April 2021

The central bearded dragon (Pogona vitticeps) is an iconic Australian species with temperature induced sex reversal, which causes genetic males to develop as phenotypic females. Because of this trait, female development in this species can occur either under the control of sex chromosomes, or via the influence of incubation temperature. Comparing gene expression patterns between these two female types during embryonic development revealed that two distinct pathways are responsible for driving female development. This showed for the first time the unique transcriptional profile of embryos undergoing sex reversal, providing new insights into the development of this fascinating species. See Whiteley et al.

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Image Credit: Arthur Georges

Viewpoints

Multiplexed assays reveal effects of missense variants in MSH2 and cancer predisposition

Sofie V. Nielsen, Rasmus Hartmann-Petersen, Amelie Stein, Kresten Lindorff-Larsen

PLOS Genetics: published April 22, 2021 | https://doi.org/10.1371/journal.pgen.1009496

Perspective

Putting the brakes on centromere drive in Mimulus

Ching-Ho Chang, Harmit S. Malik

PLOS Genetics: published April 22, 2021 | https://doi.org/10.1371/journal.pgen.1009494

Research Articles

Leveraging expression from multiple tissues using sparse canonical correlation analysis and aggregate tests improves the power of transcriptome-wide association studies

Helian Feng, Nicholas Mancuso, Alexander Gusev, Arunabha Majumdar, Megan Major, Bogdan Pasaniuc, Peter Kraft

PLOS Genetics: published April 8, 2021 | https://doi.org/10.1371/journal.pgen.1008973

Functional assessment of the “two-hit” model for neurodevelopmental defects in Drosophila and X. laevis

Lucilla Pizzo, Micaela Lasser, Tanzeen Yusuff, Matthew Jensen, Phoebe Ingraham, Emily Huber, Mayanglambam Dhruba Singh, Connor Monahan, Janani Iyer, Inshya Desai, Siddharth Karthikeyan, Dagny J. Gould, Sneha Yennawar, Alexis T. Weiner, Vijay Kumar Pounraja, Arjun Krishnan, Melissa M. Rolls, Laura Anne Lowery, Santhosh Girirajan

PLOS Genetics: published April 5, 2021 | https://doi.org/10.1371/journal.pgen.1009112

ARID1A regulates R-loop associated DNA replication stress

Shuhe Tsai, Louis-Alexandre Fournier, Emily Yun-chia Chang, James P. Wells, Sean W. Minaker, Yi Dan Zhu, Alan Ying-Hsu Wang, Yemin Wang, David G. Huntsman, Peter C. Stirling

PLOS Genetics: published April 7, 2021 | https://doi.org/10.1371/journal.pgen.1009238

Analysis of cell-type-specific chromatin modifications and gene expression in Drosophila neurons that direct reproductive behavior

Colleen M. Palmateer, Shawn C. Moseley, Surjyendu Ray, Savannah G. Brovero, Michelle N. Arbeitman

PLOS Genetics: published April 26, 2021 | https://doi.org/10.1371/journal.pgen.1009240

Ubiquitin-protein ligase Ubr5 cooperates with hedgehog signalling to promote skeletal tissue homeostasis

David Mellis, Katherine A. Staines, Silvia Peluso, Ioanna Ch. Georgiou, Natalie Dora, Malgorzata Kubiak, Rob van’t Hof, Michela Grillo, Colin Farquharson, Elaine Kinsella, Anna Thornburn, Stuart H. Ralston, Donald M. Salter, Natalia A. Riobo-Del Galdo, Robert E. Hill, Mark Ditzel

PLOS Genetics: published April 5, 2021 | https://doi.org/10.1371/journal.pgen.1009275

Virus-derived variation in diverse human genomes

Shohei Kojima, Anselmo Jiro Kamada, Nicholas F. Parrish

PLOS Genetics: published April 26, 2021 | https://doi.org/10.1371/journal.pgen.1009324

Aurora kinase A is essential for meiosis in mouse oocytes

Cecilia S. Blengini, Patricia Ibrahimian, Michaela Vaskovicova, David Drutovic, Petr Solc, Karen Schindler

PLOS Genetics: published April 26, 2021 | https://doi.org/10.1371/journal.pgen.1009327

Pathways and signatures of mutagenesis at targeted DNA nicks

Yinbo Zhang, Luther Davis, Nancy Maizels

PLOS Genetics: published April 15, 2021 | https://doi.org/10.1371/journal.pgen.1009329

LuxT controls specific quorum-sensing-regulated behaviors in Vibrionaceae spp. via repression of qrr1, encoding a small regulatory RNA

Michaela J. Eickhoff, Chenyi Fei, Xiuliang Huang, Bonnie L. Bassler

PLOS Genetics: published April 1, 2021 | https://doi.org/10.1371/journal.pgen.1009336

A complex genetic architecture in zebrafish relatives Danio quagga and D. kyathit underlies development of stripes and spots

Braedan M. McCluskey, Susumu Uji, Joseph L. Mancusi, John H. Postlethwait, David M. Parichy

PLOS Genetics: published April 26, 2021 | https://doi.org/10.1371/journal.pgen.1009364

Genetic analysis of the septal peptidoglycan synthase FtsWI complex supports a conserved activation mechanism for SEDS-bPBP complexes

Ying Li, Han Gong, Rui Zhan, Shushan Ouyang, Kyung-Tae Park, Joe Lutkenhaus, Shishen Du

PLOS Genetics: published April 15, 2021 | https://doi.org/10.1371/journal.pgen.1009366

Identification of common predisposing loci to hematopoietic cancers in four dog breeds

Benoît Hédan, Édouard Cadieu, Maud Rimbault, Amaury Vaysse, Caroline Dufaure de Citres, Patrick Devauchelle, Nadine Botherel, Jérôme Abadie, Pascale Quignon, Thomas Derrien, Catherine André

PLOS Genetics: published April 1, 2021 | https://doi.org/10.1371/journal.pgen.1009395

PLD3 is a neuronal lysosomal phospholipase D associated with β-amyloid plaques and cognitive function in Alzheimer’s disease

Alex G. Nackenoff, Timothy J. Hohman, Sarah M. Neuner, Carolyn S. Akers, Nicole C. Weitzel, Alena Shostak, Shawn M. Ferguson, Bret Mobley, David A. Bennett, Julie A. Schneider, Angela L. Jefferson, Catherine C. Kaczorowski, Matthew S. Schrag

PLOS Genetics: published April 8, 2021 | https://doi.org/10.1371/journal.pgen.1009406

Selfish chromosomal drive shapes recent centromeric histone evolution in monkeyflowers

Findley R. Finseth, Thomas C. Nelson, Lila Fishman

PLOS Genetics: published April 22, 2021 | https://doi.org/10.1371/journal.pgen.1009418

Sex-stratified genome-wide association study of multisite chronic pain in UK Biobank

Keira J. A. Johnston, Joey Ward, Pradipta R. Ray, Mark J. Adams, Andrew M. McIntosh, Blair H. Smith, Rona J. Strawbridge, Theodore J. Price, Daniel J. Smith, Barbara I. Nicholl, Mark E. S. Bailey

PLOS Genetics: published April 8, 2021 | https://doi.org/10.1371/journal.pgen.1009428

Toxic Y chromosome: Increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome

Alison H. Nguyen, Doris Bachtrog

PLOS Genetics: published April 22, 2021 | https://doi.org/10.1371/journal.pgen.1009438

ELAV/Hu RNA binding proteins determine multiple programs of neural alternative splicing

Seungjae Lee, Lu Wei, Binglong Zhang, Raeann Goering, Sonali Majumdar, Jiayu Wen, J. Matthew Taliaferro, Eric C. Lai

PLOS Genetics: published April 7, 2021 | https://doi.org/10.1371/journal.pgen.1009439

MRLocus: Identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity

Anqi Zhu, Nana Matoba, Emma P. Wilson, Amanda L. Tapia, Yun Li, Joseph G. Ibrahim, Jason L. Stein, Michael I. Love

PLOS Genetics: published April 19, 2021 | https://doi.org/10.1371/journal.pgen.1009455

Caenorhabditis elegans PTR/PTCHD PTR-18 promotes the clearance of extracellular hedgehog-related protein via endocytosis

Hirohisa Chiyoda, Masahiko Kume, Carla Cadena del Castillo, Kenji Kontani, Anne Spang, Toshiaki Katada, Masamitsu Fukuyama

PLOS Genetics: published April 19, 2021 | https://doi.org/10.1371/journal.pgen.1009457

Tissue specificity-aware TWAS (TSA-TWAS) framework identifies novel associations with metabolic, immunologic, and virologic traits in HIV-positive adults

Binglan Li, Yogasudha Veturi, Anurag Verma, Yuki Bradford, Eric S. Daar, Roy M. Gulick, Sharon A. Riddler, Gregory K. Robbins, Jeffrey L. Lennox, David W. Haas, Marylyn D. Ritchie

PLOS Genetics: published April 26, 2021 | https://doi.org/10.1371/journal.pgen.1009464

Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination

Sarah L. Whiteley, Clare E. Holleley, Susan Wagner, James Blackburn, Ira W. Deveson, Jennifer A. Marshall Graves, Arthur Georges

PLOS Genetics: published April 15, 2021 | https://doi.org/10.1371/journal.pgen.1009465

Extracellular spreading of Wingless is required for Drosophila oogenesis

Xiaoxi Wang, Kimberly S. LaFever, Indrayani Waghmare, Andrea Page-McCaw

PLOS Genetics: published April 2, 2021 | https://doi.org/10.1371/journal.pgen.1009469

Control of pre-replicative complex during the division cycle in Chlamydomonas reinhardtii

Amy E. Ikui, Noriko Ueki, Kresti Pecani, Frederick R. Cross

PLOS Genetics: published April 28, 2021 | https://doi.org/10.1371/journal.pgen.1009471

Quantifying evolutionary importance of protein sites: A Tale of two measures

Avital Sharir-Ivry, Yu Xia

PLOS Genetics: published April 7, 2021 | https://doi.org/10.1371/journal.pgen.1009476

Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease

Alvaro Ingles-Prieto, Nikolas Furthmann, Samuel H. Crossman, Alexandra-Madelaine Tichy, Nina Hoyer, Meike Petersen, Vanessa Zheden, Julia Biebl, Eva Reichhart, Attila Gyoergy, Daria E. Siekhaus, Peter Soba, Konstanze F. Winklhofer, Harald Janovjak

PLOS Genetics: published April 15, 2021 | https://doi.org/10.1371/journal.pgen.1009479

Novel Variance-Component TWAS method for studying complex human diseases with applications to Alzheimer’s dementia

Shizhen Tang, Aron S. Buchman, Philip L. De Jager, David A. Bennett, Michael P. Epstein, Jingjing Yang

PLOS Genetics: published April 2, 2021 | https://doi.org/10.1371/journal.pgen.1009482

A mouse model of Bardet-Biedl Syndrome has impaired fear memory, which is rescued by lithium treatment

Thomas K. Pak, Calvin S. Carter, Qihong Zhang, Sunny C. Huang, Charles Searby, Ying Hsu, Rebecca J. Taugher, Tim Vogel, Christopher C. Cychosz, Rachel Genova, Nina N. Moreira, Hanna Stevens, John A. Wemmie, Andrew A. Pieper, Kai Wang, Val C. Sheffield

PLOS Genetics: published April 22, 2021 | https://doi.org/10.1371/journal.pgen.1009484

Sperm acrosome overgrowth and infertility in mice lacking chromosome 18 pachytene piRNA

Heejin Choi, Zhengpin Wang, Jurrien Dean

PLOS Genetics: published April 8, 2021 | https://doi.org/10.1371/journal.pgen.1009485

Widespread imprinting of transposable elements and variable genes in the maize endosperm

Sarah N. Anderson, Peng Zhou, Kaitlin Higgins, Yaniv Brandvain, Nathan M. Springer

PLOS Genetics: published April 8, 2021 | https://doi.org/10.1371/journal.pgen.1009491

A structural signature motif enlightens the origin and diversification of nuclear receptors

Brice Beinsteiner, Gabriel V. Markov, Stéphane Erb, Yassmine Chebaro, Alastair G. McEwen, Sarah Cianférani, Vincent Laudet, Dino Moras, Isabelle M. L. Billas

PLOS Genetics: published April 21, 2021 | https://doi.org/10.1371/journal.pgen.1009492

The genomics of rapid climatic adaptation and parallel evolution in North American house mice

Kathleen G. Ferris, Andreas S. Chavez, Taichi A. Suzuki, Elizabeth J. Beckman, Megan Phifer-Rixey, Ke Bi, Michael W. Nachman

PLOS Genetics: published April 29, 2021 | https://doi.org/10.1371/journal.pgen.1009495

DNA methylation patterns expose variations in enhancer-chromatin modifications during embryonic stem cell differentiation

Adi Alajem, Hava Roth, Sofia Ratgauzer, Danny Bavli, Alex Motzik, Shlomtzion Lahav, Itay Peled, Oren Ram

PLOS Genetics: published April 12, 2021 | https://doi.org/10.1371/journal.pgen.1009498

Ionotropic Receptor-dependent cool cells control the transition of temperature preference in Drosophila larvae

Jordan J. Tyrrell, Jackson T. Wilbourne, Alisa A. Omelchenko, Jin Yoon, Lina Ni

PLOS Genetics: published April 7, 2021 | https://doi.org/10.1371/journal.pgen.1009499

Opposing roles for Egalitarian and Staufen in transport, anchoring and localization of oskar mRNA in the Drosophila oocyte

Sabine Mohr, Andrew Kenny, Simon T. Y. Lam, Miles B. Morgan, Craig A. Smibert, Howard D. Lipshitz, Paul M. Macdonald

PLOS Genetics: published April 2, 2021 | https://doi.org/10.1371/journal.pgen.1009500

ANGPTL8 protein-truncating variant associated with lower serum triglycerides and risk of coronary disease

Pyry Helkkula, Tuomo Kiiskinen, Aki S. Havulinna, Juha Karjalainen, Seppo Koskinen, Veikko Salomaa, Mark J. Daly, Aarno Palotie, Ida Surakka, Samuli Ripatti, FinnGen

PLOS Genetics: published April 28, 2021 | https://doi.org/10.1371/journal.pgen.1009501

Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology

Kohta Yoshida, Jun Kitano

PLOS Genetics: published April 16, 2021 | https://doi.org/10.1371/journal.pgen.1009502

The canonical α-SNAP is essential for gametophytic development in Arabidopsis

Fei Liu, Ji-Peng Li, Lu-Shen Li, Qi Liu, Shan-Wei Li, Ming-Lei Song, Sha Li, Yan Zhang

PLOS Genetics: published April 22, 2021 | https://doi.org/10.1371/journal.pgen.1009505

Mitogen-activated protein kinase 6 negatively regulates secondary wall biosynthesis by modulating MYB46 protein stability in Arabidopsis thaliana

Jong Hee Im, Jae-Heung Ko, Won-Chan Kim, Brent Crain, Daniel Keathley, Kyung-Hwan Han

PLOS Genetics: published April 7, 2021 | https://doi.org/10.1371/journal.pgen.1009510

The RabGAP TBC-11 controls Argonaute localization for proper microRNA function in C. elegans

Pascale Michaud, Vivek Nilesh Shah, Pauline Adjibade, Francois Houle, Miguel Quévillon Huberdeau, Rachel Rioux, Camille Lavoie-Ouellet, Weifeng Gu, Rachid Mazroui, Martin J. Simard

PLOS Genetics: published April 7, 2021 | https://doi.org/10.1371/journal.pgen.1009511

The actin nucleation factors JMY and WHAMM enable a rapid Arp2/3 complex-mediated intrinsic pathway of apoptosis

Virginia L. King, Nathan K. Leclair, Alyssa M. Coulter, Kenneth G. Campellone

PLOS Genetics: published April 19, 2021 | https://doi.org/10.1371/journal.pgen.1009512

Subunit P60 of phosphatidylinositol 3-kinase promotes cell proliferation or apoptosis depending on its phosphorylation status

Yu-Qin Di, Yu-Meng Zhao, Ke-Yan Jin, Xiao-Fan Zhao

PLOS Genetics: published April 26, 2021 | https://doi.org/10.1371/journal.pgen.1009514

CRISPR gRNA phenotypic screening in zebrafish reveals pro-regenerative genes in spinal cord injury

Marcus Keatinge, Themistoklis M. Tsarouchas, Tahimina Munir, Nicola J. Porter, Juan Larraz, Davide Gianni, Hui-Hsin Tsai, Catherina G. Becker, David A. Lyons, Thomas Becker

PLOS Genetics: published April 29, 2021 | https://doi.org/10.1371/journal.pgen.1009515

Cell volume homeostatically controls the rDNA repeat copy number and rRNA synthesis rate in yeast

José E. Pérez-Ortín, Adriana Mena, Marina Barba-Aliaga, Abhyudai Singh, Sebastián Chávez, José García-Martínez

PLOS Genetics: published April 7, 2021 | https://doi.org/10.1371/journal.pgen.1009520

Dynamic post-transcriptional regulation by Mrn1 links cell wall homeostasis to mitochondrial structure and function

Kendra Reynaud, Molly Brothers, Michael Ly, Nicholas T. Ingolia

PLOS Genetics: published April 15, 2021 | https://doi.org/10.1371/journal.pgen.1009521

Aicardi-Goutières syndrome-associated gene SAMHD1 preserves genome integrity by preventing R-loop formation at transcription–replication conflict regions

Kiwon Park, Jeongmin Ryoo, Heena Jeong, Minsu Kim, Sungwon Lee, Sung-Yeon Hwang, Jiyoung Ahn, Doyeon Kim, Hyungseok C. Moon, Daehyun Baek, Kwangsoo Kim, Hye Yoon Park, Kwangseog Ahn

PLOS Genetics: published April 15, 2021 | https://doi.org/10.1371/journal.pgen.1009523

Trehalose and α-glucan mediate distinct abiotic stress responses in Pseudomonas aeruginosa

Stuart D. Woodcock, Karl Syson, Richard H. Little, Danny Ward, Despoina Sifouna, James K. M. Brown, Stephen Bornemann, Jacob G. Malone

PLOS Genetics: published April 19, 2021 | https://doi.org/10.1371/journal.pgen.1009524

Using genetic variants to evaluate the causal effect of cholesterol lowering on head and neck cancer risk: A Mendelian randomization study

Mark Gormley, James Yarmolinsky, Tom Dudding, Kimberley Burrows, Richard M. Martin, Steven Thomas, Jessica Tyrrell, Paul Brennan, Miranda Pring, Stefania Boccia, Andrew F. Olshan, Brenda Diergaarde, Rayjean J. Hung, Geoffrey Liu, Danny Legge, Eloiza H. Tajara, Patricia Severino, Martin Lacko, Andrew R. Ness, George Davey Smith, Emma E. Vincent, Rebecca C. Richmond

PLOS Genetics: published April 22, 2021 | https://doi.org/10.1371/journal.pgen.1009525

Evolutionary dynamics of the human pseudoautosomal regions

Bruno Monteiro, Miguel Arenas, Maria João Prata, António Amorim

PLOS Genetics: published April 19, 2021 | https://doi.org/10.1371/journal.pgen.1009532

Intercellular viral spread and intracellular transposition of Drosophila gypsy

Richard M. Keegan, Lillian R. Talbot, Yung-Heng Chang, Michael J. Metzger, Josh Dubnau

PLOS Genetics: published April 22, 2021 | https://doi.org/10.1371/journal.pgen.1009535

An insulator blocks access to enhancers by an illegitimate promoter, preventing repression by transcriptional interference

Miki Fujioka, Anastasiya Nezdyur, James B. Jaynes

PLOS Genetics: published April 26, 2021 | https://doi.org/10.1371/journal.pgen.1009536

Coordinating the morphogenesis-differentiation balance by tweaking the cytokinin-gibberellin equilibrium

Alon Israeli, Yogev Burko, Sharona Shleizer-Burko, Iris Daphne Zelnik, Noa Sela, Mohammad R. Hajirezaei, Alisdair R. Fernie, Takayuki Tohge, Naomi Ori, Maya Bar

PLOS Genetics: published April 26, 2021 | https://doi.org/10.1371/journal.pgen.1009537

Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae

Kotchaphorn Mangkalaphiban, Feng He, Robin Ganesan, Chan Wu, Richard Baker, Allan Jacobson

PLOS Genetics: published April 20, 2021 | https://doi.org/10.1371/journal.pgen.1009538

Mapping the degradation pathway of a disease-linked aspartoacylase variant

Sarah K. Gersing, Yong Wang, Martin Grønbæk-Thygesen, Caroline Kampmeyer, Lene Clausen, Martin Willemoës, Claes Andréasson, Amelie Stein, Kresten Lindorff-Larsen, Rasmus Hartmann-Petersen

PLOS Genetics: published April 29, 2021 | https://doi.org/10.1371/journal.pgen.1009539

Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering

Leonor García-Bayona, Michael J. Coyne, Laurie E. Comstock

PLOS Genetics: published April 26, 2021 | https://doi.org/10.1371/journal.pgen.1009541

Genome-wide proximity between RNA polymerase and DNA topoisomerase I supports transcription in Streptococcus pneumoniae

María-José Ferrándiz, Pablo Hernández, Adela G. de la Campa

PLOS Genetics: published April 30, 2021 | https://doi.org/10.1371/journal.pgen.1009542

DNA methylation-mediated modulation of rapid desiccation tolerance acquisition and dehydration stress memory in the resurrection plant Boea hygrometrica

Run-Ze Sun, Jie Liu, Yuan-Yuan Wang, Xin Deng

PLOS Genetics: published April 30, 2021 | https://doi.org/10.1371/journal.pgen.1009549

Corrections

Correction: A missense variant in Mitochondrial Amidoxime Reducing Component 1 gene and protection against liver disease

Connor A. Emdin, Mary E. Haas, Amit V. Khera, Krishna Aragam, Mark Chaffin, Derek Klarin, George Hindy, Lan Jiang, Wei-Qi Wei, Qiping Feng, Juha Karjalainen, Aki Havulinna, Tuomo Kiiskinen, Alexander Bick, Diego Ardissino, James G. Wilson, Heribert Schunkert, Ruth McPherson, Hugh Watkins, Roberto Elosua, Matthew J. Bown, Nilesh J. Samani, Usman Baber, Jeanette Erdmann, Namrata Gupta, John Danesh, Danish Saleheen, Kyong-Mi Chang, Marijana Vujkovic, Ben Voight, Scott Damrauer, Julie Lynch, David Kaplan, Marina Serper, Philip Tsao, Million Veteran Program, Josep Mercader, Craig Hanis, Mark Daly, Joshua Denny, Stacey Gabriel, Sekar Kathiresan

PLOS Genetics: published April 6, 2021 | https://doi.org/10.1371/journal.pgen.1009503

Correction: Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data

Thibaut Paul Patrick Sellinger, Diala Abu Awad, Markus Moest, Aurélien Tellier

PLOS Genetics: published April 7, 2021 | https://doi.org/10.1371/journal.pgen.1009504

Correction: Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma

Sarah A. Gilmore, Mark Voorhies, Dana Gebhart, Anita Sil

PLOS Genetics: published April 7, 2021 | https://doi.org/10.1371/journal.pgen.1009509

Cover

Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination.

Viewpoints

Perspective

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Corrections

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