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Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing

https://doi.org/10.1101/132274
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/wrna.84openalex-snapshot
Single‐molecule direct RNA sequencing without cDNA synthesis
inferredcites →https://doi.org/10.1016/0022-2836(87)90349-4openalex-snapshot
Sites of action of two ribosomal RNA methylases responsible for resistance to aminoglycosides
inferredcites →https://doi.org/10.1016/0092-8674(86)90813-5openalex-snapshot
Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes
inferredcites →https://doi.org/10.1016/j.biochi.2014.11.019openalex-snapshot
What do we know about ribosomal RNA methylation in Escherichia coli?
inferredcites →https://doi.org/10.1016/j.drup.2012.05.001openalex-snapshot
Exogenously acquired 16S rRNA methyltransferases found in aminoglycoside-resistant pathogenic Gram-negative bacteria: An update
inferredcites →https://doi.org/10.1021/ja1087612openalex-snapshot
Processive Replication of Single DNA Molecules in a Nanopore Catalyzed by phi29 DNA Polymerase
inferredcites →https://doi.org/10.1038/327389a0openalex-snapshot
Interaction of antibiotics with functional sites in 16S ribosomal RNA
inferredcites →https://doi.org/10.1038/msb4100050openalex-snapshot
Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection
inferredcites →https://doi.org/10.1038/nbt.2147openalex-snapshot
Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision
inferredcites →https://doi.org/10.1038/nbt.2171openalex-snapshot
Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase
inferredcites →https://doi.org/10.1038/nbt.2950openalex-snapshot
Decoding long nanopore sequencing reads of natural DNA
inferredcites →https://doi.org/10.1038/ncomms11307openalex-snapshot
Fast and sensitive mapping of nanopore sequencing reads with GraphMap
inferredcites →https://doi.org/10.1038/nmeth.3290openalex-snapshot
Improved data analysis for the MinION nanopore sequencer
inferredcites →https://doi.org/10.1038/nmeth.4184openalex-snapshot
Detecting DNA cytosine methylation using nanopore sequencing
inferredcites →https://doi.org/10.1038/nmeth.4189openalex-snapshot
Mapping DNA methylation with high-throughput nanopore sequencing
inferredcites →https://doi.org/10.1038/nmeth.4577openalex-snapshot
Highly parallel direct RNA sequencing on an array of nanopores
inferredcites →https://doi.org/10.1038/nrmicro3330openalex-snapshot
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
inferredcites →https://doi.org/10.1073/pnas.1002036107openalex-snapshot
Dynamic evolution of translation initiation mechanisms in prokaryotes
inferredcites →https://doi.org/10.1073/pnas.71.4.1342openalex-snapshot
The 3′-Terminal Sequence of Escherichia coli 16S Ribosomal RNA: Complementarity to Nonsense Triplets and Ribosome Binding Sites
inferredcites →https://doi.org/10.1073/pnas.74.11.5088openalex-snapshot
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
inferredcites →https://doi.org/10.1073/pnas.93.24.13770openalex-snapshot
Characterization of individual polynucleotide molecules using a membrane channel
inferredcites →https://doi.org/10.1093/bioinformatics/btu555openalex-snapshot
Poretools: a toolkit for analyzing nanopore sequence data
inferredcites →https://doi.org/10.1093/nar/22.18.3681openalex-snapshot
The single pseudouridine residue inEscherichia coli16S RNA is located at position 516
inferredcites →https://doi.org/10.1101/094672openalex-snapshot
De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing
inferredcites →https://doi.org/10.1111/j.1365-2958.2006.05585.xopenalex-snapshot
Loss of a conserved 7‐methylguanosine modification in 16S rRNA confers low‐level streptomycin resistance in bacteria
inferredcites →https://doi.org/10.1111/j.1432-1033.1985.tb08704.xopenalex-snapshot
Specific fragmentation of tRNA and rRNA at a 7-methylguanine residue in the presence of methylated carrier RNA
inferredcites →https://doi.org/10.1128/aac.48.2.491-496.2004openalex-snapshot
Plasmid-Mediated 16S rRNA Methylase in Serratia marcescens Conferring High-Level Resistance to Aminoglycosides
inferredcites →https://doi.org/10.1128/cmr.17.4.840-862.2004openalex-snapshot
Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases
inferredcites →https://doi.org/10.1186/1477-3155-11-8openalex-snapshot
Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription
inferredcites →https://doi.org/10.1186/s13059-016-1103-0openalex-snapshot
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
inferredcites →https://doi.org/10.12688/f1000research.7201.1openalex-snapshot
MinION Analysis and Reference Consortium: Phase 1 data release and analysis
inferredcites →https://doi.org/10.3389/fbioe.2015.00091openalex-snapshot
Capture, Unfolding, and Detection of Individual tRNA Molecules Using a Nanopore Device
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.1002/wrna.1547openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s12551-017-0322-2openalex-snapshot
Protein folding and tRNA biology
inferred← citeshttps://doi.org/10.1016/b978-0-12-805364-5.00005-6openalex-snapshot
Sequencing in Precision Medicine
inferred← citeshttps://doi.org/10.1016/j.csbj.2022.05.034openalex-snapshot
Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages
inferred← citeshttps://doi.org/10.1016/j.tibtech.2018.02.009openalex-snapshot
Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods
inferred← citeshttps://doi.org/10.1016/j.tig.2018.05.008openalex-snapshot
The Third Revolution in Sequencing Technology
inferred← citeshttps://doi.org/10.1038/nature24286openalex-snapshot
DNA sequencing at 40: past, present and future
inferred← citeshttps://doi.org/10.1038/s41467-019-11713-9openalex-snapshot
Accurate detection of m6A RNA modifications in native RNA sequences
inferred← citeshttps://doi.org/10.1038/s41467-020-14665-7openalex-snapshot
A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry
inferred← citeshttps://doi.org/10.1038/s41576-018-0017-yopenalex-snapshot
Towards a complete map of the human long non-coding RNA transcriptome
inferred← citeshttps://doi.org/10.1038/s41576-019-0150-2openalex-snapshot
RNA sequencing: the teenage years
inferred← citeshttps://doi.org/10.1038/s41592-019-0617-2openalex-snapshot
Nanopore native RNA sequencing of a human poly(A) transcriptome
inferred← citeshttps://doi.org/10.1038/s41598-017-18364-0openalex-snapshot
Nanopore DNA Sequencing and Genome Assembly on the International Space Station
inferred← citeshttps://doi.org/10.1038/s41598-018-21484-wopenalex-snapshot
Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias
inferred← citeshttps://doi.org/10.1038/s41598-022-05457-8openalex-snapshot
Dual isoform sequencing reveals complex transcriptomic and epitranscriptomic landscapes of a prototype baculovirus
inferred← citeshttps://doi.org/10.1093/hmg/ddx287openalex-snapshot
The potential impact of nanopore sequencing on human genetics
inferred← citeshttps://doi.org/10.1093/jxb/erx289openalex-snapshot
A world of opportunities with nanopore sequencing
inferred← citeshttps://doi.org/10.1093/nar/gkz731openalex-snapshot
A general LC-MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures
inferred← citeshttps://doi.org/10.1098/rsob.180121openalex-snapshot
Emerging approaches for detection of methylation sites in RNA
inferred← citeshttps://doi.org/10.1101/167015openalex-snapshot
Using MinION ™ to characterize dog skin microbiota through full-length 16S rRNA gene sequencing approach
inferred← citeshttps://doi.org/10.1101/2019.12.18.880849openalex-snapshot
Exploring prokaryotic transcription, operon structures, rRNA maturation and modifications using Nanopore-based native RNA sequencing
inferred← citeshttps://doi.org/10.1101/483693openalex-snapshot
Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
inferred← citeshttps://doi.org/10.1101/487819openalex-snapshot
Decoding the Epitranscriptional Landscape from Native RNA Sequences
inferred← citeshttps://doi.org/10.1101/gr.247064.118openalex-snapshot
Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
inferred← citeshttps://doi.org/10.1111/gbb.12444openalex-snapshot
Role of RNA modifications in brain and behavior
inferred← citeshttps://doi.org/10.1146/annurev-biodatasci-072018-021255openalex-snapshot
RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis
inferred← citeshttps://doi.org/10.1261/rna.063503.117openalex-snapshot
The RNA modification landscape in human disease
inferred← citeshttps://doi.org/10.12688/f1000research.11547.1openalex-snapshot
Investigation of chimeric reads using the MinION
inferred← citeshttps://doi.org/10.17520/biods.2018201openalex-snapshot
Analysis of prospective microbiology research using third-generation sequencing technology
inferred← citeshttps://doi.org/10.21203/rs.3.rs-637036/v1openalex-snapshot
Dual Isoform Sequencing Reveals a Multifaceted Transcriptional Architecture of a Prototype Baculovirus
inferred← citeshttps://doi.org/10.3389/fgene.2019.00253openalex-snapshot
Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing
inferred← citeshttps://doi.org/10.3389/fgene.2020.00606openalex-snapshot
Methodologies for Transcript Profiling Using Long-Read Technologies
inferred← citeshttps://doi.org/10.53846/goediss-7501openalex-snapshot
Transcriptome maps of general eukaryotic RNA degradation factors and identification and functional characterization of the novel mRNA modification N3-methylcytidine
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