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Genomics & Functional Genomics

  • An evolutionary approach to systematic discovery of novel deubiquitinases, applied to <em>Legionella</em>
    Open Access
    An evolutionary approach to systematic discovery of novel deubiquitinases, applied to Legionella

    Thomas Hermanns, Ilka Woiwode, Ricardo FM Guerreiro, Robert Vogt, Michael Lammers, Kay Hofmann

    Thomas Hermanns ... Kay Hofmann

    Published 27 July 2020

    The analysis of the relationships between different deubiquitinase classes leads to the definition of an aromatic “gatekeeper” motif that distinguishes DUBs from other cysteine proteases and helps to predict new bacterial DUBs.

  • Multiple sclerosis risk variants regulate gene expression in innate and adaptive immune cells
    Open Access
    Multiple sclerosis risk variants regulate gene expression in innate and adaptive immune cells

    Melissa M Gresle, Margaret A Jordan, Jim Stankovich, Tim Spelman, Laura J Johnson, Louise Laverick, Alison Hamlett, Letitia D Smith, Vilija G Jokubaitis, Josephine Baker, Jodi Haartsen, Bruce Taylor, Jac Charlesworth, Melanie Bahlo, Terence P Speed, Matthew A Brown, Judith Field, Alan G Baxter, Helmut Butzkueven

    Melissa M Gresle ... Helmut Butzkueven

    Published 9 June 2020

    This comprehensive study identifies multiple sclerosis risk expression quantitative trait loci in purified immune cell types.

  • MAPK pathway mutations in head and neck cancer affect immune microenvironments and ErbB3 signaling
    Open Access
    MAPK pathway mutations in head and neck cancer affect immune microenvironments and ErbB3 signaling

    Hoi-Lam Ngan, Yuchen Liu, Andrew Yuon Fong, Peony Hiu Yan Poon, Chun Kit Yeung, Sharon Suet Man Chan, Alexandria Lau, Wenying Piao, Hui Li, Jessie Sze Wing Tse, Kwok-Wai Lo, Sze Man Chan, Yu-Xiong Su, Jason Ying Kuen Chan, Chin Wang Lau, Gordon B Mills, Jennifer Rubin Grandis, Vivian Wai Yan Lui

    Hoi-Lam Ngan ... Vivian Wai Yan Lui

    Published 7 May 2020

    MAPK mutations favor HNSCC survival, revealing the broad clinical utility of MAPK pathway mutations in prognosis and potentially in precision immunotherapy.

  • A novel class of polymorphic toxins in Bacteroidetes
    Open Access
    A novel class of polymorphic toxins in Bacteroidetes

    Biswanath Jana, Dor Salomon, Eran Bosis

    Biswanath Jana ... Eran Bosis

    Published 13 March 2020

    Bacteria often use toxins to mediate their interaction with the environment. This study reveals a new class of polymorphic toxins, which contain an N-terminal TANFOR domain, in Bacteroidetes.

  • Splicing of enhancer-associated lincRNAs contributes to enhancer activity
    Open Access
    Splicing of enhancer-associated lincRNAs contributes to enhancer activity

    Jennifer Y Tan, Adriano Biasini, Robert S Young, Ana C Marques

    Jennifer Y Tan ... Ana C Marques

    Published 21 February 2020

    Analysis of enhancer-associated lincRNA transcripts shows their efficient and conserved splicing contributes to cognate enhancer activity and cis-regulation of target gene expression.

  • Oxidised metabolites of the omega-6 fatty acid linoleic acid activate dFOXO
    Open Access
    Oxidised metabolites of the omega-6 fatty acid linoleic acid activate dFOXO

    So Yeon Kwon, Karen Massey, Mark A Watson, Tayab Hussain, Giacomo Volpe, Christopher D Buckley, Anna Nicolaou, Paul Badenhorst

    So Yeon Kwon ... Paul Badenhorst

    Published 28 January 2020

    Oxidised omega-6 fatty acids activate the FOXO transducers of the Insulin signaling pathway potentially linking changes in dietary fatty acid balance and proinflammatory states with insulin resistance.

  • Virus-induced transposable element expression up-regulation in human and mouse host cells
    Open Access
    Virus-induced transposable element expression up-regulation in human and mouse host cells

    Marissa G Macchietto, Ryan A Langlois, Steven S Shen

    Marissa G Macchietto ... Steven S Shen

    Published 21 January 2020

    Genome-wide transposon expression up-regulation in host cells regardless of virus, species, and host cell tissue types occurs early during viral infection and likely contributes to promoting the host innate immune response.

  • TRAP1 chaperone protein mutations and autoinflammation
    Open Access
    TRAP1 chaperone protein mutations and autoinflammation

    Ariane SI Standing, Ying Hong, Coro Paisan-Ruiz, Ebun Omoyinmi, Alan Medlar, Horia Stanescu, Robert Kleta, Dorota Rowcenzio, Philip Hawkins, Helen Lachmann, Michael F McDermott, Despina Eleftheriou, Nigel Klein, Paul A Brogan

    Ariane SI Standing ... Paul A Brogan

    Published 27 December 2019

    This study identifies patients with autoinflammation and mutations affecting the mitochondrial/ER protein chaperone TRAP1, either alone or digenic, with MEFV mutation possibly synergizing to produce severe disease. TRAP1 mutations lead to increased mitochondrial reactive oxygen species and may contribute to autoinflammation.

  • In vivo and in vitro knockout system labelled using fluorescent protein via microhomology-mediated end joining
    Open Access
    In vivo and in vitro knockout system labelled using fluorescent protein via microhomology-mediated end joining

    Shota Katayama, Kota Sato, Toru Nakazawa

    Shota Katayama ... Toru Nakazawa

    Published 24 December 2019

    This study provides a new method that enables the labelling of knockout cells with fluorescent protein through microhomology-mediated end joining (MMEJ)–based knock-in.

  • Metabolome-based prediction of yield heterosis contributes to the breeding of elite rice
    Open Access
    Metabolome-based prediction of yield heterosis contributes to the breeding of elite rice

    Zhiwu Dan, Yunping Chen, Weibo Zhao, Qiong Wang, Wenchao Huang

    Zhiwu Dan ... Wenchao Huang

    Published 13 December 2019

    Metabolite profiles obtained from parental seedlings can predict yield heterosis of rice hybrids with correctly dissected population structure across different growth conditions.

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