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Common analysis of direct RNA sequencinG CUrrently leads to misidentification of m5C at GCU motifs.
Watson, Kaylee J; Bromley, Robin E; Sparklin, Benjamin C; Gasser, Mark T; Bhattacharya, Tamanash; Lebov, Jarrett F; Tyson, Tyonna; Dai, Nan; Teigen, Laura E; Graf, Karen T; Foster, Jeremy M; Michalski, Michelle; Bruno, Vincent M; Lindsey, Amelia Ri; Corrêa, Ivan R; Hardy, Richard W; Newton, Irene Lg; Dunning Hotopp, Julie C.
Afiliación
  • 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.
  • Lindsey AR; https://ror.org/04rq5mt64 Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
  • Corrêa IR; https://ror.org/01kg8sb98 Department of Biology, Indiana University, Bloomington, IN, USA.
  • Hardy RW; https://ror.org/04ywg3445 New England Biolabs, Ipswich, MA, USA.
  • Newton IL; https://ror.org/01kg8sb98 Department of Biology, Indiana University, Bloomington, IN, USA.
  • Dunning Hotopp JC; https://ror.org/01kg8sb98 Department of Biology, Indiana University, Bloomington, IN, USA.
Life Sci Alliance ; 7(2)2024 02.
Article en En | MEDLINE | ID: mdl-38030223
ABSTRACT
RNA modifications, such as methylation, can be detected with Oxford Nanopore Technologies direct RNA sequencing. One commonly used tool for detecting 5-methylcytosine (m5C) 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 m5C at the central position of a GCU motif. However, it also identified a m5C 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 m5C in a GCU context should be reconsidered, including those from human coronavirus and human cerebral organoid samples.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Algoritmos / ARN Límite: Animals / Humans Idioma: En Revista: Life Sci Alliance Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos
Texto completo
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XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Algoritmos / ARN Límite: Animals / Humans Idioma: En Revista: Life Sci Alliance Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos