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Table of Contents

October 2019 | Volume 2, No. 5

Research Articles

  • Targeting plasma membrane phosphatidylserine content to inhibit oncogenic KRAS function
    Open Access
    Targeting plasma membrane phosphatidylserine content to inhibit oncogenic KRAS function

    Walaa E Kattan, Wei Chen, Xiaoping Ma, Tien Hung Lan, Dharini van der Hoeven, Ransome van der Hoeven, John F Hancock

    Walaa E Kattan ... John F Hancock

    Published 26 August 2019

    KRAS-dependent cancer cell growth is inhibited by disrupting phosphatidylserine transport to the plasma membrane by genetic knockdown of lipid exchangers ORP5 and ORP8 or by inhibition of PI4KIIIα.

  • Mutagenesis of the ADAM17-phosphatidylserine–binding motif leads to embryonic lethality in mice
    Open Access
    Mutagenesis of the ADAM17-phosphatidylserine–binding motif leads to embryonic lethality in mice

    Martin Veit, Björn Ahrens, Jana Seidel, Anselm Sommer, Sucharit Bhakdi, Karina Reiss

    Martin Veit ... Karina Reiss

    Published 27 August 2019

    Mutation of three cationic amino acids previously identified as an extracellular phosphatidylserine-binding motif abrogates ADAM17 sheddase function and causes early embryonic death in mice.

  • Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptome
    Open Access
    Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptome

    Ugo Szachnowski, Sara Andjus, Dominika Foretek, Antonin Morillon, Maxime Wery

    Ugo Szachnowski ... Maxime Wery

    Published 28 August 2019

    A genome-wide comparative analysis of “cryptic” aslncRNAs decay in RNAi-capable and RNAi-deficient budding yeasts suggests an evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.

  • Structural and functional characterization of the mitochondrial complex IV assembly factor Coa6
    Open Access
    Structural and functional characterization of the mitochondrial complex IV assembly factor Coa6

    Shadi Maghool, N Dinesha G Cooray, David A Stroud, David Aragão, Michael T Ryan, Megan J Maher

    Shadi Maghool ... Megan J Maher

    Published 12 September 2019

    The structures of the mitochondrial complex IV assembly factor Coa6 and a pathogenic mutant variant (W59CCoa6) are reported, providing molecular mechanisms for its mode of action and the loss-of-function mutation.

  • The huntingtin inclusion is a dynamic phase-separated compartment
    Open Access
    The huntingtin inclusion is a dynamic phase-separated compartment

    Fahmida Aktar, Chakkapong Burudpakdee, Mercedes Polanco, Sen Pei, Theresa C Swayne, Peter N Lipke, Lesley Emtage

    Fahmida Aktar ... Lesley Emtage

    Published 16 September 2019

    When expressed in yeast, mutant Htt-GFP forms an inclusion that is mobile, gel-like, and releases material; evidence suggests that it grows through collision and coalescence with small aggregates.

  • Pleiotropic requirements for human TDP-43 in the regulation of cell and organelle homeostasis
    Open Access
    Pleiotropic requirements for human TDP-43 in the regulation of cell and organelle homeostasis

    Agnes Roczniak-Ferguson, Shawn M Ferguson

    Agnes Roczniak-Ferguson ... Shawn M Ferguson

    Published 16 September 2019

    Comprehensive analysis of human TDP-43 knockout cells revealed that TDP-43 regulates hundreds of transcripts and is critical for maintaining the homeostasis of multiple subcellular organelles.

  • Mechanistic insights into the protective roles of polyphosphate against amyloid cytotoxicity
    Open Access
    Mechanistic insights into the protective roles of polyphosphate against amyloid cytotoxicity

    Justine Lempart, Eric Tse, James A Lauer, Magdalena I Ivanova, Alexandra Sutter, Nicholas Yoo, Philipp Huettemann, Daniel Southworth, Ursula Jakob

    Justine Lempart ... Ursula Jakob

    Published 18 September 2019

    This study provides novel insights into the mechanisms by which presence of polyP alters the formation, structural properties, and cytotoxic effects of α-synuclein fibers.

  • Engineering <em>Photorhabdus luminescens</em> toxin complex (PTC) into a recombinant injection nanomachine
    Open Access
    Engineering Photorhabdus luminescens toxin complex (PTC) into a recombinant injection nanomachine

    Peter Njenga Ng´ang´a, Julia K Ebner, Matthias Plessner, Klaus Aktories, Gudula Schmidt

    Peter Njenga Ng´ang´a ... Gudula Schmidt

    Published 20 September 2019

    The article shows successful engineering of the syringe-like injection apparatus of Photorhabdus luminescens as standalone nanomachine for delivery of protein toxins and enzymes from different species into mammalian cells.

  • Glycine cleavage system determines the fate of pluripotent stem cells via the regulation of senescence and epigenetic modifications
    Open Access
    Glycine cleavage system determines the fate of pluripotent stem cells via the regulation of senescence and epigenetic modifications

    Shengya Tian, Junru Feng, Yang Cao, Shengqi Shen, Yongping Cai, Dongdong Yang, Ronghui Yan, Lihua Wang, Huafeng Zhang, Xiuying Zhong, Ping Gao

    Shengya Tian ... Ping Gao

    Published 27 September 2019

    The glycine cleavage system (GCS) is highly activated to promote stem cell pluripotency. The GCS catabolizes glycine to prevent methylglyoxal accumulation and to fuel H3K4me3 modification, promoting the expression of pluripotency genes.

  • Sufficiency analysis of estrogen responsive enhancers using synthetic activators
    Open Access
    Sufficiency analysis of estrogen responsive enhancers using synthetic activators

    Matthew Ginley-Hidinger, Julia B Carleton, Adriana C Rodriguez, Kristofer C Berrett, Jason Gertz

    Matthew Ginley-Hidinger ... Jason Gertz

    Published 30 September 2019

    Enhancers bound by synthetic activators can recreate a transcriptional response to estrogen, drive different levels of gene expression, and work independently to regulate transcription.

  • HELZ directly interacts with CCR4–NOT and causes decay of bound mRNAs
    Open Access
    HELZ directly interacts with CCR4–NOT and causes decay of bound mRNAs

    Aoife Hanet, Felix Räsch, Ramona Weber, Vincenzo Ruscica, Maria Fauser, Tobias Raisch, Duygu Kuzuoğlu-Öztürk, Chung-Te Chang, Dipankar Bhandari, Cátia Igreja, Lara Wohlbold

    Aoife Hanet ... Lara Wohlbold

    Published 30 September 2019

    The putative UPF1-like SF1 helicase HELZ directly interacts with the CCR4–NOT deadenylase complex to induce translational repression and 5′-to-3′ decay of bound mRNAs.

  • Chromatin remodeler Fft3 plays a dual role at blocked DNA replication forks
    Open Access
    Chromatin remodeler Fft3 plays a dual role at blocked DNA replication forks

    Anissia Ait-Saada, Olga Khorosjutina, Jiang Chen, Karol Kramarz, Vladimir Maksimov, J Peter Svensson, Sarah Lambert, Karl Ekwall

    Anissia Ait-Saada ... Karl Ekwall

    Published 1 October 2019

    Fft3, a member of the SNF2 family of ATPase-dependent enzymes, plays a dual role at DNA replication barriers in fission yeast by promoting both DNA resection and restart of blocked DNA replication forks.

  • Endogenous epitope-tagging of <em>Tet1</em>, <em>Tet2</em> and <em>Tet3</em> identifies TET2 as a naïve pluripotency marker
    Open Access
    Endogenous epitope-tagging of Tet1, Tet2 and Tet3 identifies TET2 as a naïve pluripotency marker

    Raphaël Pantier, Tülin Tatar, Douglas Colby, Ian Chambers

    Raphaël Pantier ... Ian Chambers

    Published 3 October 2019

    Expression of TET proteins in pluripotent cell types is visualised by epitope tagging of endogenous alleles.

  • Ligand-induced IFNGR1 down-regulation calibrates myeloid cell IFNγ responsiveness
    Open Access
    Ligand-induced IFNGR1 down-regulation calibrates myeloid cell IFNγ responsiveness

    William J Crisler, Emily M Eshleman, Laurel L Lenz

    William J Crisler ... Laurel L Lenz

    Published 4 October 2019

    IFNγ is shown to silence Ifngr1 transcription by altering enhancer occupancy, reducing myeloid cell IFNGR1 as a feedback mechanism to attenuate macrophage responses associated with inflammation.

  • Enhanced carbonyl stress induces irreversible multimerization of CRMP2 in schizophrenia pathogenesis
    Open Access
    Enhanced carbonyl stress induces irreversible multimerization of CRMP2 in schizophrenia pathogenesis

    Manabu Toyoshima, Xuguang Jiang, Tadayuki Ogawa, Tetsuo Ohnishi, Shogo Yoshihara, Shabeesh Balan, Takeo Yoshikawa, Nobutaka Hirokawa

    Manabu Toyoshima ... Nobutaka Hirokawa

    Published 7 October 2019

    Enhanced carbonyl stress results in neurodevelopmental deficits by affecting microtubule function through the formation of irreversible dysfunctional multimer of carbonylated CRMP2.

  • Oct4 mediates Müller glia reprogramming and cell cycle exit during retina regeneration in zebrafish
    Open Access
    Oct4 mediates Müller glia reprogramming and cell cycle exit during retina regeneration in zebrafish

    Poonam Sharma, Shivangi Gupta, Mansi Chaudhary, Soumitra Mitra, Bindia Chawla, Mohammad Anwar Khursheed, Rajesh Ramachandran

    Poonam Sharma ... Rajesh Ramachandran

    Published 8 October 2019

    The rapid induction of pluripotency-inducing factor Oct4 in the injured retina necessitates the de novo induction of stem cells and their subsequent cell cycle exit.

  • Resolving kinesin stepping: one head at a time
    Open Access
    Resolving kinesin stepping: one head at a time

    Willi L Stepp, Zeynep Ökten

    Willi L Stepp ... Zeynep Ökten

    Published 10 October 2019

    This study shows for the first time a qualitative difference in the stepping of a heterodimeric motor and the asymmetric influence of autoinhibition on the stepping of one of the heads.

  • Unfolded protein-independent IRE1 activation contributes to multifaceted developmental processes in Arabidopsis
    Open Access
    Unfolded protein-independent IRE1 activation contributes to multifaceted developmental processes in Arabidopsis

    Kei-ichiro Mishiba, Yuji Iwata, Tomofumi Mochizuki, Atsushi Matsumura, Nanami Nishioka, Rikako Hirata, Nozomu Koizumi

    Kei-ichiro Mishiba ... Nozomu Koizumi

    Published 10 October 2019

    The Arabidopsis unfolded protein response transducer IRE1 contributes to male gametophyte development using an alternative activation mechanism bypassing the unfolded protein-sensing domain.

  • Drug-induced chromatin accessibility changes associate with sensitivity to liver tumor promotion
    Open Access
    Drug-induced chromatin accessibility changes associate with sensitivity to liver tumor promotion

    Antonio Vitobello, Juliane Perner, Johanna Beil, Jiang Zhu, Alberto Del Río-Espínola, Laurent Morawiec, Magdalena Westphal, Valérie Dubost, Marc Altorfer, Ulrike Naumann, Arne Mueller, Karen Kapur, Mark Borowsky, Colin Henderson, C Roland Wolf, Michael Schwarz, Jonathan Moggs, Rémi Terranova

    Antonio Vitobello ... Rémi Terranova

    Published 15 October 2019

    This work explores quantitative chromatin accessibility, transcriptional and cis-acting gene regulatory variations underlying mouse strain–specific differences in drug-induced liver tumor promotion sensitivity.

  • Nrf2 signaling links ER oxidative protein folding and calcium homeostasis in health and disease
    Open Access
    Nrf2 signaling links ER oxidative protein folding and calcium homeostasis in health and disease

    Veronica Granatiero, Csaba Konrad, Kirsten Bredvik, Giovanni Manfredi, Hibiki Kawamata

    Veronica Granatiero ... Hibiki Kawamata

    Published 28 October 2019

    Oxidative protein folding in the ER generates ROS, leading to Nrf2-dependent feedback on protein folding via ER calcium level modulation. This feedback loop is suppressed in ALS-associated mutant astrocytes but can be rescued by dimethyl fumarate.

Methods

  • Detecting sequence signals in targeting peptides using deep learning
    Open Access
    Detecting sequence signals in targeting peptides using deep learning

    Jose Juan Almagro Armenteros, Marco Salvatore, Olof Emanuelsson, Ole Winther, Gunnar von Heijne, Arne Elofsson, Henrik Nielsen

    Jose Juan Almagro Armenteros ... Henrik Nielsen

    Published 30 September 2019

    During the development of TargetP 2.0, a state-of-the-art method to predict targeting signal, we find a previously overlooked biological signal for subcellular targeting using the output from a deep learning method.

Resource

  • Defining the expression of piRNA and transposable elements in <em>Drosophila</em> ovarian germline stem cells and somatic support cells
    Open Access
    Defining the expression of piRNA and transposable elements in Drosophila ovarian germline stem cells and somatic support cells

    Benjamin Story, Xing Ma, Kazue Ishihara, Hua Li, Kathryn Hall, Allison Peak, Perera Anoja, Jungeun Park, Jeff Haug, Marco Blanchette, Ting Xie

    Benjamin Story ... Ting Xie

    Published 16 October 2019

    Comprehensive transcriptional characterization of mRNA and small RNA in early Drosophila germline stem cells reveals novel piRNA clusters, transposon dynamics, and alternative splicing events.

  • Conservation of cell-intrinsic immune responses in diverse nonhuman primate species
    Open Access
    Conservation of cell-intrinsic immune responses in diverse nonhuman primate species

    Jenna M Gaska, Lance Parsons, Metodi Balev, Ann Cirincione, Wei Wang, Robert E Schwartz, Alexander Ploss

    Jenna M Gaska ... Alexander Ploss

    Published 24 October 2019

    The transcriptomic response of diverse nonhuman primate (NHP) species to poly(I:C) is highly conserved, and this novel RNA sequencing dataset will help improve NHP genome annotations.

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Volume 2, No. 5
October 2019
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