Publications - Published papers

Please find below publications of our group. Currently, we list 496 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

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Comparison of splice sites reveals that long non-coding RNAs are evolutionarily well conserved

Anne Nitsche, Dominic Rose, Mario Fasold, Kristin Reiche, and Peter F. Stadler

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RNA May 2015 21: 801-812; Published in Advance March 23, 2015

Abstract


Large-scale RNA sequencing has revealed a large number of long mRNA-like transcripts (lncRNAs) that do not code for proteins. The evolutionary history of these lncRNAs has been notoriously hard to study systematically due to their low level of sequence conservation that precludes comprehensive homology-based surveys and makes them nearly impossible to align. Several special cases, however, have been shown to be at least as old as the vertebrate lineage. Here we use the conservation of splice sites to trace the evolution of lncRNAs. We show that more than 50% of the human GENCODE lncRNAs were already present at the divergence of placental mammals and many hundreds of these RNAs are even older. Nevertheless, we observe a fast turnover of intron/exon structures. We conclude that lncRNA genes are evolutionary ancient components of vertebrate genomes that show an unexpected and unprecedented evolutionary plasticity. We offer a public web service (http://splicemap.bioinf.uni-leipzig.de) that allows to retrieve sets of orthologous splice sites and to produce overview maps of evolutionarily conserved splice sites for visualization and further analysis. An electronic supplement containing the ncRNA data sets used in this study is available at http://www.bioinf.uni-leipzig.de/publications/supplements/12-001.

Keywords


long non-coding RNAs, lncRNA, splice sites, multiple sequence alignments, evolution, evolutionary plasticity.