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Decoding the Epitranscriptional Landscape from Native RNA Sequences

https://doi.org/10.1101/487819
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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/anie.201410647openalex-snapshot
High‐Resolution N6‐Methyladenosine (m6A) Map Using Photo‐Crosslinking‐Assisted m6A Sequencing
inferredcites →https://doi.org/10.1007/s12035-018-1138-1openalex-snapshot
m6A RNA Methylation Controls Neural Development and Is Involved in Human Diseases
inferredcites →https://doi.org/10.1016/j.bbagrm.2018.09.010openalex-snapshot
It's complicated… m6A-dependent regulation of gene expression in cancer
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.cell.2012.05.003openalex-snapshot
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons
inferredcites →https://doi.org/10.1016/j.cell.2015.08.011openalex-snapshot
HNRNPA2B1 Is a Mediator of m6A-Dependent Nuclear RNA Processing Events
inferredcites →https://doi.org/10.1016/j.copbio.2012.09.004openalex-snapshot
Transcriptome analysis using next-generation sequencing
inferredcites →https://doi.org/10.1016/j.gpb.2018.04.002openalex-snapshot
YTH Domain: A Family of N 6 -Methyladenosine (m 6 A) Readers
inferredcites →https://doi.org/10.1016/j.molcel.2016.01.012openalex-snapshot
Nuclear m6A Reader YTHDC1 Regulates mRNA Splicing
inferredcites →https://doi.org/10.1016/j.stem.2014.09.019openalex-snapshot
m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.tcb.2017.10.001openalex-snapshot
Reading m6A in the Transcriptome: m6A-Binding Proteins
inferredcites →https://doi.org/10.1038/nature23883openalex-snapshot
m6A modulates haematopoietic stem and progenitor cell specification
inferredcites →https://doi.org/10.1038/nature24482openalex-snapshot
Visualization of chemical modifications in the human 80S ribosome structure
inferredcites →https://doi.org/10.1038/nchembio.1654openalex-snapshot
Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain
inferredcites →https://doi.org/10.1038/nchembio.2569openalex-snapshot
Structural and evolutionary insights into ribosomal RNA methylation
inferredcites →https://doi.org/10.1038/nmeth.1459openalex-snapshot
Direct detection of DNA methylation during single-molecule, real-time sequencing
inferredcites →https://doi.org/10.1038/nmeth.3453openalex-snapshot
Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome
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/nrg.2016.169openalex-snapshot
Detecting RNA modifications in the epitranscriptome: predict and validate
inferredcites →https://doi.org/10.1038/s41592-019-0617-2openalex-snapshot
Nanopore native RNA sequencing of a human poly(A) transcriptome
inferredcites →https://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
inferredcites →https://doi.org/10.1073/pnas.1707674114openalex-snapshot
Evidence for rRNA 2′-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes
inferredcites →https://doi.org/10.1093/bib/bby017openalex-snapshot
Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btx364openalex-snapshot
UpSetR: an R package for the visualization of intersecting sets and their properties
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/nar/gkq1028openalex-snapshot
The RNA modification database, RNAMDB: 2011 update
inferredcites →https://doi.org/10.1093/nar/gkq224openalex-snapshot
Biases in Illumina transcriptome sequencing caused by random hexamer priming
inferredcites →https://doi.org/10.1093/nar/gks602openalex-snapshot
The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences
inferredcites →https://doi.org/10.1093/nar/gks804openalex-snapshot
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1093/nar/gkt111openalex-snapshot
Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods
inferredcites →https://doi.org/10.1093/nar/gku710openalex-snapshot
Distinctive structural motifs of RNA G-quadruplexes composed of AGG, CGG and UGG trinucleotide repeats
inferredcites →https://doi.org/10.1093/nar/gkw482openalex-snapshot
Profiling of 2′- O -Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity
inferredcites →https://doi.org/10.1093/nar/gkx1030openalex-snapshot
MODOMICS: a database of RNA modification pathways. 2017 update
inferredcites →https://doi.org/10.1093/nar/gkx934openalex-snapshot
RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data
inferredcites →https://doi.org/10.1093/nar/gky014openalex-snapshot
Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D
inferredcites →https://doi.org/10.1101/132274openalex-snapshot
Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing
inferredcites →https://doi.org/10.1101/gad.269415.115openalex-snapshot
A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation
inferredcites →https://doi.org/10.1101/gad.305862.117openalex-snapshot
RNA G-quadruplex secondary structure promotes alternative splicing via the RNA-binding protein hnRNPF
inferredcites →https://doi.org/10.1126/science.278.5338.680openalex-snapshot
Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale
inferredcites →https://doi.org/10.1155/2013/340620openalex-snapshot
State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity
inferredcites →https://doi.org/10.1186/1471-2105-11-237openalex-snapshot
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
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/gb-2012-13-10-175openalex-snapshot
The birth of the Epitranscriptome: deciphering the function of RNA modifications
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1186/s13059-018-1462-9openalex-snapshot
From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy
inferredcites →https://doi.org/10.1261/rna.063503.117openalex-snapshot
The RNA modification landscape in human disease
inferredcites →https://doi.org/10.1261/rna.2142810openalex-snapshot
Functional implications of the emergence of alternative splicing in hnRNP A/B transcripts
inferredcites →https://doi.org/10.1371/journal.pcbi.1003118openalex-snapshot
Software for Computing and Annotating Genomic Ranges
inferredcites →https://doi.org/10.1371/journal.pone.0168873openalex-snapshot
Mapping of Complete Set of Ribose and Base Modifications of Yeast rRNA by RP-HPLC and Mung Bean Nuclease Assay
inferredcites →https://doi.org/10.2210/pdb6ek0/pdbopenalex-snapshot
High-resolution cryo-EM structure of the human 80S ribosome

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s11033-021-06963-0openalex-snapshot
RNA sequencing and its applications in cancer and rare diseases
inferred← citeshttps://doi.org/10.1007/s13238-020-00733-7openalex-snapshot
Mapping the epigenetic modifications of DNA and RNA
inferred← citeshttps://doi.org/10.1016/j.tibtech.2020.06.002openalex-snapshot
New Twists in Detecting mRNA Modification Dynamics
inferred← citeshttps://doi.org/10.1021/acscentsci.1c00788openalex-snapshot
Nanopore Dwell Time Analysis Permits Sequencing and Conformational Assignment of Pseudouridine in SARS-CoV-2
inferred← citeshttps://doi.org/10.1038/s10038-019-0679-0openalex-snapshot
Recent advances in the detection of base modifications using the Nanopore sequencer
inferred← citeshttps://doi.org/10.1038/s41576-019-0150-2openalex-snapshot
RNA sequencing: the teenage years
inferred← citeshttps://doi.org/10.1038/s41587-021-00915-6openalex-snapshot
Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing
inferred← citeshttps://doi.org/10.1093/nar/gkaa588openalex-snapshot
New insights into Arabidopsis transcriptome complexity revealed by direct sequencing of native RNAs
inferred← citeshttps://doi.org/10.1093/nar/gkad044openalex-snapshot
Nanopore sequencing for N1-methylpseudouridine in RNA reveals sequence-dependent discrimination of the modified nucleotide triphosphate during transcription
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/10.1101/2021.04.28.441767openalex-snapshot
Thermodynamic stability of G-quadruplex and overlapping m6A: Position-dependent collaborators in allele frequency and fitness?
inferred← citeshttps://doi.org/10.1101/2023.03.12.532289openalex-snapshot
Nanopore sequencing for the 17 modification types in 36 locations in E. coli ribosomal RNA enables monitoring of stress-dependent changes
inferred← citeshttps://doi.org/10.1101/2024.08.26.609766openalex-snapshot
CO 2 protects cells from iron-Fenton oxidative DNA damage in E. coli and humans
inferred← citeshttps://doi.org/10.1261/rna.078777.121openalex-snapshot
The m 6 A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication
inferred← citeshttps://doi.org/10.14232/phd.10517openalex-snapshot
Comprehensive characterization of viral transcriptomes using long-read sequencing
inferred← citeshttps://doi.org/10.26650/jarhs2023-1349345openalex-snapshot
THE FREQUENCY AND FITNESS OF m6A-ASSOCIATED VARIANTS COULD BE MODULATED BY THE THERMODYNAMIC STABILITY OF AN OVERLAPPING G-QUADRUPLEX
inferred← citeshttps://doi.org/10.3389/fgene.2019.00834openalex-snapshot
Multiple Long-Read Sequencing Survey of Herpes Simplex Virus Dynamic Transcriptome
inferred← citeshttps://doi.org/10.3389/fgene.2020.00076openalex-snapshot
Nanopore Sequencing in Blood Diseases: A Wide Range of Opportunities
inferred← citeshttps://doi.org/10.3389/fgene.2020.00394openalex-snapshot
Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts
inferred← citeshttps://doi.org/10.3389/fmicb.2019.00260openalex-snapshot
Rapid Sequencing of Multiple RNA Viruses in Their Native Form
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