2019
DOI: 10.1101/843136
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RNA modifications detection by comparative Nanopore direct RNA sequencing

Abstract: RNA molecules undergo a vast array of chemical post-transcriptional modifications (PTMs) that can affect their structure and interaction properties. To date, over 150 naturally occurring PTMs have been identified, however the overwhelming majority of their functions remain elusive. In recent years, a small number of PTMs have been successfully mapped to the transcriptome using experimental approaches relying on high-throughput sequencing. Oxford Nanopore direct-RNA sequencing (DRS) technology has been shown to… Show more

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Cited by 75 publications
(151 citation statements)
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“…In this study, we focused on the 16S rRNA which is known to carry different types of RNA modifications which are introduced at different positions and different stages of the small ribosomal subunit maturation 73,107 . Our study provides evidence that RNA modification detection benefits of the use of unmodified/hypo-modified references (in agreement with recent studies 15,106 ). In this study, we have used a sample-compare approach analysing pre-rRNAs, which are expected to contain incomplete modification patterns, in comparison to mature rRNAs, which are expected to harbor a completed modification pattern.…”
Section: Discussionsupporting
confidence: 92%
See 1 more Smart Citation
“…In this study, we focused on the 16S rRNA which is known to carry different types of RNA modifications which are introduced at different positions and different stages of the small ribosomal subunit maturation 73,107 . Our study provides evidence that RNA modification detection benefits of the use of unmodified/hypo-modified references (in agreement with recent studies 15,106 ). In this study, we have used a sample-compare approach analysing pre-rRNAs, which are expected to contain incomplete modification patterns, in comparison to mature rRNAs, which are expected to harbor a completed modification pattern.…”
Section: Discussionsupporting
confidence: 92%
“…Several recent focused analyses have explored different strategies to evaluate the capacity of ONT to accurately detect RNA modifications (e.g. m6A) 14,15,55,105,106 . In this study, we focused on the 16S rRNA which is known to carry different types of RNA modifications which are introduced at different positions and different stages of the small ribosomal subunit maturation 73,107 .…”
Section: Discussionmentioning
confidence: 99%
“…Direct RNA-Seq applies a fundamentally unique principle for base identification: as RNA passes through the pore, the magnitudes of electric intensity across the nanopore surface are recorded and used to identify the corresponding nucleotide sequence. RNA modifications cause shifts in the intensity levels which are used to computationally identify modified bases (H. Liu et al 2019;Lorenz et al 2020;Leger et al 2019;Stoiber et al 2017) . Identification of m6A modifications can be achieved using a supervised learning approach that heavily relies on basecalling accuracy or training data from synthetic sequences (H. Liu et al 2019) .…”
Section: Introductionmentioning
confidence: 99%
“…Identification of m6A modifications can be achieved using a supervised learning approach that heavily relies on basecalling accuracy or training data from synthetic sequences (H. Liu et al 2019) . An alternative approach is the detection of modifications by comparison to a non-modified control sample, thereby removing the requirements of training data, and potentially enabling the identification of non-m6A modifications (Stoiber et al 2017;Leger et al 2019) . However, such samples are difficult to generate, they are affected by artifacts from various depletion methods, require prior knowledge about enzymes, and are still influenced by non-depleted modifications.…”
Section: Introductionmentioning
confidence: 99%
“…In 2017, the direct RNA sequencing (dRNAseq) technology appeared, making it possible for the first time to sequence native RNA molecules. Importantly, this technology could also identify chemical RNA modifications present in the native RNA molecules (4,5,8,15) , as well as estimations for their polyA-tail lengths (16,17) . However, a major caveat of dRNAseq is the amount of poly(A)-selected RNA material that is needed, i.e., typically 500ng of poly Compounding this fact, many of the recently developed DNA base-callers for nanopore signals rely on the use of DNNs, such as DeepNano (19) , DeepSignal (20) or Chiron (21) .…”
Section: Discussionmentioning
confidence: 99%