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  • 1.
    Kärblane, Kairi
    et al.
    Tallinn University of Technology, Tallinn, Estonia / Competence Centre for Cancer Research, Tallinn, Estonia .
    Gerassimenko, Jelena
    Tallinn University of Technology, Tallinn, Estonia / Competence Centre for Cancer Research, Tallinn, Estonia .
    Nigul, Lenne
    Tallinn University of Technology, Tallinn, Estonia.
    Piirsoo, Alla
    Tallinn University of Technology, Tallinn, Estonia.
    Smialowska, Agata
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska Institutet.
    Vinkel, Kadri
    Tallinn University of Technology, Tallinn, Estonia .
    Kylsten, Per
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Ekwall, Karl
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska Institutet.
    Swoboda, Peter
    Karolinska Institutet.
    Truve, Erkki
    Tallinn University of Technology, Tallinn, Estonia / Competence Centre for Cancer Research, Tallinn, Estonia .
    Sarmiento, Cecilia
    Tallinn University of Technology, Tallinn, Estonia / Competence Centre for Cancer Research, Tallinn, Estonia .
    ABCE1 Is a Highly Conserved RNA Silencing Suppressor2015In: PLOS ONE, E-ISSN 1932-6203, Vol. 10, no 2, article id e0116702Article in journal (Refereed)
    Abstract [en]

    ATP-binding cassette sub-family E member 1 (ABCE1) is a highly conserved protein among eukaryotes and archaea. Recent studies have identified ABCE1 as a ribosome-recycling factor important for translation termination in mammalian cells, yeast and also archaea. Here we report another conserved function of ABCE1. We have previously described AtRLI2, the homolog of ABCE1 in the plant Arabidopsis thaliana, as an endogenous suppressor of RNA silencing. In this study we show that this function is conserved: human ABCE1 is able to suppress RNA silencing in Nicotiana benthamiana plants, in mammalian HEK293 cells and in the worm Caenorhabditis elegans. Using co-immunoprecipitation and mass spectrometry, we found a number of potential ABCE1-interacting proteins that might support its function as an endogenous suppressor of RNA interference. The interactor candidates are associated with epigenetic regulation, transcription, RNA processing and mRNA surveillance. In addition, one of the identified proteins is translin, which together with its binding partner TRAX supports RNA interference.

  • 2. Rhind, Nicholas
    et al.
    Chen, Zehua
    Yassour, Moran
    Thompson, Dawn A.
    Haas, Brian J.
    Habib, Naomi
    Wapinski, Ilan
    Roy, Sushmita
    Lin, Michael F.
    Heiman, David I.
    Young, Sarah K.
    Furuya, Kanji
    Guo, Yabin
    Pidoux, Alison
    Chen, Huei Mei
    Robbertse, Barbara
    Goldberg, Jonathan M.
    Aoki, Keita
    Bayne, Elizabeth H.
    Berlin, Aaron M.
    Desjardins, Christopher A.
    Dobbs, Edward
    Dukaj, Livio
    Fan, Lin
    FitzGerald, Michael G.
    French, Courtney
    Gujja, Sharvari
    Hansen, Klavs
    Keifenheim, Dan
    Levin, Joshua Z.
    Mosher, Rebecca A.
    Mueller, Carolin A.
    Pfiffner, Jenna
    Priest, Margaret
    Russ, Carsten
    Smialowska, Agata
    Södertörn University, School of Life Sciences, Molecular biology.
    Swoboda, Peter
    Sykes, Sean M.
    Vaughn, Matthew
    Vengrova, Sonya
    Yoder, Ryan
    Zeng, Qiandong
    Allshire, Robin
    Baulcombe, David
    Birren, Bruce W.
    Brown, William
    Ekwall, Karl
    Södertörn University, School of Life Sciences, Molecular biology.
    Kellis, Manolis
    Leatherwood, Janet
    Levin, Henry
    Margalit, Hanah
    Martienssen, Rob
    Nieduszynski, Conrad A.
    Spatafora, Joseph W.
    Friedman, Nir
    Dalgaard, Jacob Z.
    Baumann, Peter
    Niki, Hironori
    Regev, Aviv
    Nusbaum, Chad
    Comparative Functional Genomics of the Fission Yeasts2011In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 332, no 6032, p. 930-936Article in journal (Refereed)
    Abstract [en]

    The fission yeast clade-comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S. japonicus-occupies the basal branch of Ascomycete fungi and is an important model of eukaryote biology. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres. Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, which suggests a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response. Differences in gene content and regulation also explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade.

  • 3.
    Smialowska, Agata
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Karolinska instiutet.
    Djupedal, Ingela
    Karolinska instiutet.
    Wang, Jingwen
    Karolinska instiutet.
    Kylsten, Per
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Swoboda, Peter
    Karolinska instiutet.
    Ekwall, Karl
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Karolinska instiutet.
    RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe2014In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 444, no 2, p. 254-259Article in journal (Other academic)
    Abstract [en]

    RNA interference (RNAi) is a gene silencing mechanism conserved from fungi to mammals. Small interfering RNAs are products and mediators of the RNAi pathway and act as specificity factors in recruiting effector complexes. The Schizosaccharomyces pombe genome encodes one of each of the core RNAi proteins, Dicer, Argonaute and RNA-dependent RNA polymerase (dcr1, ago1, rdp1). Even though the function of RNAi in heterochromatin assembly in S. pombe is established, its role in controlling gene expression is elusive. Here, we report the identification of small RNAs mapped anti-sense to protein coding genes in fission yeast. We demonstrate that these genes are up-regulated at the protein level in RNAi mutants, while their mRNA levels are not significantly changed. We show that the repression by RNAi is not a result of heterochromatin formation. Thus, we conclude that RNAi is involved in post-transcriptional gene silencing in S. pombe.

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