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Table of Contents

January 2021

Cephalochordates (amphioxus) are early-branching chordates. Using RNA-seq analysis on separated blastomeres, Lin et al generated a spatial transcriptomic map for the cleavage stage amphioxus embryos and identified clear molecular asymmetries that might control axial patterning or germ line formation. This dataset provides a global transcriptomic blueprint for guiding future functional studies in amphioxus and comparative studies to understand the evolution of developmental mechanisms. See Lin et al.

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Image Credit: Che-Yi Lin and Jr-Kai Yu

Research Articles

Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins

Alexey D. Neverov, Anfisa V. Popova, Gennady G. Fedonin, Evgeny A. Cheremukhin, Galya V. Klink, Georgii A. Bazykin

Polygenic adaptation of rosette growth in Arabidopsis thaliana

Benedict Wieters, Kim A. Steige, Fei He, Evan M. Koch, Sebastián E. Ramos-Onsins, Hongya Gu, Ya-Long Guo, Shamil Sunyaev, Juliette de Meaux

Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and in trans effects on the protein regulatory network

Laura Natalia Balarezo-Cisneros, Steven Parker, Marcin G. Fraczek, Soukaina Timouma, Ping Wang, Raymond T. O’Keefe, Catherine B. Millar, Daniela Delneri

Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans

Shelby J. Priest, Marco A. Coelho, Verónica Mixão, Shelly Applen Clancey, Yitong Xu, Sheng Sun, Toni Gabaldón, Joseph Heitman

Predicting evolutionary change at the DNA level in a natural Mimulus population

Patrick J. Monnahan, Jack Colicchio, Lila Fishman, Stuart J. Macdonald, John K. Kelly

Differential role of cytosolic Hsp70s in longevity assurance and protein quality control

Rebecca Andersson, Anna Maria Eisele-Bürger, Sarah Hanzén, Katarina Vielfort, David Öling, Frederik Eisele, Gustav Johansson, Tobias Gustafsson, Kristian Kvint, Thomas Nyström

Essentiality of c-di-AMP in Bacillus subtilis: Bypassing mutations converge in potassium and glutamate homeostasis

Larissa Krüger, Christina Herzberg, Hermann Rath, Tiago Pedreira, Till Ischebeck, Anja Poehlein, Jan Gundlach, Rolf Daniel, Uwe Völker, Ulrike Mäder, Jörg Stülke

Impaired tumor immune response in metastatic tumors is a selective pressure for neutral evolution in CRC cases

Shotaro Sakimura, Satoshi Nagayama, Mitsuko Fukunaga, Qingjiang Hu, Akihiro Kitagawa, Yuta Kobayashi, Takanori Hasegawa, Miwa Noda, Yuta Kouyama, Dai Shimizu, Tomoko Saito, Atsushi Niida, Yusuke Tsuruda, Hajime Otsu, Yoshihiro Matsumoto, Hiroki Uchida, Takaaki Masuda, Keishi Sugimachi, Shin Sasaki, Kazutaka Yamada, Kazuki Takahashi, Hideki Innan, Yutaka Suzuki, Hiromi Nakamura, Yasushi Totoki, Shinichi Mizuno, Masanobu Ohshima, Tatsuhiro Shibata, Koshi Mimori

Phase-related differences in egg production of the migratory locust regulated by differential oosorption through microRNA-34 targeting activinβ

Lianfeng Zhao, Wei Guo, Feng Jiang, Jing He, Hongran Liu, Juan Song, Dan Yu, Le Kang

Aberrant regulation of a poison exon caused by a non-coding variant in a mouse model of Scn1a-associated epileptic encephalopathy

Yuliya Voskobiynyk, Gopal Battu, Stephanie A. Felker, J. Nicholas Cochran, Megan P. Newton, Laura J. Lambert, Robert A. Kesterson, Richard M. Myers, Gregory M. Cooper, Erik D. Roberson, Gregory S. Barsh

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Runx1 is a central regulator of osteogenesis for bone homeostasis by orchestrating BMP and WNT signaling pathways

Chen-Yi Tang, Mengrui Wu, Dongfeng Zhao, Diep Edwards, Abigail McVicar, Yuan Luo, Guochun Zhu, Yongjun Wang, Hou-De Zhou, Wei Chen, Yi-Ping Li

Human genome diversity data reveal that L564P is the predominant TPC2 variant and a prerequisite for the blond hair associated M484L gain-of-function effect

Julia Böck, Einar Krogsaeter, Marcel Passon, Yu-Kai Chao, Sapna Sharma, Harald Grallert, Annette Peters, Christian Grimm

Estimating FST and kinship for arbitrary population structures

Alejandro Ochoa, John D. Storey

Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus

Xavier Grau-Bové, Eric Lucas, Dimitra Pipini, Emily Rippon, Arjèn E. van ‘t Hof, Edi Constant, Samuel Dadzie, Alexander Egyir-Yawson, John Essandoh, Joseph Chabi, Luc Djogbénou, Nicholas J. Harding, Alistair Miles, Dominic Kwiatkowski, Martin J. Donnelly, David Weetman, The Anopheles gambiae 1000 Genomes Consortium

Dynamic regulation of CTCF stability and sub-nuclear localization in response to stress

Bettina J. Lehman, Fernando J. Lopez-Diaz, Thom P. Santisakultarm, Linjing Fang, Maxim N. Shokhirev, Kenneth E. Diffenderfer, Uri Manor, Beverly M. Emerson

A rare coding mutation in the MAST2 gene causes venous thrombosis in a French family with unexplained thrombophilia: The Breizh MAST2 Arg89Gln variant

Pierre-Emmanuel Morange, Franck Peiretti, Lenaick Gourhant, Carole Proust, Omar Soukarieh, Anne-Sophie Pulcrano-Nicolas, Ganapathi-Varma Saripella, Luca Stefanucci, Romaric Lacroix, Manal Ibrahim-Kosta, Catherine A. Lemarié, Mattia Frontini, Marie-Christine Alessi, David-Alexandre Trégouët, Francis Couturaud

Genome-scale CRISPR screening for modifiers of cellular LDL uptake

Brian T. Emmer, Emily J. Sherman, Paul J. Lascuna, Sarah E. Graham, Cristen J. Willer, David Ginsburg

Htt is a repressor of Abl activity required for APP-induced axonal growth

Claire Marquilly, Germain U. Busto, Brittany S. Leger, Ana Boulanger, Edward Giniger, James A. Walker, Lee G. Fradkin, Jean-Maurice Dura

Natural variation in temperature-modulated immunity uncovers transcription factor bHLH059 as a thermoresponsive regulator in Arabidopsis thaliana

Friederike Bruessow, Jaqueline Bautor, Gesa Hoffmann, Ipek Yildiz, Jürgen Zeier, Jane E. Parker

Temperature regulates synaptic subcellular specificity mediated by inhibitory glutamate signaling

Mengqing Wang, Daniel Witvliet, Mengting Wu, Lijun Kang, Zhiyong Shao

Immune fingerprinting through repertoire similarity

Thomas Dupic, Meriem Bensouda Koraichi, Anastasia A. Minervina, Mikhail V. Pogorelyy, Thierry Mora, Aleksandra M. Walczak

UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin

Natalie Saini, Camille K. Giacobone, Leszek J. Klimczak, Brian N. Papas, Adam B. Burkholder, Jian-Liang Li, David C. Fargo, Re Bai, Kevin Gerrish, Cynthia L. Innes, Shepherd H. Schurman, Dmitry A. Gordenin

Kinetochore-independent mechanisms of sister chromosome separation

Hannah Vicars, Travis Karg, Brandt Warecki, Ian Bast, William Sullivan

Ciona Brachyury proximal and distal enhancers have different FGF dose-response relationships

Matthew J. Harder, Julie Hix, Wendy M. Reeves, Michael T. Veeman

Pleiotropy and epistasis within and between signaling pathways defines the genetic architecture of fungal virulence

Cullen Roth, Debra Murray, Alexandria Scott, Ci Fu, Anna F. Averette, Sheng Sun, Joseph Heitman, Paul M. Magwene

RAFFI: Accurate and fast familial relationship inference in large scale biobank studies using RaPID

Ardalan Naseri, Junjie Shi, Xihong Lin, Shaojie Zhang, Degui Zhi

Natural variations of TFIIAγ gene and LOB1 promoter contribute to citrus canker disease resistance in Atalantia buxifolia

Xiaomei Tang, Xia Wang, Yue Huang, Ling Ma, Xiaolin Jiang, Muhammad Junaid Rao, Yuantao Xu, Ping Yin, Meng Yuan, Xiuxin Deng, Qiang Xu

Regulating the expression of gene drives is key to increasing their invasive potential and the mitigation of resistance

Andrew Hammond, Xenia Karlsson, Ioanna Morianou, Kyros Kyrou, Andrea Beaghton, Matthew Gribble, Nace Kranjc, Roberto Galizi, Austin Burt, Andrea Crisanti, Tony Nolan

Ablation of DNA-methyltransferase 3A in skeletal muscle does not affect energy metabolism or exercise capacity

Lewin Small, Lars R. Ingerslev, Eleonora Manitta, Rhianna C. Laker, Ann N. Hansen, Brendan Deeney, Alain Carrié, Philippe Couvert, Romain Barrès