MicroRNAs in Amoebozoa: Deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs
- 1Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, S-75124 Uppsala, Sweden
- 2Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, S-75124 Uppsala, Sweden
- 3Science for Life Laboratory, SE-75124 Uppsala, Sweden
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
Footnotes
-
↵4 The authors wish it to be known that the first two authors should be regarded as joint First Authors.
-
↵8 Corresponding author
E-mail fredde{at}xray.bmc.uu.se
-
Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.033175.112.
- Received March 9, 2012.
- Accepted June 11, 2012.
- Copyright © 2012 RNA Society