Published online 27 August 2004
Nucleic Acids Research, Vol. 32 No. 15 © Oxford University Press 2004; all rights reserved
Novel non-coding RNAs in Dictyostelium discoideum and their expression during development
Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, Box 590, S-75124 Uppsala, Sweden and 1 Institute of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, S-75124 Uppsala, Sweden
* To whom correspondence should be addressed. Tel: +46 18 471 4901; Fax: +46 18 536971; Email: Fredrik.Soderbom{at}molbio.slu.se
Present address: Anders Aspegren, AstraZeneca, R&D, Department of Molecular Pharmacology, Pepparedsleden 1, S-431 83 Mölndal, Sweden
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
+AJ698945–AJ698946, AJ703792–AJ703794, AJ699367–AJ699397
Received May 26, 2004; Revised and Accepted August 17, 2004
The quest for non-coding RNAs (ncRNAs) in the last few years has revealed a surprisingly large number of small RNAs belonging to previously known as well as entirely novel classes. Computational and experimental approaches have uncovered new ncRNAs in all kingdoms of life. In this work, we used a shotgun cloning approach to construct full-length cDNA libraries of small RNAs from the eukaryotic model organism Dictyostelium discoideum. Interestingly, two entirely novel classes of RNAs were identified of which one is developmentally regulated. The RNAs within each class share conserved 5'- and 3'-termini that can potentially form stem structures. RNAs of both classes show predominantly cytoplasmic localization. In addition, based on conserved structure and/or sequence motifs, several of the identified ncRNAs could be divided into classes known from other organisms, e.g. 18 small nucleolar RNA candidates (17 box C/D, of which a few are developmentally regulated, and one box H/ACA). Two ncRNAs showed a high degree of similarity to the small nuclear U2 RNA and signal recognition particle RNA (SRP RNA), respectively. Furthermore, the majority of the regions upstream of the sequences encoding the isolated RNAs share conserved motifs that may constitute new promoter elements.
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