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bioRxiv · 10.1101/2023.05.25.542276

MRT-ModSeq - Rapid detection of RNA modifications with MarathonRT

Araujo Tavares, R. d. C.·Mahadeshwar, G.·Wan, H.·Pyle, A. M.
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Abstract

Chemical modifications are essential regulatory elements that modulate the behavior and function of cellular RNAs. Despite recent advances in sequencing-based RNA modification mapping, methods combining accuracy and speed are still lacking. Here, we introduce MRT- ModSeq for rapid, simultaneous detection of multiple RNA modifications using MarathonRT. MRT-ModSeq employs distinct divalent cofactors to generate 2-D mutational profiles that are highly dependent on nucleotide identity and modification type. As a proof of concept, we use the MRT fingerprints of well-studied rRNAs to implement a general workflow for detecting RNA modifications. MRT-ModSeq rapidly detects positions of diverse modifications across a RNA transcript, enabling assignment of m1acp3Y, m1A, m3U, m7G and 2-OMe locations through mutation-rate filtering and machine learning. m1A sites in sparsely modified targets, such as MALAT1 and PRUNE1 could also be detected. MRT-ModSeq can be trained on natural and synthetic transcripts to expedite detection of diverse RNA modification subtypes across targets of interest.

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Araujo Tavares, R. d. C., Mahadeshwar, G., Wan, H., Pyle, A. M.. 2023-05-25. MRT-ModSeq - Rapid detection of RNA modifications with MarathonRT. https://doi.org/10.1101/2023.05.25.542276

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