August 2018

The image summarizes our study of a neuropeptide receptor that modulates flight behavior in the fruit fly, Drosophila melanogaster. The various hexagons with images depict the depth of our investigation from behavior, to neurons and finally the molecular details. Images from top, running clockwise are: a silhouette of a fly in flight, schematic of the fly head with its brain shown in red, central dopaminergic neurons of the fly brain, PPL1 cluster of dopaminergic neurons, a neuropeptide ligand with its GPCR and a voltage gated-Ca²⁺ channel on the plasma membrane. See Ravi et al.

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Image Credit: Preethi Ravi

Perspective

C. elegans RAB-35: Dual roles in apoptotic cell clearance

Christian E. Rocheleau

PLOS Genetics: published August 23, 2018 | https://doi.org/10.1371/journal.pgen.1007534

Review

The last universal common ancestor between ancient Earth chemistry and the onset of genetics

Madeline C. Weiss, Martina Preiner, Joana C. Xavier, Verena Zimorski, William F. Martin

PLOS Genetics: published August 16, 2018 | https://doi.org/10.1371/journal.pgen.1007518

Research Articles

Investigating the shared genetics of non-syndromic cleft lip/palate and facial morphology

Laurence J. Howe, Myoung Keun Lee, Gemma C. Sharp, George Davey Smith, Beate St Pourcain, John R. Shaffer, Kerstin U. Ludwig, Elisabeth Mangold, Mary L. Marazita, Eleanor Feingold, Alexei Zhurov, Evie Stergiakouli, Jonathan Sandy, Stephen Richmond, Seth M. Weinberg, Gibran Hemani, Sarah J. Lewis

PLOS Genetics: published August 1, 2018 | https://doi.org/10.1371/journal.pgen.1007501

Overlapping open reading frames strongly reduce human and yeast STN1 gene expression and affect telomere function

Victoria Torrance, David Lydall

PLOS Genetics: published August 1, 2018 | https://doi.org/10.1371/journal.pgen.1007523

Progressive ataxia of Charolais cattle highlights a role of KIF1C in sustainable myelination

Amandine Duchesne, Anne Vaiman, Magali Frah, Sandrine Floriot, Sabrina Legoueix-Rodriguez, Anne Desmazières, Sébastien Fritz, Christian Beauvallet, Olivier Albaric, Eric Venot, Maud Bertaud, Romain Saintilan, Raphaël Guatteo, Diane Esquerré, Julien Branchu, Anaïs Fleming, Alexis Brice, Frédéric Darios, Jean-Luc Vilotte, Giovanni Stevanin, Didier Boichard, Khalid Hamid El Hachimi

PLOS Genetics: published August 1, 2018 | https://doi.org/10.1371/journal.pgen.1007550

bric à brac (bab), a central player in the gene regulatory network that mediates thermal plasticity of pigmentation in Drosophila melanogaster

Sandra De Castro, Frédérique Peronnet, Jean-François Gilles, Emmanuèle Mouchel-Vielh, Jean-Michel Gibert

PLOS Genetics: published August 1, 2018 | https://doi.org/10.1371/journal.pgen.1007573

Dynamic expression patterns of Irx3 and Irx5 during germline nest breakdown and primordial follicle formation promote follicle survival in mouse ovaries

Anqi Fu, Sydney M. Oberholtzer, Stefan Bagheri-Fam, Raphael H. Rastetter, Claire Holdreith, Valeria L. Caceres, Steven V. John, Sarah A. Shaw, Kathleen J. Krentz, Xiaoyun Zhang, Chi-chung Hui, Dagmar Wilhelm, Joan S. Jorgensen

PLOS Genetics: published August 2, 2018 | https://doi.org/10.1371/journal.pgen.1007488

Enhanced uptake of potassium or glycine betaine or export of cyclic-di-AMP restores osmoresistance in a high cyclic-di-AMP Lactococcus lactis mutant

Huong Thi Pham, Nguyen Thi Hanh Nhiep, Thu Ngoc Minh Vu, TuAnh Ngoc Huynh, Yan Zhu, Anh Le Diep Huynh, Alolika Chakrabortti, Esteban Marcellin, Raquel Lo, Christopher B. Howard, Nidhi Bansal, Joshua J. Woodward, Zhao-Xun Liang, Mark S. Turner

PLOS Genetics: published August 3, 2018 | https://doi.org/10.1371/journal.pgen.1007574

Mutational analysis of dishevelled genes in zebrafish reveals distinct functions in embryonic patterning and gastrulation cell movements

Yan-Yi Xing, Xiao-Ning Cheng, Yu-Long Li, Chong Zhang, Audrey Saquet, Yuan-Yuan Liu, Ming Shao, De-Li Shi

PLOS Genetics: published August 6, 2018 | https://doi.org/10.1371/journal.pgen.1007551

Multilevel effects of light on ribosome dynamics in chloroplasts program genome-wide and psbA-specific changes in translation

Prakitchai Chotewutmontri, Alice Barkan

PLOS Genetics: published August 6, 2018 | https://doi.org/10.1371/journal.pgen.1007555

Baldspot/ELOVL6 is a conserved modifier of disease and the ER stress response

Rebecca A. S. Palu, Clement Y. Chow

PLOS Genetics: published August 6, 2018 | https://doi.org/10.1371/journal.pgen.1007557

Complexin in ivermectin resistance in body lice

Nadia Amanzougaghene, Florence Fenollar, Claude Nappez, Amira Ben-Amara, Philippe Decloquement, Said Azza, Yassina Bechah, Eric Chabrière, Didier Raoult, Oleg Mediannikov

PLOS Genetics: published August 6, 2018 | https://doi.org/10.1371/journal.pgen.1007569

Drosophila Ca_V2 channels harboring human migraine mutations cause synapse hyperexcitability that can be suppressed by inhibition of a Ca²⁺ store release pathway

Douglas J. Brusich, Ashlyn M. Spring, Thomas D. James, Catherine J. Yeates, Timothy H. Helms, C. Andrew Frank

PLOS Genetics: published August 6, 2018 | https://doi.org/10.1371/journal.pgen.1007577

Cooperation, cis-interactions, versatility and evolutionary plasticity of multiple cis-acting elements underlie krox20 hindbrain regulation

Patrick Torbey, Elodie Thierion, Samuel Collombet, Anne de Cian, Carole Desmarquet-Trin-Dinh, Mathilde Dura, Jean-Paul Concordet, Patrick Charnay, Pascale Gilardi-Hebenstreit

PLOS Genetics: published August 6, 2018 | https://doi.org/10.1371/journal.pgen.1007581

UBTOR/KIAA1024 regulates neurite outgrowth and neoplasia through mTOR signaling

Hefei Zhang, Quan Zhang, Ge Gao, Xinjian Wang, Tiantian Wang, Zhitao Kong, Guoxiang Wang, Cuizhen Zhang, Yun Wang, Gang Peng

PLOS Genetics: published August 6, 2018 | https://doi.org/10.1371/journal.pgen.1007583

The transcription factor Dysfusion promotes fold and joint morphogenesis through regulation of Rho1

Sergio Córdoba, Carlos Estella

PLOS Genetics: published August 6, 2018 | https://doi.org/10.1371/journal.pgen.1007584

Naturally-occurring canine invasive urothelial carcinoma harbors luminal and basal transcriptional subtypes found in human muscle invasive bladder cancer

Deepika Dhawan, Noah M. Hahn, José A. Ramos-Vara, Deborah W. Knapp

PLOS Genetics: published August 8, 2018 | https://doi.org/10.1371/journal.pgen.1007571

Heterochromatin and RNAi regulate centromeres by protecting CENP-A from ubiquitin-mediated degradation

Jinpu Yang, Siyu Sun, Shu Zhang, Marlyn Gonzalez, Qianhua Dong, Zhongxuan Chi, Yu-hang Chen, Fei Li

PLOS Genetics: published August 8, 2018 | https://doi.org/10.1371/journal.pgen.1007572

A ZIP1 separation-of-function allele reveals that centromere pairing drives meiotic segregation of achiasmate chromosomes in budding yeast

Emily L. Kurdzo, Hoa H. Chuong, Jared M. Evatt, Dean S. Dawson

PLOS Genetics: published August 9, 2018 | https://doi.org/10.1371/journal.pgen.1007513

Single-strand annealing between inverted DNA repeats: Pathway choice, participating proteins, and genome destabilizing consequences

Sreejith Ramakrishnan, Zachary Kockler, Robert Evans, Brandon D. Downing, Anna Malkova

PLOS Genetics: published August 9, 2018 | https://doi.org/10.1371/journal.pgen.1007543

Characterizing genetic and environmental influences on variable DNA methylation using monozygotic and dizygotic twins

Eilis Hannon, Olivia Knox, Karen Sugden, Joe Burrage, Chloe C. Y. Wong, Daniel W. Belsky, David L. Corcoran, Louise Arseneault, Terrie E. Moffitt, Avshalom Caspi, Jonathan Mill

PLOS Genetics: published August 9, 2018 | https://doi.org/10.1371/journal.pgen.1007544

Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions

Yan Zhao, Hongliang Zhang, Jianlong Xu, Conghui Jiang, Zhigang Yin, Haiyan Xiong, Jianyin Xie, Xueqiang Wang, Xiaoyang Zhu, Yang Li, Weipeng Zhao, Muhammad Abdul Rehman Rashid, Jinjie Li, Wensheng Wang, Binying Fu, Guoyou Ye, Yan Guo, Zhiqiang Hu, Zhikang Li, Zichao Li

PLOS Genetics: published August 10, 2018 | https://doi.org/10.1371/journal.pgen.1007521

Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression

Rachel Kaletsky, Victoria Yao, April Williams, Alexi M. Runnels, Alicja Tadych, Shiyi Zhou, Olga G. Troyanskaya, Coleen T. Murphy

PLOS Genetics: published August 10, 2018 | https://doi.org/10.1371/journal.pgen.1007559

Genetic architecture of gene expression traits across diverse populations

Lauren S. Mogil, Angela Andaleon, Alexa Badalamenti, Scott P. Dickinson, Xiuqing Guo, Jerome I. Rotter, W. Craig Johnson, Hae Kyung Im, Yongmei Liu, Heather E. Wheeler

PLOS Genetics: published August 10, 2018 | https://doi.org/10.1371/journal.pgen.1007586

Transcription factor ASCL2 is required for development of the glycogen trophoblast cell lineage

Aaron B. Bogutz, Rosemary Oh-McGinnis, Karen J. Jacob, Rita Ho-Lau, Ting Gu, Marina Gertsenstein, Andras Nagy, Louis Lefebvre

PLOS Genetics: published August 10, 2018 | https://doi.org/10.1371/journal.pgen.1007587

Wdr62 is involved in female meiotic initiation via activating JNK signaling and associated with POI in humans

Yang Zhou, Yan Qin, Yingying Qin, Binyang Xu, Ting Guo, Hanni Ke, Min Chen, Lianjun Zhang, Feng Han, Yaqiong Li, Min Chen, Axel Behrens, Yaqing Wang, Zhiheng Xu, Zi-Jiang Chen, Fei Gao

PLOS Genetics: published August 13, 2018 | https://doi.org/10.1371/journal.pgen.1007463

A genome-wide association study identifies a susceptibility locus for biliary atresia on 2p16.1 within the gene EFEMP1

Ying Chen, Melissa A. Gilbert, Christopher M. Grochowski, Deborah McEldrew, Jessica Llewellyn, Orith Waisbourd-Zinman, Hakon Hakonarson, Joan E. Bailey-Wilson, Pierre Russo, Rebecca G. Wells, Kathleen M. Loomes, Nancy B. Spinner, Marcella Devoto

PLOS Genetics: published August 13, 2018 | https://doi.org/10.1371/journal.pgen.1007532

Combinations of DIPs and Dprs control organization of olfactory receptor neuron terminals in Drosophila

Scott Barish, Sarah Nuss, Ilya Strunilin, Suyang Bao, Sayan Mukherjee, Corbin D. Jones, Pelin C. Volkan

PLOS Genetics: published August 13, 2018 | https://doi.org/10.1371/journal.pgen.1007560

Seven-transmembrane receptor protein RgsP and cell wall-binding protein RgsM promote unipolar growth in Rhizobiales

Simon Schäper, Hamish C. L. Yau, Elizaveta Krol, Dorota Skotnicka, Thomas Heimerl, Joe Gray, Volkhard Kaever, Lotte Søgaard-Andersen, Waldemar Vollmer, Anke Becker

PLOS Genetics: published August 13, 2018 | https://doi.org/10.1371/journal.pgen.1007594

The bithorax complex iab-7 Polycomb response element has a novel role in the functioning of the Fab-7 chromatin boundary

Olga Kyrchanova, Amina Kurbidaeva, Marat Sabirov, Nikolay Postika, Daniel Wolle, Tsutomu Aoki, Oksana Maksimenko, Vladic Mogila, Paul Schedl, Pavel Georgiev

PLOS Genetics: published August 15, 2018 | https://doi.org/10.1371/journal.pgen.1007442

FMRFa receptor stimulated Ca²⁺ signals alter the activity of flight modulating central dopaminergic neurons in Drosophila melanogaster

Preethi Ravi, Deepti Trivedi, Gaiti Hasan

PLOS Genetics: published August 15, 2018 | https://doi.org/10.1371/journal.pgen.1007459

The roles of SMYD4 in epigenetic regulation of cardiac development in zebrafish

Deyong Xiao, Huijun Wang, Lili Hao, Xiao Guo, Xiaojing Ma, Yanyan Qian, Hongbo Chen, Jing Ma, Jin Zhang, Wei Sheng, Weinian Shou, Guoying Huang, Duan Ma

PLOS Genetics: published August 15, 2018 | https://doi.org/10.1371/journal.pgen.1007578

Lactosylceramide synthases encoded by B4galt5 and 6 genes are pivotal for neuronal generation and myelin formation in mice

Toru Yoshihara, Hiroyuki Satake, Toshikazu Nishie, Nozomu Okino, Toshihisa Hatta, Hiroki Otani, Chie Naruse, Hiroshi Suzuki, Kazushi Sugihara, Eikichi Kamimura, Noriyo Tokuda, Keiko Furukawa, Koichi Fururkawa, Makoto Ito, Masahide Asano

PLOS Genetics: published August 16, 2018 | https://doi.org/10.1371/journal.pgen.1007545

AAV9-mediated telomerase activation does not accelerate tumorigenesis in the context of oncogenic K-Ras-induced lung cancer

Miguel A. Muñoz-Lorente, Paula Martínez, Águeda Tejera, Kurt Whittemore, Ana Carolina Moisés-Silva, Fàtima Bosch, Maria A. Blasco

PLOS Genetics: published August 16, 2018 | https://doi.org/10.1371/journal.pgen.1007562

The methyltransferase HEN1 is required in Nematostella vectensis for microRNA and piRNA stability as well as larval metamorphosis

Vengamanaidu Modepalli, Arie Fridrich, Maayan Agron, Yehu Moran

PLOS Genetics: published August 17, 2018 | https://doi.org/10.1371/journal.pgen.1007590

E-cadherin bridges cell polarity and spindle orientation to ensure prostate epithelial integrity and prevent carcinogenesis in vivo

Xue Wang, Baijun Dong, Kai Zhang, Zhongzhong Ji, Chaping Cheng, Huifang Zhao, Yaru Sheng, Xiaoxia Li, Liancheng Fan, Wei Xue, Wei-Qiang Gao, Helen He Zhu

PLOS Genetics: published August 17, 2018 | https://doi.org/10.1371/journal.pgen.1007609

A novel gene-diet pair modulates C. elegans aging

Sonia Verma, Urmila Jagtap, Anita Goyala, Arnab Mukhopadhyay

PLOS Genetics: published August 20, 2018 | https://doi.org/10.1371/journal.pgen.1007608

Specification of Drosophila neuropeptidergic neurons by the splicing component brr2

Ignacio Monedero Cobeta, Caroline Bivik Stadler, Jin Li, Peng Yu, Stefan Thor, Jonathan Benito-Sipos

PLOS Genetics: published August 22, 2018 | https://doi.org/10.1371/journal.pgen.1007496

The small GTPase RAB-35 defines a third pathway that is required for the recognition and degradation of apoptotic cells

Ryan Haley, Ying Wang, Zheng Zhou

PLOS Genetics: published August 23, 2018 | https://doi.org/10.1371/journal.pgen.1007558

The thirsty fly: Ion transport peptide (ITP) is a novel endocrine regulator of water homeostasis in Drosophila

Martina Gáliková, Heinrich Dircksen, Dick R. Nässel

PLOS Genetics: published August 23, 2018 | https://doi.org/10.1371/journal.pgen.1007618

cis-regulatory architecture of a short-range EGFR organizing center in the Drosophila melanogaster leg

Susan Newcomb, Roumen Voutev, Aurelie Jory, Rebecca K. Delker, Matthew Slattery, Richard S. Mann

PLOS Genetics: published August 24, 2018 | https://doi.org/10.1371/journal.pgen.1007568

Whi2 is a conserved negative regulator of TORC1 in response to low amino acids

Xianghui Chen, Guiqin Wang, Yu Zhang, Margaret Dayhoff-Brannigan, Nicola L. Diny, Mingjun Zhao, Ge He, Cierra N. Sing, Kyle A. Metz, Zachary D. Stolp, Abdel Aouacheria, Wen-Chih Cheng, J. Marie Hardwick, Xinchen Teng

PLOS Genetics: published August 24, 2018 | https://doi.org/10.1371/journal.pgen.1007592

Identification of expression quantitative trait loci associated with schizophrenia and affective disorders in normal brain tissue

Oneil G. Bhalala, Artika P. Nath, UK Brain Expression Consortium, Michael Inouye, Christopher R. Sibley

PLOS Genetics: published August 24, 2018 | https://doi.org/10.1371/journal.pgen.1007607

The uterine epithelial loss of Pten is inefficient to induce endometrial cancer with intact stromal Pten

Xiaohuan Liang, Takiko Daikoku, Jumpei Terakawa, Yuya Ogawa, Ayesha R. Joshi, Lora H. Ellenson, Xiaofei Sun, Sudhansu K. Dey

PLOS Genetics: published August 24, 2018 | https://doi.org/10.1371/journal.pgen.1007630

The temporal landscape of recursive splicing during Pol II transcription elongation in human cells

Xiao-Ou Zhang, Yu Fu, Haiwei Mou, Wen Xue, Zhiping Weng

PLOS Genetics: published August 27, 2018 | https://doi.org/10.1371/journal.pgen.1007579

Numerous recursive sites contribute to accuracy of splicing in long introns in flies

Athma A. Pai, Joseph M. Paggi, Paul Yan, Karen Adelman, Christopher B. Burge

PLOS Genetics: published August 27, 2018 | https://doi.org/10.1371/journal.pgen.1007588

Tdp1 processes chromate-induced single-strand DNA breaks that collapse replication forks

Abantika Ganguly, Lan Guo, Lingling Sun, Fang Suo, Li-Lin Du, Paul Russell

PLOS Genetics: published August 27, 2018 | https://doi.org/10.1371/journal.pgen.1007595

Homozygous loss-of-function mutations in MNS1 cause laterality defects and likely male infertility

Asaf Ta-Shma, Rim Hjeij, Zeev Perles, Gerard W. Dougherty, Ibrahim Abu Zahira, Stef J. F. Letteboer, Dinu Antony, Alaa Darwish, Dorus A. Mans, Sabrina Spittler, Christine Edelbusch, Sandra Cindrić, Tabea Nöthe-Menchen, Heike Olbrich, Friederike Stuhlmann, Isabella Aprea, Petra Pennekamp, Niki T. Loges, Oded Breuer, Avraham Shaag, Azaria J. J. T. Rein, Elif Yilmaz Gulec, Alper Gezdirici, Revital Abitbul, Nael Elias, Israel Amirav, Miriam Schmidts, Ronald Roepman, Orly Elpeleg, Heymut Omran

PLOS Genetics: published August 27, 2018 | https://doi.org/10.1371/journal.pgen.1007602

Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme

JohnCarlo Kristofich, Andrew B. Morgenthaler, Wallis R. Kinney, Christopher C. Ebmeier, Daniel J. Snyder, William M. Old, Vaughn S. Cooper, Shelley D. Copley

PLOS Genetics: published August 27, 2018 | https://doi.org/10.1371/journal.pgen.1007615

Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosa

Lin Li, Xiaodong Jiao, Ilaria D’Atri, Fumihito Ono, Ralph Nelson, Chi-Chao Chan, Naoki Nakaya, Zhiwei Ma, Yan Ma, Xiaoying Cai, Longhua Zhang, Siying Lin, Abdul Hameed, Barry A. Chioza, Holly Hardy, Gavin Arno, Sarah Hull, Muhammad Imran Khan, James Fasham, Gaurav V. Harlalka, Michel Michaelides, Anthony T. Moore, Zeynep Hande Coban Akdemir, Shalini Jhangiani, James R. Lupski, Frans P. M. Cremers, Raheel Qamar, Ahmed Salman, John Chilton, Jay Self, Radha Ayyagari, Firoz Kabir, Muhammad Asif Naeem, Muhammad Ali, Javed Akram, Paul A. Sieving, Sheikh Riazuddin, Emma L. Baple, S. Amer Riazuddin, Andrew H. Crosby, J. Fielding Hejtmancik

PLOS Genetics: published August 29, 2018 | https://doi.org/10.1371/journal.pgen.1007504

Corrections

Correction: Deletion of Nkx2-5 in trabecular myocardium reveals the developmental origins of pathological heterogeneity associated with ventricular non-compaction cardiomyopathy

Caroline Choquet, Thi Hong Minh Nguyen, Pierre Sicard, Emeline Buttigieg, Thi Thom Tran, Frank Kober, Isabelle Varlet, Rachel Sturny, Mauro W. Costa, Richard P. Harvey, Catherine Nguyen, Pascal Rihet, Sylvain Richard, Monique Bernard, Robert G. Kelly, Nathalie Lalevée, Lucile Miquerol

PLOS Genetics: published August 15, 2018 | https://doi.org/10.1371/journal.pgen.1007610

Correction: FIN219/JAR1 and cryptochrome1 antagonize each other to modulate photomorphogenesis under blue light in Arabidopsis

Huai-Ju Chen, Tsu-Yu Fu, Shao-Li Yang, Hsu-Liang Hsieh

PLOS Genetics: published August 16, 2018 | https://doi.org/10.1371/journal.pgen.1007606

Correction: The TIE1 transcriptional repressor controls shoot branching by directly repressing BRANCHED1 in Arabidopsis

Yan Yang, Michael Nicolas, Jinzhe Zhang, Hao Yu, Dongshu Guo, Rongrong Yuan, Tiantian Zhang, Jianzhao Yang, Pilar Cubas, Genji Qin

PLOS Genetics: published August 24, 2018 | https://doi.org/10.1371/journal.pgen.1007565

Correction: The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation

Khanh Dao Duc, Yun S. Song

PLOS Genetics: published August 24, 2018 | https://doi.org/10.1371/journal.pgen.1007620

Correction: Velvet domain protein VosA represses the zinc cluster transcription factor SclB regulatory network for Aspergillus nidulans asexual development, oxidative stress response and secondary metabolism

Karl G. Thieme, Jennifer Gerke, Christoph Sasse, Oliver Valerius, Sabine Thieme, Razieh Karimi, Antje K. Heinrich, Florian Finkernagel, Kristina Smith, Helge B. Bode, Michael Freitag, Arthur F. J. Ram, Gerhard H. Braus

PLOS Genetics: published August 29, 2018 | https://doi.org/10.1371/journal.pgen.1007638

Cover

Neuropeptidergic modulation of flight in Drosophila

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