Abstract

The RNA interference machinery has served as a guardian of eukaryotic genomes since the divergence from prokaryotes. Although the basic components have a shared origin, silencing pathways directed by small RNAs have evolved in diverse directions in different eukaryotic lineages. Micro (mi)RNAs regulate protein-coding genes and play vital roles in plants and animals, but less is known about their functions in other organisms. Here, we report, for the first time, deep sequencing of small RNAs from the social amoeba Dictyostelium discoideum. RNA from growing single-cell amoebae as well as from two multicellular developmental stages was sequenced. Computational analyses combined with experimental data reveal the expression of miRNAs, several of them exhibiting distinct expression patterns during development. To our knowledge, this is the first report of miRNAs in the Amoebozoa supergroup. We also show that overexpressed miRNA precursors generate miRNAs and, in most cases, miRNA* sequences, whose biogenesis is dependent on the Dicer-like protein DrnB, further supporting the presence of miRNAs in D. discoideum. In addition, we find miRNAs processed from hairpin structures originating from an intron as well as from a class of repetitive elements. We believe that these repetitive elements are sources for newly evolved miRNAs.

Keywords

microRNA; Dictyostelium discoideum; high-throughput sequencing; small RNA; development

Published in

RNA
2012, Volume: 18, number: 10, pages: 1771-1782
Publisher: COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT

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

Biological Systematics
Genetics


Publication identifier

DOI: https://doi.org/10.1261/rna.033175.112

Permanent link to this page (URI)

https://res.slu.se/id/publ/43079