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Genomics & Functional Genomics

  • The cation exchanger Letm1, circadian rhythms, and NAD(H) levels interconnect in diurnal zebrafish
    Open Access
    The cation exchanger Letm1, circadian rhythms, and NAD(H) levels interconnect in diurnal zebrafish

    Pauline Dao, Stefan Hajny, Ronald Mekis, Lukas Orel, Nora Dinhopl, Kristin Tessmar-Raible, Karin Nowikovsky

    Pauline Dao ... Karin Nowikovsky

    Published 13 June 2022

    The mitochondrial osmoregulator Letm1 exhibits a diel regulation, impacts on NAD+/H levels, circadian genes, and its study allows new perspectives on possible genetic compensation mechanisms.

  • LncRNA <em>RUS</em> shapes the gene expression program towards neurogenesis
    Open Access
    LncRNA RUS shapes the gene expression program towards neurogenesis

    Marius F Schneider, Veronika Müller, Stephan A Müller, Stefan F Lichtenthaler, Peter B Becker, Johanna C Scheuermann

    Marius F Schneider ... Johanna C Scheuermann

    Published 10 June 2022

    The chromatin-associated lncRNA RUS binds in the vicinity to neural differentiation-associated genes and regulates them in a context-dependent manner to enable proper neuron development.

  • miR-486 is essential for muscle function and suppresses a dystrophic transcriptome
    Open Access
    miR-486 is essential for muscle function and suppresses a dystrophic transcriptome

    Adrienne Samani, Rylie M Hightower, Andrea L Reid, Katherine G English, Michael A Lopez, J Scott Doyle, Michael J Conklin, David A Schneider, Marcas M Bamman, Jeffrey J Widrick, David K Crossman, Min Xie, David Jee, Eric C Lai, Matthew S Alexander

    Adrienne Samani ... Matthew S Alexander

    Published 5 May 2022

    The authors identify miR-486 as essential for normal muscle function and a driver of dystrophic transcriptomic pathways using mir-486 knockout mice and multiple sequencing platforms.

  • Exploring YAP1-centered networks linking dysfunctional CFTR to epithelial–mesenchymal transition
    Open Access
    Exploring YAP1-centered networks linking dysfunctional CFTR to epithelial–mesenchymal transition

    Margarida C Quaresma, Hugo M Botelho, Ines Pankonien, Cláudia S Rodrigues, Madalena C Pinto, Pau R Costa, Aires Duarte, Margarida D Amaral

    Margarida C Quaresma ... Margarida D Amaral

    Published 2 May 2022

    In this work, a systems biology approach identifies potentially dysregulated EMT signaling in CF (including the Hippo, Wnt, TGF-β, p53, and MYC pathways), integrated by YAP1 and TEAD4.

  • The value of genotype-specific reference for transcriptome analyses in barley
    Open Access
    The value of genotype-specific reference for transcriptome analyses in barley

    Wenbin Guo, Max Coulter, Robbie Waugh, Runxuan Zhang

    Wenbin Guo ... Runxuan Zhang

    Published 22 April 2022

    We demonstrate in this study that using a common reference genome may lead to loss of genotype-specific information in the assembled Reference Transcript Dataset (RTD) and the generation of erroneous, incomplete, or misleading transcriptomics analysis results in barley.

  • Phylogenetic profiling resolves early emergence of PRC2 and illuminates its functional core
    Open Access
    Phylogenetic profiling resolves early emergence of PRC2 and illuminates its functional core

    Abdoallah Sharaf, Mallika Vijayanathan, Miroslav Oborník, Iva Mozgová

    Abdoallah Sharaf ... Iva Mozgová

    Published 19 April 2022

    This study strengthens the support for PRC2 emergence before the diversification of eukaryotes, detects a common presence of E(z) and ESC, indicating a conserved core, identifies diverse VEFS-Box Su(z)12 candidate proteins, and proposes a substrate specificity shift during E(z) evolution.

  • Intensive single-cell analysis reveals immune-cell diversity among healthy individuals
    Open Access
    Intensive single-cell analysis reveals immune-cell diversity among healthy individuals

    Yukie Kashima, Keiya Kaneko, Patrick Reteng, Nina Yoshitake, Lucky Ronald Runtuwene, Satoi Nagasawa, Masaya Onishi, Masahide Seki, Ayako Suzuki, Sumio Sugano, Mamiko Sakata-Yanagimoto, Yumiko Imai, Kaori Nakayama-Hosoya, Ai Kawana-Tachikawa, Taketoshi Mizutani, Yutaka Suzuki

    Yukie Kashima ... Yutaka Suzuki

    Published 5 April 2022

    This study describes the diversity of the immune-cell profiling in healthy adults at the single-cell level using RNA-seq, VDJ repertoires, and proteome.

  • Profiles of telomeric repeats in Insecta reveal diverse forms of telomeric motifs in Hymenopterans
    Open Access
    Profiles of telomeric repeats in Insecta reveal diverse forms of telomeric motifs in Hymenopterans

    Yihang Zhou, Yi Wang, Xiao Xiong, Arthur G Appel, Chao Zhang, Xu Wang

    Yihang Zhou ... Xu Wang

    Published 1 April 2022

    A bioinformatic pipeline for telomeric repeat motif detection was applied to 129 insect species and identified diverse forms of telomeric motifs in Hymenopterans, including canonical 5-bp, novel 8- and 9-bp forms, suggesting extraordinary evolutionary fluidity of telomeric repeat in Hymenopterans.

  • DNA methylation–independent long-term epigenetic silencing with dCRISPR/Cas9 fusion proteins
    Open Access
    DNA methylation–independent long-term epigenetic silencing with dCRISPR/Cas9 fusion proteins

    Li Ding, Lukas Theo Schmitt, Melanie Brux, Duran Sürün, Martina Augsburg, Felix Lansing, Jovan Mircetic, Mirko Theis, Frank Buchholz

    Li Ding ... Frank Buchholz

    Published 14 March 2022

    Long-term epigenetic gene silencing can be induced independently of DNA methylation by dCas9-KRABd-MeCP2 fusion proteins.

  • Genome analysis of <em>Legionella pneumophila</em> ST23 from various countries reveals highly similar strains
    Open Access
    Genome analysis of Legionella pneumophila ST23 from various countries reveals highly similar strains

    Maria Luisa Ricci, Silvia Fillo, Andrea Ciammaruconi, Florigio Lista, Christophe Ginevra, Sophie Jarraud, Antonietta Girolamo, Fabrizio Barbanti, Maria Cristina Rota, Diane Lindsay, Jamie Gorzynski, Søren A Uldum, Sharmin Baig, Marina Foti, Giancarlo Petralito, Stefania Torri, Marino Faccini, Maira Bonini, Gabriella Gentili, Sabrina Senatore, Anna Lamberti, Joao André Carrico, Maria Scaturro

    Maria Luisa Ricci ... Maria Scaturro

    Published 2 March 2022

    ST23 isolated in Italy are analysed by cgMLST and SNP approaches and they are also compared with ST23 from other countries. They are found to be phylogenetically related independently on year, town, or country of isolation.

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