De novo basecalling of RNA modifications at single molecule and nucleotide resolution
Abstract RNA modifications influence RNA function and fate, but detecting them in individual molecules remains challenging for most modifications. Here we present a novel methodology to generate training sets and build modification-aware basecalling models. Using this approach, we develop the m 6 AB...
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| Format: | Article |
| Language: | English |
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BMC
2025-02-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-025-03498-6 |
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| author | Sonia Cruciani Anna Delgado-Tejedor Leszek P. Pryszcz Rebeca Medina Laia Llovera Eva Maria Novoa |
| author_facet | Sonia Cruciani Anna Delgado-Tejedor Leszek P. Pryszcz Rebeca Medina Laia Llovera Eva Maria Novoa |
| author_sort | Sonia Cruciani |
| collection | DOAJ |
| description | Abstract RNA modifications influence RNA function and fate, but detecting them in individual molecules remains challenging for most modifications. Here we present a novel methodology to generate training sets and build modification-aware basecalling models. Using this approach, we develop the m 6 ABasecaller, a basecalling model that predicts m6A modifications from raw nanopore signals. We validate its accuracy in vitro and in vivo, revealing stable m6A modification stoichiometry across isoforms, m6A co-occurrence within RNA molecules, and m6A-dependent effects on poly(A) tails. Finally, we demonstrate that our method generalizes to other RNA and DNA modifications, paving the path towards future efforts detecting other modifications. |
| format | Article |
| id | doaj-art-9b1daf4e53d046968add11dd4bd87490 |
| institution | DOAJ |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-9b1daf4e53d046968add11dd4bd874902025-08-20T03:04:34ZengBMCGenome Biology1474-760X2025-02-0126113610.1186/s13059-025-03498-6De novo basecalling of RNA modifications at single molecule and nucleotide resolutionSonia Cruciani0Anna Delgado-Tejedor1Leszek P. Pryszcz2Rebeca Medina3Laia Llovera4Eva Maria Novoa5Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyAbstract RNA modifications influence RNA function and fate, but detecting them in individual molecules remains challenging for most modifications. Here we present a novel methodology to generate training sets and build modification-aware basecalling models. Using this approach, we develop the m 6 ABasecaller, a basecalling model that predicts m6A modifications from raw nanopore signals. We validate its accuracy in vitro and in vivo, revealing stable m6A modification stoichiometry across isoforms, m6A co-occurrence within RNA molecules, and m6A-dependent effects on poly(A) tails. Finally, we demonstrate that our method generalizes to other RNA and DNA modifications, paving the path towards future efforts detecting other modifications.https://doi.org/10.1186/s13059-025-03498-6Nanopore sequencingNative RNARNA modificationsMachine learningN6-methyladenosineBasecalling |
| spellingShingle | Sonia Cruciani Anna Delgado-Tejedor Leszek P. Pryszcz Rebeca Medina Laia Llovera Eva Maria Novoa De novo basecalling of RNA modifications at single molecule and nucleotide resolution Genome Biology Nanopore sequencing Native RNA RNA modifications Machine learning N6-methyladenosine Basecalling |
| title | De novo basecalling of RNA modifications at single molecule and nucleotide resolution |
| title_full | De novo basecalling of RNA modifications at single molecule and nucleotide resolution |
| title_fullStr | De novo basecalling of RNA modifications at single molecule and nucleotide resolution |
| title_full_unstemmed | De novo basecalling of RNA modifications at single molecule and nucleotide resolution |
| title_short | De novo basecalling of RNA modifications at single molecule and nucleotide resolution |
| title_sort | de novo basecalling of rna modifications at single molecule and nucleotide resolution |
| topic | Nanopore sequencing Native RNA RNA modifications Machine learning N6-methyladenosine Basecalling |
| url | https://doi.org/10.1186/s13059-025-03498-6 |
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