Nucleic Acids Research Advance Access originally published online on October 4, 2007
Nucleic Acids Research 2007 35(20):6714-6726; doi:10.1093/nar/gkm707
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Nucleic Acids Research, 2007, Vol. 35, No. 20 6714-6726
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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The small RNA repertoire of Dictyostelium discoideum and its regulation by components of the RNAi pathway
1Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, Box 590, SE-75124 Uppsala, Sweden, 2Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-75124 Uppsala, Sweden, 3Department of Genetics, Kassel University, Heinrich Plett Strasse 40, 34132 Kassel, Germany and 4Department of Genetics, Dartmouth Medical School, Hanover, NH 03755, USA
*To whom correspondence should be addressed. Tel: +46 18 471 4901; Fax: +46 18 536971; Email: fredde{at}xray.bmc.uu.se
Received July 15, 2007. Revised August 23, 2007. Accepted August 24, 2007.
Small RNAs play crucial roles in regulation of gene expression in many eukaryotes. Here, we report the cloning and characterization of 18–26 nt RNAs in the social amoeba Dictyostelium discoideum. This survey uncovered developmentally regulated microRNA candidates whose biogenesis, at least in one case, is dependent on a Dicer homolog, DrnB. Furthermore, we identified a large number of 21 nt RNAs originating from the DIRS-1 retrotransposon, clusters of which have been suggested to constitute centromeres. Small RNAs from another retrotransposon, Skipper, were significantly up-regulated in strains depleted of the second Dicer-like protein, DrnA, and a putative RNA-dependent RNA polymerase, RrpC. In contrast, the expression of DIRS-1 small RNAs was not altered in any of the analyzed strains. This suggests the presence of multiple RNAi pathways in D. discoideum. In addition, we isolated several small RNAs with antisense complementarity to mRNAs. Three of these mRNAs are developmentally regulated. Interestingly, all three corresponding genes express longer antisense RNAs from which the small RNAs may originate. In at least one case, the longer antisense RNA is complementary to the spliced but not the unspliced pre-mRNA, indicating synthesis by an RNA-dependent RNA polymerase.
Present address: Andrea Hinas, Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Ave, Cambridge, MA 02138, USA.
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