title: The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals.
abstract: Dictyostelium intermediate repeat sequence 1 (DIRS-1) is the founding member of a poorly characterized class of retrotransposable elements that contain inverse long terminal repeats and tyrosine recombinase instead of DDE-type integrase enzymes. In Dictyostelium discoideum, DIRS-1 forms clusters that adopt the function of centromeres, rendering tight retrotransposition control critical to maintaining chromosome integrity. We report that in deletion strains of the RNA-dependent RNA polymerase RrpC, full-length and shorter DIRS-1 messenger RNAs are strongly enriched. Shorter versions of a hitherto unknown long non-coding RNA in DIRS-1 antisense orientation are also enriched in rrpC- strains. Concurrent with the accumulation of long transcripts, the vast majority of small (21 mer) DIRS-1 RNAs vanish in rrpC- strains. RNASeq reveals an asymmetric distribution of the DIRS-1 small RNAs, both along DIRS-1 and with respect to sense and antisense orientation. We show that RrpC is required for post-transcriptional DIRS-1 silencing and also for spreading of RNA silencing signals. Finally, DIRS-1 mis-regulation in the absence of RrpC leads to retrotransposon mobilization. In summary, our data reveal RrpC as a key player in the silencing of centromeric retrotransposon DIRS-1. RrpC acts at the post-transcriptional level and is involved in spreading of RNA silencing signals, both in the 5' and 3' directions.
authors.affiliation: Ribogenetics@Biochemistry Lab, School of Engineering and Science, Molecular Life Sciences Research Center, Jacobs University Bremen, Campus Ring 1, DE-28759 Bremen, Germany, Abteilung Genetik, Universität Kassel, Heinrich-Plett-Strasse 40, DE-34132 Kassel, Germany, Friedrich-Schiller-Universität Jena, Institut für Pharmazie, Lehrstuhl für Pharmazeutische Biologie, Semmelweisstraße 10, DE-07743 Jena, Germany, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory (SciLifeLab Stockholm), School of Biotechnology, SE-171 65 Solna, Sweden, Garvan Institute of Medical Research, 384 Victoria St Darlinghurst, NSW 2010, Australia, Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, PO Box 596, S-75124 Uppsala, Sweden and Science for Life Laboratory, SE-75124 Uppsala, Sweden.
authors.forename: Stephan
authors.initials: S
authors.lastname: Wiegand
authors.forename: Doreen
authors.initials: D
authors.lastname: Meier
authors.forename: Carsten
authors.initials: C
authors.lastname: Seehafer
authors.forename: Marek
authors.initials: M
authors.lastname: Malicki
authors.forename: Patrick
authors.initials: P
authors.lastname: Hofmann
authors.forename: Anika
authors.initials: A
authors.lastname: Schmith
authors.forename: Thomas
authors.initials: T
authors.lastname: Winckler
authors.forename: Balint
authors.initials: B
authors.lastname: Földesi
authors.forename: Benjamin
authors.initials: B
authors.lastname: Boesler
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Nellen
authors.forename: Johan
authors.initials: J
authors.lastname: Reimegård
authors.forename: Max
authors.initials: M
authors.lastname: Käller
authors.forename: Jimmie
authors.initials: J
authors.lastname: Hällman
authors.forename: Olof
authors.initials: O
authors.lastname: Emanuelsson
authors.forename: Lotta
authors.initials: L
authors.lastname: Avesson
authors.forename: Fredrik
authors.initials: F
authors.lastname: Söderbom
authors.forename: Christian
authors.initials: C
authors.lastname: Hammann
mesh_terms: D002467:Cell Nucleus / Q000235:genetics; D004023:Dictyostelium / Q000201:enzymology / Q000235:genetics*; D016678:Genome; D011401:Promoter Regions, Genetic; D034622:RNA Interference; D016372:RNA, Antisense / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000378:metabolism; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics / Q000502:physiology*; D018626:Retroelements; D020079:Terminal Repeat Sequences
chemical_list: D016372:RNA, Antisense; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D018626:Retroelements; D012324:RNA-Dependent RNA Polymerase