Engines of change: Transposable element mutation rates are high and variable within Daphnia magna

Eddie K. H. Ho, Emily S. Bellis, Jaclyn Calkins, Jeffrey R. Adrion, Leigh C. Latta IV, Sarah Schaack

PLOS Genetics: published November 1, 2021 | https://doi.org/10.1371/journal.pgen.1009827

FOXR1 regulates stress response pathways and is necessary for proper brain development

Andressa Mota, Hannah K. Waxman, Rui Hong, Gavin D. Lagani, Sheng-Yong Niu, Féodora L. Bertherat, Lynne Wolfe, Christine May Malicdan, Thomas C. Markello, David R. Adams, William A. Gahl, Christine S. Cheng, Uwe Beffert, Angela Ho

PLOS Genetics: published November 1, 2021 | https://doi.org/10.1371/journal.pgen.1009854

Two oppositely-charged sf3b1 mutations cause defective development, impaired immune response, and aberrant selection of intronic branch sites in Drosophila

Bei Zhang, Zhan Ding, Liang Li, Ling-Kun Xie, Yu-Jie Fan, Yong-Zhen Xu

PLOS Genetics: published November 1, 2021 | https://doi.org/10.1371/journal.pgen.1009861

A behavioral screen for mediators of age-dependent TDP-43 neurodegeneration identifies SF2/SRSF1 among a group of potent suppressors in both neurons and glia

Jorge Azpurua, Enas Gad El-Karim, Marvel Tranquille, Josh Dubnau

PLOS Genetics: published November 1, 2021 | https://doi.org/10.1371/journal.pgen.1009882

A nuclear pore sub-complex restricts the propagation of Ty retrotransposons by limiting their transcription

Amandine Bonnet, Carole Chaput, Noé Palmic, Benoit Palancade, Pascale Lesage

PLOS Genetics: published November 1, 2021 | https://doi.org/10.1371/journal.pgen.1009889

Histone deacetylase 1 controls cardiomyocyte proliferation during embryonic heart development and cardiac regeneration in zebrafish

Anja Bühler, Bernd M. Gahr, Deung-Dae Park, Alberto Bertozzi, Alena Boos, Mohankrishna Dalvoy, Alexander Pott, Franz Oswald, Rhett A. Kovall, Bernhard Kühn, Gilbert Weidinger, Wolfgang Rottbauer, Steffen Just

PLOS Genetics: published November 1, 2021 | https://doi.org/10.1371/journal.pgen.1009890

Analysis of growth cone extension in standardized coordinates highlights self-organization rules during wiring of the Drosophila visual system

Weiyue Ji, Lani F. Wu, Steven J. Altschuler

PLOS Genetics: published November 3, 2021 | https://doi.org/10.1371/journal.pgen.1009857

M-DATA: A statistical approach to jointly analyzing de novo mutations for multiple traits

Yuhan Xie, Mo Li, Weilai Dong, Wei Jiang, Hongyu Zhao

PLOS Genetics: published November 4, 2021 | https://doi.org/10.1371/journal.pgen.1009849

Prediction of heterosis in the recent rapeseed (Brassica napus) polyploid by pairing parental nucleotide sequences

Qian Wang, Tao Yan, Zhengbiao Long, Luna Yue Huang, Yang Zhu, Ying Xu, Xiaoyang Chen, Haksong Pak, Jiqiang Li, Dezhi Wu, Yang Xu, Shuijin Hua, Lixi Jiang

PLOS Genetics: published November 4, 2021 | https://doi.org/10.1371/journal.pgen.1009879

Assortative mating and within-spouse pair comparisons

Laurence J. Howe, Thomas Battram, Tim T. Morris, Fernando P. Hartwig, Gibran Hemani, Neil M. Davies, George Davey Smith

PLOS Genetics: published November 4, 2021 | https://doi.org/10.1371/journal.pgen.1009883

Serotonin transporter-mediated molecular axis regulates regional retinal ganglion cell vulnerability and axon regeneration after nerve injury

Rody Kingston, Dwarkesh Amin, Sneha Misra, Jeffrey M. Gross, Takaaki Kuwajima

PLOS Genetics: published November 4, 2021 | https://doi.org/10.1371/journal.pgen.1009885

Mutation rate dynamics reflect ecological change in an emerging zoonotic pathogen

Gemma G. R. Murray, Andrew J. Balmer, Josephine Herbert, Nazreen F. Hadjirin, Caroline L. Kemp, Marta Matuszewska, Sebastian Bruchmann, A. S. Md. Mukarram Hossain, Marcelo Gottschalk, Alexander W. Tucker, Eric Miller, Lucy A. Weinert

PLOS Genetics: published November 8, 2021 | https://doi.org/10.1371/journal.pgen.1009864

The FASTK family proteins fine-tune mitochondrial RNA processing

Akira Ohkubo, Lindsey Van Haute, Danielle L. Rudler, Maike Stentenbach, Florian A. Steiner, Oliver Rackham, Michal Minczuk, Aleksandra Filipovska, Jean-Claude Martinou

PLOS Genetics: published November 8, 2021 | https://doi.org/10.1371/journal.pgen.1009873

Signaling via the FLP-14/FRPR-19 neuropeptide pathway sustains nociceptive response to repeated noxious stimuli in C. elegans

Filipe Marques, Laurent Falquet, Elke Vandewyer, Isabel Beets, Dominique A. Glauser

PLOS Genetics: published November 8, 2021 | https://doi.org/10.1371/journal.pgen.1009880

The effects of introgression across thousands of quantitative traits revealed by gene expression in wild tomatoes

Mark S. Hibbins, Matthew W. Hahn

PLOS Genetics: published November 8, 2021 | https://doi.org/10.1371/journal.pgen.1009892

The ZO-1 protein Polychaetoid as an upstream regulator of the Hippo pathway in Drosophila

Qingliang Sang, Gang Wang, David B. Morton, Hui Wu, Baotong Xie

PLOS Genetics: published November 8, 2021 | https://doi.org/10.1371/journal.pgen.1009894

Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model

Bryan J. Matthews, Tisha Melia, David J. Waxman

PLOS Genetics: published November 9, 2021 | https://doi.org/10.1371/journal.pgen.1009588

The H3.3K27M oncohistone affects replication stress outcome and provokes genomic instability in pediatric glioma

Irena Bočkaj, Tosca E. I. Martini, Eduardo S. de Camargo Magalhães, Petra L. Bakker, Tiny G. J. Meeuwsen-de Boer, Inna Armandari, Saskia L. Meuleman, Marin T. Mondria, Colin Stok, Yannick P. Kok, Bjorn Bakker, René Wardenaar, Jonas Seiler, Mathilde J. C. Broekhuis, Hilda van den Bos, Diana C. J. Spierings, Femke C. A. Ringnalda, Hans Clevers, Ulrich Schüller, Marcel A. T. M. van Vugt, Floris Foijer, Sophia W. M. Bruggeman

PLOS Genetics: published November 9, 2021 | https://doi.org/10.1371/journal.pgen.1009868

Ploidy and recombination proficiency shape the evolutionary adaptation to constitutive DNA replication stress

Marco Fumasoni, Andrew W. Murray

PLOS Genetics: published November 9, 2021 | https://doi.org/10.1371/journal.pgen.1009875

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1. Correction: Ploidy and recombination proficiency shape the evolutionary adaptation to constitutive DNA replication stress

Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle

Mads Bengtsen, Ivan Myhre Winje, Einar Eftestøl, Johannes Landskron, Chengyi Sun, Kamilla Nygård, Diana Domanska, Douglas P. Millay, Leonardo A. Meza-Zepeda, Kristian Gundersen

PLOS Genetics: published November 9, 2021 | https://doi.org/10.1371/journal.pgen.1009907

Mad1’s ability to interact with Mad2 is essential to regulate and monitor meiotic synapsis in C. elegans

Alice Devigne, Needhi Bhalla

PLOS Genetics: published November 11, 2021 | https://doi.org/10.1371/journal.pgen.1009598

Convergent adaptation of Saccharomyces uvarum to sulfite, an antimicrobial preservative widely used in human-driven fermentations

Laura G. Macías, Melisa González Flores, Ana Cristina Adam, María E. Rodríguez, Amparo Querol, Eladio Barrio, Christian Ariel Lopes, Roberto Pérez-Torrado

PLOS Genetics: published November 11, 2021 | https://doi.org/10.1371/journal.pgen.1009872

Positive correlation between transcriptomic stemness and PI3K/AKT/mTOR signaling scores in breast cancer, and a counterintuitive relationship with PIK3CA genotype

Ralitsa R. Madsen, Emily C. Erickson, Oscar M. Rueda, Xavier Robin, Carlos Caldas, Alex Toker, Robert K. Semple, Bart Vanhaesebroeck

PLOS Genetics: published November 11, 2021 | https://doi.org/10.1371/journal.pgen.1009876

Deficiency of ASGR1 in pigs recapitulates reduced risk factor for cardiovascular disease in humans

Baocai Xie, Xiaochen Shi, Yan Li, Bo Xia, Jia Zhou, Minjie Du, Xiangyang Xing, Liang Bai, Enqi Liu, Fernando Alvarez, Long Jin, Shaoping Deng, Grant A. Mitchell, Dengke Pan, Mingzhou Li, Jiangwei Wu

PLOS Genetics: published November 11, 2021 | https://doi.org/10.1371/journal.pgen.1009891

Targeted chromosomal Escherichia coli:dnaB exterior surface residues regulate DNA helicase behavior to maintain genomic stability and organismal fitness

Megan S. Behrmann, Himasha M. Perera, Joy M. Hoang, Trisha A. Venkat, Bryan J. Visser, David Bates, Michael A. Trakselis

PLOS Genetics: published November 12, 2021 | https://doi.org/10.1371/journal.pgen.1009886

Repression of the Hox gene abd-A by ELAV-mediated Transcriptional Interference

Javier J. Castro Alvarez, Maxime Revel, Judit Carrasco, Fabienne Cléard, Daniel Pauli, Valérie Hilgers, François Karch, Robert K. Maeda

PLOS Genetics: published November 15, 2021 | https://doi.org/10.1371/journal.pgen.1009843

daf-16/FOXO blocks adult cell fate in Caenorhabditis elegans dauer larvae via lin-41/TRIM71

Matthew J. Wirick, Allison R. Cale, Isaac T. Smith, Amelia F. Alessi, Margaret R. Starostik, Liberta Cuko, Kyal Lalk, Mikayla N. Schmidt, Benjamin S. Olson, Payton M. Salomon, Alexis Santos, Axel Schmitter-Sánchez, Himani Galagali, Kevin J. Ranke, Payton A. Wolbert, Macy L. Knoblock, John K. Kim, Xantha Karp

PLOS Genetics: published November 15, 2021 | https://doi.org/10.1371/journal.pgen.1009881

JNK and Yorkie drive tumor malignancy by inducing L-amino acid transporter 1 in Drosophila

Bojie Cong, Mai Nakamura, Yukari Sando, Takefumi Kondo, Shizue Ohsawa, Tatsushi Igaki

PLOS Genetics: published November 15, 2021 | https://doi.org/10.1371/journal.pgen.1009893

ATRX proximal protein associations boast roles beyond histone deposition

William A. Scott, Erum Z. Dhanji, Boris J. A. Dyakov, Ema S. Dreseris, Jonathon S. Asa, Laura J. Grange, Mila Mirceta, Christopher E. Pearson, Grant S. Stewart, Anne-Claude Gingras, Eric I. Campos

PLOS Genetics: published November 15, 2021 | https://doi.org/10.1371/journal.pgen.1009909

The genome variation and developmental transcriptome maps reveal genetic differentiation of skeletal muscle in pigs

Yalan Yang, Junyu Yan, Xinhao Fan, Jiaxing Chen, Zishuai Wang, Xiaoqin Liu, Guoqiang Yi, Yuwen Liu, Yongchao Niu, Longchao Zhang, Lixian Wang, ShuaiCheng Li, Kui Li, Zhonglin Tang

PLOS Genetics: published November 15, 2021 | https://doi.org/10.1371/journal.pgen.1009910

Ca²⁺ administration prevents α-synuclein proteotoxicity by stimulating calcineurin-dependent lysosomal proteolysis

Lukas Habernig, Filomena Broeskamp, Andreas Aufschnaiter, Jutta Diessl, Carlotta Peselj, Elisabeth Urbauer, Tobias Eisenberg, Ana de Ory, Sabrina Büttner

PLOS Genetics: published November 15, 2021 | https://doi.org/10.1371/journal.pgen.1009911

A large-scale transgenic RNAi screen identifies transcription factors that modulate myofiber size in Drosophila

Flavia A. Graca, Natalie Sheffield, Melissa Puppa, David Finkelstein, Liam C. Hunt, Fabio Demontis

PLOS Genetics: published November 15, 2021 | https://doi.org/10.1371/journal.pgen.1009926

Salt responsive alternative splicing of a RING finger E3 ligase modulates the salt stress tolerance by fine-tuning the balance of COP9 signalosome subunit 5A

Yuan Zhou, Xiao-Hu Li, Qian-Huan Guo, Peng Liu, Ying Li, Chang-Ai Wu, Guo-Dong Yang, Jin-Guang Huang, Shi-Zhong Zhang, Cheng-Chao Zheng, Kang Yan

PLOS Genetics: published November 16, 2021 | https://doi.org/10.1371/journal.pgen.1009898

Alternative poly-adenylation modulates α1-antitrypsin expression in chronic obstructive pulmonary disease

Lela Lackey, Aaztli Coria, Auyon J. Ghosh, Phil Grayeski, Abigail Hatfield, Vijay Shankar, John Platig, Zhonghui Xu, Silvia B. V. Ramos, Edwin K. Silverman, Victor E. Ortega, Michael H. Cho, Craig P. Hersh, Brian D. Hobbs, Peter Castaldi, Alain Laederach

PLOS Genetics: published November 16, 2021 | https://doi.org/10.1371/journal.pgen.1009912

Abnormal accumulation of lipid droplets in neurons induces the conversion of alpha-Synuclein to proteolytic resistant forms in a Drosophila model of Parkinson’s disease

Victor Girard, Florence Jollivet, Oskar Knittelfelder, Marion Celle, Jean-Noel Arsac, Gilles Chatelain, Daan M. Van den Brink, Thierry Baron, Andrej Shevchenko, Ronald P. Kühnlein, Nathalie Davoust, Bertrand Mollereau

PLOS Genetics: published November 17, 2021 | https://doi.org/10.1371/journal.pgen.1009921

The pleiotropic functions of intracellular hydrophobins in aerial hyphae and fungal spores

Feng Cai, Zheng Zhao, Renwei Gao, Peijie Chen, Mingyue Ding, Siqi Jiang, Zhifei Fu, Pingyong Xu, Komal Chenthamara, Qirong Shen, Günseli Bayram Akcapinar, Irina S. Druzhinina

PLOS Genetics: published November 17, 2021 | https://doi.org/10.1371/journal.pgen.1009924

Nucleoporin TPR promotes tRNA nuclear export and protein synthesis in lung cancer cells

Miao Chen, Qian Long, Melinda S. Borrie, Haohui Sun, Changlin Zhang, Han Yang, Dingbo Shi, Marc R. Gartenberg, Wuguo Deng

PLOS Genetics: published November 18, 2021 | https://doi.org/10.1371/journal.pgen.1009899

EHMT2 suppresses the variation of transcriptional switches in the mouse embryo

Tie-Bo Zeng, Nicholas Pierce, Ji Liao, Purnima Singh, Kin Lau, Wanding Zhou, Piroska E. Szabó

PLOS Genetics: published November 18, 2021 | https://doi.org/10.1371/journal.pgen.1009908

Combining the strengths of inverse-variance weighting and Egger regression in Mendelian randomization using a mixture of regressions model

Zhaotong Lin, Yangqing Deng, Wei Pan

PLOS Genetics: published November 18, 2021 | https://doi.org/10.1371/journal.pgen.1009922

PQN-59 antagonizes microRNA-mediated repression during post-embryonic temporal patterning and modulates translation and stress granule formation in C. elegans

Colleen Carlston, Robin Weinmann, Natalia Stec, Simona Abbatemarco, Francoise Schwager, Jing Wang, Huiwu Ouyang, Collin Y. Ewald, Monica Gotta, Christopher M. Hammell

PLOS Genetics: published November 22, 2021 | https://doi.org/10.1371/journal.pgen.1009599

The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters

Jelly H. M. Soffers, Sergio G-M Alcantara, Xuanying Li, Wanqing Shao, Christopher W. Seidel, Hua Li, Julia Zeitlinger, Susan M. Abmayr, Jerry L. Workman

PLOS Genetics: published November 22, 2021 | https://doi.org/10.1371/journal.pgen.1009668

Cascading epigenomic analysis for identifying disease genes from the regulatory landscape of GWAS variants

Bernard Ng, William Casazza, Nam Hee Kim, Chendi Wang, Farnush Farhadi, Shinya Tasaki, David A. Bennett, Philip L. De Jager, Christopher Gaiteri, Sara Mostafavi

PLOS Genetics: published November 22, 2021 | https://doi.org/10.1371/journal.pgen.1009918

NF-κB modifies the mammalian circadian clock through interaction with the core clock protein BMAL1

Yang Shen, Mehari Endale, Wei Wang, Andrew R. Morris, Lauren J. Francey, Rachel L. Harold, David W. Hammers, Zhiguang Huo, Carrie L. Partch, John B. Hogenesch, Zhao-Hui Wu, Andrew C. Liu

PLOS Genetics: published November 22, 2021 | https://doi.org/10.1371/journal.pgen.1009933

Taming active transposons at Drosophila telomeres: The interconnection between HipHop’s roles in capping and transcriptional silencing

Min Cui, Yaofu Bai, Kaili Li, Yikang S. Rong

PLOS Genetics: published November 23, 2021 | https://doi.org/10.1371/journal.pgen.1009925

rab-27 acts in an intestinal pathway to inhibit axon regeneration in C. elegans

Alexander T. Lin-Moore, Motunrayo J. Oyeyemi, Marc Hammarlund

PLOS Genetics: published November 24, 2021 | https://doi.org/10.1371/journal.pgen.1009877

Co-option of immune effectors by the hormonal signalling system triggering metamorphosis in Drosophila melanogaster

Catarina Nunes, Takashi Koyama, Élio Sucena

PLOS Genetics: published November 29, 2021 | https://doi.org/10.1371/journal.pgen.1009916

Epithelial-specific ERBB3 deletion results in a genetic background-dependent increase in intestinal and colon polyps that is mediated by EGFR

Carolina Mantilla Rojas, Michael P. McGill, Anna C. Salvador, David Bautz, David W. Threadgill

PLOS Genetics: published November 29, 2021 | https://doi.org/10.1371/journal.pgen.1009931

Maternal starvation primes progeny response to nutritional stress

Kelly Voo, Jeralyn Wen Hui Ching, Joseph Wee Hao Lim, Seow Neng Chan, Amanda Yunn Ee Ng, Jasmine Yi Ying Heng, Shiao See Lim, Jun Wei Pek

PLOS Genetics: published November 29, 2021 | https://doi.org/10.1371/journal.pgen.1009932

Dynamic genome plasticity during unisexual reproduction in the human fungal pathogen Cryptococcus deneoformans

Ci Fu, Aaliyah Davy, Simeon Holmes, Sheng Sun, Vikas Yadav, Asiya Gusa, Marco A. Coelho, Joseph Heitman

PLOS Genetics: published November 29, 2021 | https://doi.org/10.1371/journal.pgen.1009935

An optimal growth law for RNA composition and its partial implementation through ribosomal and tRNA gene locations in bacterial genomes

Xiao-Pan Hu, Martin J. Lercher

PLOS Genetics: published November 29, 2021 | https://doi.org/10.1371/journal.pgen.1009939

Motor domain-mediated autoinhibition dictates axonal transport by the kinesin UNC-104/KIF1A

Dezi Cong, Jinqi Ren, Yurong Zhou, Shuang Wang, Jingjing Liang, Mei Ding, Wei Feng

PLOS Genetics: published November 29, 2021 | https://doi.org/10.1371/journal.pgen.1009940

Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance

Manuel Ares-Arroyo, Eduardo P. C. Rocha, Bruno Gonzalez-Zorn

PLOS Genetics: published November 30, 2021 | https://doi.org/10.1371/journal.pgen.1009919

Retraction: 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, the PLOS Genetics Editors

PLOS Genetics: published November 4, 2021 | https://doi.org/10.1371/journal.pgen.1009895

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1. 24-Hour Rhythms of DNA Methylation and Their Relation with Rhythms of RNA Expression in the Human Dorsolateral Prefrontal Cortex

Network-based protein-protein interaction prediction method maps perturbations of cancer interactome

Jiajun Qiu, Kui Chen, Chunlong Zhong, Sihao Zhu, Xiao Ma

PLOS Genetics: published November 2, 2021 | https://doi.org/10.1371/journal.pgen.1009869

High-efficiency CRISPR gene editing in C. elegans using Cas9 integrated into the genome

Matthew L. Schwartz, M. Wayne Davis, Matthew S. Rich, Erik M. Jorgensen

PLOS Genetics: published November 8, 2021 | https://doi.org/10.1371/journal.pgen.1009755