Common analysis of direct RNA sequencinG CUrrently leads to misidentification of m 5 C at GCU motifs.

Autor:	Watson KJ; https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA., Bromley RE; https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA., Sparklin BC; https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA., Gasser MT; https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA., Bhattacharya T; https://ror.org/01kg8sb98 Department of Biology, Indiana University, Bloomington, IN, USA., Lebov JF; https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA., Tyson T; https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA., Dai N; https://ror.org/04ywg3445 New England Biolabs, Ipswich, MA, USA., Teigen LE; https://ror.org/05w22af52 Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA., Graf KT; https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA., Foster JM; https://ror.org/04ywg3445 New England Biolabs, Ipswich, MA, USA., Michalski M; https://ror.org/05w22af52 Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA., Bruno VM; https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.; https://ror.org/04rq5mt64 Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA., Lindsey AR; https://ror.org/01kg8sb98 Department of Biology, Indiana University, Bloomington, IN, USA., Corrêa IR Jr; https://ror.org/04ywg3445 New England Biolabs, Ipswich, MA, USA., Hardy RW; https://ror.org/01kg8sb98 Department of Biology, Indiana University, Bloomington, IN, USA., Newton IL; https://ror.org/01kg8sb98 Department of Biology, Indiana University, Bloomington, IN, USA., Dunning Hotopp JC; https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA jdhotopp@som.umaryland.edu.; https://ror.org/04rq5mt64 Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.; https://ror.org/04rq5mt64 Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.
Jazyk:	angličtina
Zdroj:	Life science alliance [Life Sci Alliance] 2023 Nov 29; Vol. 7 (2). Date of Electronic Publication: 2023 Nov 29 (Print Publication: 2024).
DOI:	10.26508/lsa.202302201
Abstrakt:	RNA modifications, such as methylation, can be detected with Oxford Nanopore Technologies direct RNA sequencing. One commonly used tool for detecting 5-methylcytosine (m 5 C) modifications is Tombo, which uses an "Alternative Model" to detect putative modifications from a single sample. We examined direct RNA sequencing data from diverse taxa including viruses, bacteria, fungi, and animals. The algorithm consistently identified a m 5 C at the central position of a GCU motif. However, it also identified a m 5 C in the same motif in fully unmodified in vitro transcribed RNA, suggesting that this is a frequent false prediction. In the absence of further validation, several published predictions of m 5 C in a GCU context should be reconsidered, including those from human coronavirus and human cerebral organoid samples. (© 2023 Watson et al.)
Databáze:	MEDLINE
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