, Milan K. Bagchi

PLOS Genetics: published March 9, 2017 | https://doi.org/10.1371/journal.pgen.1006654

Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization

Xiaoquan Wen, Roger Pique-Regi, Francesca Luca

PLOS Genetics: published March 9, 2017 | https://doi.org/10.1371/journal.pgen.1006646

A new mode of DNA binding distinguishes Capicua from other HMG-box factors and explains its mutation patterns in cancer

Marta Forés, Lucía Simón-Carrasco, Leiore Ajuria, Núria Samper, Sergio González-Crespo, Matthias Drosten, Mariano Barbacid, Gerardo Jiménez

PLOS Genetics: published March 9, 2017 | https://doi.org/10.1371/journal.pgen.1006622

Drosophila TRF2 and TAF9 regulate lipid droplet size and phospholipid fatty acid composition

Wei Fan, Sin Man Lam, Jingxue Xin, Xiao Yang, Zhonghua Liu, Yuan Liu, Yong Wang, Guanghou Shui, Xun Huang

PLOS Genetics: published March 8, 2017 | https://doi.org/10.1371/journal.pgen.1006664

Depletion of Arabidopsis SC35 and SC35-like serine/arginine-rich proteins affects the transcription and splicing of a subset of genes

Qingqing Yan, Xi Xia, Zhenfei Sun, Yuda Fang

PLOS Genetics: published March 8, 2017 | https://doi.org/10.1371/journal.pgen.1006663

A rare IL33 loss-of-function mutation reduces blood eosinophil counts and protects from asthma

Dirk Smith, Hannes Helgason, Patrick Sulem, Unnur Steina Bjornsdottir, Ai Ching Lim, Gardar Sveinbjornsson, Haruki Hasegawa, Michael Brown, Randal R. Ketchem, Monica Gavala, Logan Garrett, Adalbjorg Jonasdottir, Aslaug Jonasdottir, Asgeir Sigurdsson, Olafur T. Magnusson, Gudmundur I. Eyjolfsson, Isleifur Olafsson, Pall Torfi Onundarson, Olof Sigurdardottir, David Gislason, Thorarinn Gislason, Bjorn Runar Ludviksson, Dora Ludviksdottir, H. Marike Boezen, Andrea Heinzmann, Marcus Krueger, Celeste Porsbjerg, Tarunveer S. Ahluwalia, Johannes Waage, Vibeke Backer, Klaus A. Deichmann, Gerard H. Koppelman, Klaus Bønnelykke, Hans Bisgaard, Gisli Masson, Unnur Thorsteinsdottir, Daniel F. Gudbjartsson, James A. Johnston, Ingileif Jonsdottir, Kari Stefansson

PLOS Genetics: published March 8, 2017 | https://doi.org/10.1371/journal.pgen.1006659

DUX4-induced dsRNA and MYC mRNA stabilization activate apoptotic pathways in human cell models of facioscapulohumeral dystrophy

Sean C. Shadle, Jun Wen Zhong, Amy E. Campbell, Melissa L. Conerly, Sujatha Jagannathan, Chao-Jen Wong, Timothy D. Morello, Silvère M. van der Maarel, Stephen J. Tapscott

PLOS Genetics: published March 8, 2017 | https://doi.org/10.1371/journal.pgen.1006658

SRC-2-mediated coactivation of anti-tumorigenic target genes suppresses MYC-induced liver cancer

Shruthy Suresh, Deniz Durakoglugil, Xiaorong Zhou, Bokai Zhu, Sarah A. Comerford, Chao Xing, Xian-Jin Xie, Brian York, Kathryn A. O’Donnell

PLOS Genetics: published March 8, 2017 | https://doi.org/10.1371/journal.pgen.1006650

Inferring fitness landscapes and selection on phenotypic states from single-cell genealogical data

Takashi Nozoe, Edo Kussell, Yuichi Wakamoto

PLOS Genetics: published March 7, 2017 | https://doi.org/10.1371/journal.pgen.1006653

dMyc is required in retinal progenitors to prevent JNK-mediated retinal glial activation

Lígia Tavares, Andreia Correia, Marília A. Santos, João B. Relvas, Paulo S. Pereira

PLOS Genetics: published March 7, 2017 | https://doi.org/10.1371/journal.pgen.1006647

Mutations in mitochondrial DNA causing tubulointerstitial kidney disease

Thomas M. Connor, Simon Hoer, Andrew Mallett, Daniel P. Gale, Aurora Gomez-Duran, Viktor Posse, Robin Antrobus, Pablo Moreno, Marco Sciacovelli, Christian Frezza, Jennifer Duff, Neil S. Sheerin, John A. Sayer, Margaret Ashcroft, Michael S. Wiesener, Gavin Hudson, Claes M. Gustafsson, Patrick F. Chinnery, Patrick H. Maxwell

PLOS Genetics: published March 7, 2017 | https://doi.org/10.1371/journal.pgen.1006620

TDRD6 mediates early steps of spliceosome maturation in primary spermatocytes

Müge Akpınar, Mathias Lesche, Grigorios Fanourgakis, Jun Fu, Konstantinos Anasstasiadis, Andreas Dahl, Rolf Jessberger

PLOS Genetics: published March 6, 2017 | https://doi.org/10.1371/journal.pgen.1006660

Overexpression of the WOX gene STENOFOLIA improves biomass yield and sugar release in transgenic grasses and display altered cytokinin homeostasis

Hui Wang, Lifang Niu, Chunxiang Fu, Yingying Meng, Dajun Sang, Pengcheng Yin, Jinxia Wu, Yuhong Tang, Tiegang Lu, Zeng-Yu Wang, Million Tadege, Hao Lin

PLOS Genetics: published March 6, 2017 | https://doi.org/10.1371/journal.pgen.1006649

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease

J. Kenneth Baillie, Erik Arner, Carsten Daub, Michiel De Hoon, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki, FANTOM Consortium, Geoffrey J. Faulkner, Christine A. Wells, Michael Rehli, Paul Pavli, Kim M. Summers, David A. Hume

PLOS Genetics: published March 6, 2017 | https://doi.org/10.1371/journal.pgen.1006641

Robust stratification of breast cancer subtypes using differential patterns of transcript isoform expression

Thomas P. Stricker, Christopher D. Brown, Chaitanya Bandlamudi, Megan McNerney, Ralf Kittler, Vanessa Montoya, April Peterson, Robert Grossman, Kevin P. White

PLOS Genetics: published March 6, 2017 | https://doi.org/10.1371/journal.pgen.1006589

Analysis of large versus small dogs reveals three genes on the canine X chromosome associated with body weight, muscling and back fat thickness

Jocelyn Plassais, Maud Rimbault, Falina J. Williams, Brian W. Davis, Jeffrey J. Schoenebeck, Elaine A. Ostrander

PLOS Genetics: published March 3, 2017 | https://doi.org/10.1371/journal.pgen.1006661

Excess of genomic defects in a woolly mammoth on Wrangel island

Rebekah L. Rogers, Montgomery Slatkin

PLOS Genetics: published March 2, 2017 | https://doi.org/10.1371/journal.pgen.1006601

Direct Keap1-Nrf2 disruption as a potential therapeutic target for Alzheimer’s disease

Fiona Kerr, Oyinkan Sofola-Adesakin, Dobril K. Ivanov, Jemma Gatliff, Beatriz Gomez Perez-Nievas, Hélène C. Bertrand, Pedro Martinez, Rebecca Callard, Inge Snoeren, Helena M. Cochemé, Jennifer Adcott, Mobina Khericha, Jorge Iván Castillo-Quan, Geoffrey Wells, Wendy Noble, Janet Thornton, Linda Partridge

PLOS Genetics: published March 2, 2017 | https://doi.org/10.1371/journal.pgen.1006593

Cover

Climate adaptation may have driven nostril width differentiation among human populations.

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