Publications - Published papers
Please find below publications of our group. Currently, we list 565 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 (
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©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.
Traces of Post-Transcriptional RNA Modifications in Deep Sequencing Data
Sven Findeiß, David Langenberger, Peter F. Stadler, Steve Hoffmann
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Status: Published
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