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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Traces of Post-Transcriptional RNA Modifications in Deep Sequencing Data

Sven Findeiß, David Langenberger, Peter F. Stadler, Steve Hoffmann

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Biol. Chem., Vol. 392 (April 2011)

Abstract


Many aspects of the RNA maturation leave their traces in RNA sequencing data in the form of deviations from the reference genomic DNA. This includes in particular genomically non-encoded nucleotides and chemical modifications. The latter leave their signatures in forms of mismatches and conspicuous patterns of sequencing reads. Modified mapping procedures that focus on particular types of deviations can help to unearth this hidden treasure. Here, we focus on small RNA sequencing data that are produced in large quantities aiming at the analysis of microRNA expression. Starting from the recovery of many well-known modified sites in tRNAs we provide evidence that modified nucleotides are a pervasive phenomenon in these data sets. Regarding non-encoded nucleotides we concentrate on CCA tails, which, surprisingly, can be found in a diverse collection of transcripts, including sub-populations of mature microRNAs. Although small RNA sequencing libraries alone are insufficient to obtain a complete picture, they can inform on many aspects of the complex processes of RNA maturation.

Keywords


High throughout sequencing, RNA editing, tRNAs, microRNAs, CCA enyzme, RNA modification