Novel non-coding RNAs in Dictyostelium discoideum and their expression during development

Aspegren, Anders; Hinas, Andrea; Larsson, Pontus; Larsson, Anders; Söderbom, Fredrik

doi:10.1093/nar/gkh804

Cited by 51 publications

(83 citation statements)

References 53 publications

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“…Northern blots to verify newly discovered miRNA candidates were performed essentially as previously described [83]. Briefly, 20 μg total RNA was separated on 12.5% denaturing polyacrylamide gels and transferred to Hybond N+ nylon membranes (GE Healthcare).…”

Section: Rt-pcrmentioning

confidence: 99%

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

et al. 2018

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Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. The generation of the 3ʹ-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.

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Section: Rt-pcrmentioning

confidence: 99%

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

et al. 2018

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“…Many of the sequences matched annotated loci (Fig. 1B), i.e., complex repeats, noncoding RNAs (ncRNAs) such as rRNA, tRNAs, snRNAs, SRP RNAs, and Class I RNAs (Aspegren et al 2004;Eichinger et al 2005;Hinas et al 2006Larsson et al 2008;Avesson et al 2011;Boesler et al 2011), and protein-coding genes (mRNAs and antisense RNAs, depending on which strand they matched). Reads were also found mapping intergenic regions.…”

Section: Resultsmentioning

confidence: 99%

MicroRNAs in Amoebozoa: Deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs

Avesson

Reimegård

Wagner

et al. 2012

RNA

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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.

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“…Alternatively, the physiology of the Amoebozoa may be more strongly influenced by RNAbased effectors than other eukaryotes. Earlier scans for short noncoding RNAs in D. discoideum identified novel species unreported in other organisms [19]. Perhaps a closer inspection of the nonprotein coding regions of the genome will unearth conserved motifs indicative of strongly conserved RNA-based physiology distinct from other eukaryotes.…”

Section: Discussionmentioning

confidence: 99%

Comparing the Dictyostelium and Entamoeba Genomes Reveals an Ancient Split in the Conosa Lineage

Song¹,

Xu²,

Olsen³

et al. 2005

PLoS Comp Biol

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The Amoebozoa are a sister clade to the fungi and the animals, but are poorly sampled for completely sequenced genomes. The social amoeba Dictyostelium discoideum and amitochondriate pathogen Entamoeba histolytica are the first Amoebozoa with genomes completely sequenced. Both organisms are classified under the Conosa subphylum. To identify Amoebozoa-specific genomic elements, we compared these two genomes to each other and to other eukaryotic genomes. An expanded phylogenetic tree built from the complete predicted proteomes of 23 eukaryotes places the two amoebae in the same lineage, although the divergence is estimated to be greater than that between animals and fungi, and probably happened shortly after the Amoebozoa split from the opisthokont lineage. Most of the 1,500 orthologous gene families shared between the two amoebae are also shared with plant, animal, and fungal genomes. We found that only 42 gene families are distinct to the amoeba lineage; among these are a large number of proteins that contain repeats of the FNIP domain, and a putative transcription factor essential for proper cell type differentiation in D. discoideum. These Amoebozoa-specific genes may be useful in the design of novel diagnostics and therapies for amoebal pathologies.Citation: Song J, Xu Q, Olsen R, Loomis WF, Shaulsky G, et al. (2005) Comparing the Dictyostelium and Entamoeba genomes reveals an ancient split in the conosa lineage. PLoS Comput Biol 1(7): e71.

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Novel non-coding RNAs in Dictyostelium discoideum and their expression during development

Cited by 51 publications

References 53 publications

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

MicroRNAs in Amoebozoa: Deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs

Comparing the Dictyostelium and Entamoeba Genomes Reveals an Ancient Split in the Conosa Lineage

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