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bioRxiv · 10.1101/501668

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry

Wein, S.·Andrews, B.·Sachsenberg, T.·Santos-Rosa, H.·Kohlbacher, O.·Kouzarides, T.·Garcia, B. A.·Weisser, H.
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Abstract

The field of epitranscriptomics is growing in importance, with chemical modification of RNA being associated with a wide variety of biological phenomena. A pivotal challenge in this area is the identification of modified RNA residues within their sequence contexts. Next-generation sequencing approaches are generally unable to capture modifications, although workarounds for some epigenetic marks exist. Mass spectrometry (MS) offers a comprehensive solution by using analogous approaches to shotgun proteomics. However, software support for the analysis of RNA MS data is inadequate at present and does not allow high-throughput processing. In particular, existing software solutions lack the raw performance and statistical grounding to efficiently handle the large variety of modifications present on RNA. We present a free and open-source database search engine for RNA MS data, called NucleicAcidSearchEngine (NASE), that addresses these shortcomings. We demonstrate the capability of NASE to reliably identify a wide range of modified RNA sequences in three original datasets of varying complexity. In a human tRNA sample, we characterize over 20 different modification types simultaneously and find many cases of incomplete modification.

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Wein, S., Andrews, B., Sachsenberg, T., Santos-Rosa, H., Kohlbacher, O., Kouzarides, T., Garcia, B. A., Weisser, H.. 2018-12-19. A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry. https://doi.org/10.1101/501668

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