Dicty News Electronic Edition Volume 23, number 7 August 20, 2004 Please submit abstracts of your papers as soon as they have been accepted for publication by sending them to dicty@northwestern.edu or by using the form at http://dictybase.org/db/cgi-bin/dictyBase/abstract_submit. Back issues of Dicty-News, the Dicty Reference database and other useful information is available at dictyBase - http://dictybase.org. ============= Abstracts ============= A database search for double-strand containing RNAs in Dictyostelium discoideum Stefan GrŠf1, Branimira E. Borisova2, Wolfgang Nellen3, Gerhard Steger1, Christian Hammann2 Biological Chemistry, in press 1Institut fŸr Physikalische Biologie, Heinrich-Heine-UniversitŠt, 40225 DŸsseldorf, Germany 2Department of Genetics, AG Molecular Interactions, UniversitŠt Kassel, 34132 Kassel, Germany 3Department of Genetics, UniversitŠt Kassel Corresponding author: Christian Hammann, Department of Genetics, AG Molecular Interactions In eukaryotic cells, double-stranded RNA is degraded to 21mers and triggers RNA interference. Using a pattern description language, we have searched the EMBL database for sequences with the potential to form double strands in cis in Dictyostelium discoideum. No extended inverted repeats were found in mRNAs. However, the antisense direction of some mRNAs encoding regulatory or developmentally regulated proteins, showed the ability to form double stranded regions. In EST archives, we find potential double strands derived from a few genes but these transcripts are not continuously encoded in the genome. Most likely, they represent hybrid molecules of sense and antisense RNAs. Submitted by: Wolfgang Nellen [nellen@uni-kassel.de] ----------------------------------------------------------------------------- Novel non-coding RNAs in Dictyostelium discoideum and their expression during development. Anders Aspegren1,2,4, Andrea Hinas1,2, Pontus Larsson3, Anders Larsson3, and Fredrik Sšderbom1,* 1Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, Box 590, S-75124 Uppsala, Sweden, 3Institute of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, S-75124 Uppsala, Sweden. 4Present address: AstraZeneca, R&D, Department of Molecular Pharmacology, Pepparedsleden 1, S-431 83 Mšlndal, Sweden 2 The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors. Nucleic Acids Research, In Press The last few yearsâ quest for non-coding RNAs (ncRNAs) 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 shot-gun 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 5â and 3â termini that potentially can 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 (snoRNA) candidates (17 box C/D, of which a few are developmentally regulated, and one box H/ACA). Two ncRNAs showed high degree of similarity to the small nuclear U2 RNA and 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. Submitted by: Fredrik Sšderbom