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MRT-ModSeq – Rapid detection of RNA modifications with MarathonRT
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 detec...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10245971/ https://www.ncbi.nlm.nih.gov/pubmed/37292902 http://dx.doi.org/10.1101/2023.05.25.542276 |
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author | Tavares, Rafael de Cesaris Araujo Mahadeshwar, Gandhar Wan, Han Pyle, Anna Marie |
author_facet | Tavares, Rafael de Cesaris Araujo Mahadeshwar, Gandhar Wan, Han Pyle, Anna Marie |
author_sort | Tavares, Rafael de Cesaris Araujo |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-10245971 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Cold Spring Harbor Laboratory |
record_format | MEDLINE/PubMed |
spelling | pubmed-102459712023-06-08 MRT-ModSeq – Rapid detection of RNA modifications with MarathonRT Tavares, Rafael de Cesaris Araujo Mahadeshwar, Gandhar Wan, Han Pyle, Anna Marie bioRxiv Article 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. Cold Spring Harbor Laboratory 2023-05-25 /pmc/articles/PMC10245971/ /pubmed/37292902 http://dx.doi.org/10.1101/2023.05.25.542276 Text en https://creativecommons.org/licenses/by-nc/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License (https://creativecommons.org/licenses/by-nc/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator. |
spellingShingle | Article Tavares, Rafael de Cesaris Araujo Mahadeshwar, Gandhar Wan, Han Pyle, Anna Marie MRT-ModSeq – Rapid detection of RNA modifications with MarathonRT |
title | MRT-ModSeq – Rapid detection of RNA modifications with MarathonRT |
title_full | MRT-ModSeq – Rapid detection of RNA modifications with MarathonRT |
title_fullStr | MRT-ModSeq – Rapid detection of RNA modifications with MarathonRT |
title_full_unstemmed | MRT-ModSeq – Rapid detection of RNA modifications with MarathonRT |
title_short | MRT-ModSeq – Rapid detection of RNA modifications with MarathonRT |
title_sort | mrt-modseq – rapid detection of rna modifications with marathonrt |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10245971/ https://www.ncbi.nlm.nih.gov/pubmed/37292902 http://dx.doi.org/10.1101/2023.05.25.542276 |
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