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MicroRNAs in Amoebozoa: Deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs
Uppsala University.
2012 (English)In: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 18, no 10, 1771-1782 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2012. Vol. 18, no 10, 1771-1782 p.
Keyword [en]
Development, Dictyostelium discoideum, High-throughput sequencing, MicroRNA, Small RNA
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-131354DOI: 10.1261/rna.033175.112ISI: 000309002700003PubMedID: 22875808Scopus ID: 2-s2.0-84866631065OAI: oai:DiVA.org:kth-131354DiVA: diva2:656509
Funder
Swedish Research CouncilFormas
Note

QC 20131016

Available from: 2013-10-16 Created: 2013-10-14 Last updated: 2017-12-06Bibliographically approved

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