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Research article2011Peer reviewedOpen access

Abundant class of non-coding RNA regulates development in the social amoeba Dictyostelium discoideum

Avesson, Lotta; Schumacher, Heiko; Fetcher, Pierre; Romby, Pascale; Hellman, Ulf; Söderbom, Fredrik

Abstract

Non-coding (nc)RNAs are important players in most biological processes. Although small RNAs such as microRNAs and small interfering RNAs have emerged as exceptionally important regulators of gene expression, great numbers of larger ncRNAs have also been identified. Many of these are abundant and differentially expressed but their functions have in most cases not been elucidated. The social amoeba Dictyostelium discoideum contain the ncRNAs commonly found in eukaryotes. In addition, we previously reported the identification of two novel classes of 42-65 nt long stem-loop forming RNAs, Class I and Class II RNAs, with unknown function. In this study we have further characterized these abundant ncRNAs, which are downregulated during development. We have confirmed expression of 29 Class I RNAs and experimentally verified the formation of the computationally predicted short conserved stem structure. Furthermore, we have for the first time created knockout strains for several small ncRNA genes in D. discoideum and found that deletion of one of the Class I RNAs, DdR-21, results in aberrant development. In addition we have shown that this Class I RNA forms a complex with one or several proteins but do not appear to be associated with ribosomes or polysomes. In a pull down assay, several proteins interacting with DdR-21 were identified, one of these has two RNA recognition motifs (RRMs). The purified RRM containing protein was demonstrated to bind directly and specifically to DdR-21.

Keywords

non coding RNA; RNA-binding protein; regulation; Dictyostelium discoideum; development; gene knockout

Published in

RNA Biology
2011, Volume: 8, number: 6, pages: 1094-1104
Publisher: LANDES BIOSCIENCE

      SLU Authors

    • Avesson, Lotta

      • Department of Molecular Biology, Swedish University of Agricultural Sciences

      • Söderbom, Fredrik

        • Department of Molecular Biology, Swedish University of Agricultural Sciences

      UKÄ Subject classification

      Microbiology

      Publication identifier

      DOI: https://doi.org/10.4161/rna.8.6.17214

      Permanent link to this page (URI)

      https://res.slu.se/id/publ/58545