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DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing

MOTIVATION: The chemical modification of ribonucleotides regulates the structure, stability and interactions of RNAs. Profiling of these modifications using short-read (Illumina) sequencing techniques provides high sensitivity but low-to-medium resolution i.e. modifications cannot be assigned to spe...

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Autores principales: Abebe, Jonathan S, Price, Alexander M, Hayer, Katharina E, Mohr, Ian, Weitzman, Matthew D, Wilson, Angus C, Depledge, Daniel P
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9154255/
https://www.ncbi.nlm.nih.gov/pubmed/35426900
http://dx.doi.org/10.1093/bioinformatics/btac274
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author Abebe, Jonathan S
Price, Alexander M
Hayer, Katharina E
Mohr, Ian
Weitzman, Matthew D
Wilson, Angus C
Depledge, Daniel P
author_facet Abebe, Jonathan S
Price, Alexander M
Hayer, Katharina E
Mohr, Ian
Weitzman, Matthew D
Wilson, Angus C
Depledge, Daniel P
author_sort Abebe, Jonathan S
collection PubMed
description MOTIVATION: The chemical modification of ribonucleotides regulates the structure, stability and interactions of RNAs. Profiling of these modifications using short-read (Illumina) sequencing techniques provides high sensitivity but low-to-medium resolution i.e. modifications cannot be assigned to specific transcript isoforms in regions of sequence overlap. An alternative strategy uses current fluctuations in nanopore-based long read direct RNA sequencing (DRS) to infer the location and identity of nucleotides that differ between two experimental conditions. While highly sensitive, these signal-level analyses require high-quality transcriptome annotations and thus are best suited to the study of model organisms. By contrast, the detection of RNA modifications in microbial organisms which typically have no or low-quality annotations requires an alternative strategy. Here, we demonstrate that signal fluctuations directly influence error rates during base-calling and thus provides an alternative approach for identifying modified nucleotides. RESULTS: DRUMMER (Detection of Ribonucleic acid Modifications Manifested in Error Rates) (i) utilizes a range of statistical tests and background noise correction to identify modified nucleotides with high confidence, (ii) operates with similar sensitivity to signal-level analysis approaches and (iii) correlates very well with orthogonal approaches. Using well-characterized DRS datasets supported by independent meRIP-Seq and miCLIP-Seq datasets we demonstrate that DRUMMER operates with high sensitivity and specificity. AVAILABILITY AND IMPLEMENTATION: DRUMMER is written in Python 3 and is available as open source in the GitHub repository: https://github.com/DepledgeLab/DRUMMER. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-91542552022-06-04 DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing Abebe, Jonathan S Price, Alexander M Hayer, Katharina E Mohr, Ian Weitzman, Matthew D Wilson, Angus C Depledge, Daniel P Bioinformatics Applications Notes MOTIVATION: The chemical modification of ribonucleotides regulates the structure, stability and interactions of RNAs. Profiling of these modifications using short-read (Illumina) sequencing techniques provides high sensitivity but low-to-medium resolution i.e. modifications cannot be assigned to specific transcript isoforms in regions of sequence overlap. An alternative strategy uses current fluctuations in nanopore-based long read direct RNA sequencing (DRS) to infer the location and identity of nucleotides that differ between two experimental conditions. While highly sensitive, these signal-level analyses require high-quality transcriptome annotations and thus are best suited to the study of model organisms. By contrast, the detection of RNA modifications in microbial organisms which typically have no or low-quality annotations requires an alternative strategy. Here, we demonstrate that signal fluctuations directly influence error rates during base-calling and thus provides an alternative approach for identifying modified nucleotides. RESULTS: DRUMMER (Detection of Ribonucleic acid Modifications Manifested in Error Rates) (i) utilizes a range of statistical tests and background noise correction to identify modified nucleotides with high confidence, (ii) operates with similar sensitivity to signal-level analysis approaches and (iii) correlates very well with orthogonal approaches. Using well-characterized DRS datasets supported by independent meRIP-Seq and miCLIP-Seq datasets we demonstrate that DRUMMER operates with high sensitivity and specificity. AVAILABILITY AND IMPLEMENTATION: DRUMMER is written in Python 3 and is available as open source in the GitHub repository: https://github.com/DepledgeLab/DRUMMER. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2022-04-15 /pmc/articles/PMC9154255/ /pubmed/35426900 http://dx.doi.org/10.1093/bioinformatics/btac274 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Abebe, Jonathan S
Price, Alexander M
Hayer, Katharina E
Mohr, Ian
Weitzman, Matthew D
Wilson, Angus C
Depledge, Daniel P
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing
title DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing
title_full DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing
title_fullStr DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing
title_full_unstemmed DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing
title_short DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing
title_sort drummer—rapid detection of rna modifications through comparative nanopore sequencing
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9154255/
https://www.ncbi.nlm.nih.gov/pubmed/35426900
http://dx.doi.org/10.1093/bioinformatics/btac274
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