RNA modifications and cancer

ModkitOpt: An optimised workflow for RNA modification stoichiometry estimation and site calling from nanopore sequencing

ModkitOpt optimizes RNA modification site calling by selecting the best parameters and stoichiometry cutoff for nanopore sequencing data, improving precision and recall across modification types.

Nanopore Direct RNA Sequencing Enables Reproducible, Site-Resolved Pseudouridine Quantification in Human Ribosomal RNA

This study benchmarks nanopore direct RNA sequencing for pseudouridine quantification in human ribosomal RNA, showing high accuracy and reproducibility across multiple cell types.

Transcript architecture sets the m6A landscape: CSTF2 and CSTF2T reshape m6A through cleavage-dependent and -independent mechanisms

The paper identifies CSTF2 and CSTF2T as factors that shape the m6A landscape through cleavage-dependent and -independent mechanisms by altering transcript architecture and polyadenylation sites.

SWARM resolves nanopore signal interference between RNA modification types and reveals splicing-shaped pseudouridylation

SWARM improves detection of RNA modifications by reducing false positives and reveals new splicing-related pseudouridylation patterns.

Integrating mass spectrometry with Nanopore direct RNA sequencing for de novo modification profiling of bacteriophage MS2

The paper profiles RNA modifications in MS2 bacteriophage using LC-MS/MS and Nanopore DRS, finding {Psi} as the predominant modification.

Cytosolic and ER-associated ribosomes share rRNA 2'-O-methylation landscapes across human cell types

The paper compares 2'-O-methylation patterns of cytosolic and ER-associated ribosomes across human cell types and finds minimal compartment-specific differences.

FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling

FIRST-seq uses nanopore cDNA sequencing to profile RNA modifications and structures by analyzing RT errors, achieving single-nucleotide resolution without PCR or second-strand synthesis.

Molecular grammar of RNA m6A modification in ribonucleoprotein granules

The paper uses SMART-epi to study how m6A modification affects RNP granule assembly and RNA interactions, revealing functional divergence among YTHDF proteins.

m1A58 governs two steps of human initiator-methionine tRNA metabolism: maturation and XRN2-mediated decay

This study shows m1A58 regulates tRNA maturation and XRN2-mediated decay in human cells, maintaining tRNA homeostasis.

RNase 4 improves bottom-up modification mapping of E. coli total tRNAs using HILIC-MS/MS

This paper introduces a method using RNase 4 and HILIC-MS/MS to map tRNA modifications in E. coli with high coverage and without ion-pairing reagents.

SnoRNA Expression and RNA 2'-O-Methylation in Drosophila melanogaster S2 Cells

This study identifies 239 snoRNAs in Drosophila S2 cells and maps 2-O-methylation sites using RibOxi-seq2, revealing widespread Nm modifications in rRNAs and mRNAs.

tRNA-derived fragments are elevated in the aging brain and may contribute to neurodegeneration

This study shows that tRNA-derived fragments (tRFs) accumulate in aging mouse brains and are elevated in human neurodegenerative conditions, suggesting a role in neurodegeneration.

TRMT6/61A-mediated m1A methylation facilitates human pre-tRNA maturation and prevents surveillance by XRN2

This study shows TRMT6/61A-mediated m1A methylation on pre-tRNAs is essential for their maturation and prevents XRN2-mediated degradation, maintaining translational homeostasis.

m6A positions polyadenylation in Plasmodium falciparum

The paper investigates m6A methylation in Plasmodium falciparum, showing its role in polyadenylation and transcription termination.

FTO separation-of-function mutations alter m6A versus m6Am demethylation selectivity on RNA

This paper reports engineered FTO mutants that selectively demethylate m6A or m6Am RNA modifications, enabling study of their distinct biological roles.

Transcript architecture predetermines m6A remodeling and sensory neuron vulnerability in chemotherapy-induced peripheral neuropathy

The paper shows transcript architecture determines m6A loss and sensory neuron vulnerability in chemotherapy-induced neuropathy using nanopore RNA sequencing and machine learning.

The m6A reader protein YTHDF2 facilitates HTLV-1 infectious and mitotic propagation by stabilizing Tax RNA

This study identifies YTHDF2 as a host factor that stabilizes Tax RNA through m6A modification, promoting HTLV-1 replication and persistence.

Identification of rare pseudouridylated microRNA by comprehensive small RNA bisulfite sequencing of mouse and human tissues

The paper identifies rare pseudouridylated microRNA using bisulfite sequencing in mouse and human tissues, finding miR-3068-5p as a modified miRNA with altered target repression.

Deciphering the epitranscriptomic code of RNA degradation with nanopore direct RNA sequencing

This study uses nanopore direct RNA sequencing to analyze how m6A modifications and poly(A) tail dynamics influence RNA degradation kinetics and isoform-specific decay.

Evaluation of Nanopore direct RNA sequencing updates for modification detection

This paper evaluates updates to Nanopore direct RNA sequencing for detecting RNA modifications, showing improved accuracy in identifying pseudouridine and N6-methyladenosine.

EvoRMD: Integrating Biological Context and Evolutionary RNA Language Models for Interpretable Prediction of RNA Modifications

EvoRMD predicts RNA modification types using a model that integrates sequence data and biological context, achieving strong performance and interpretability.

Contribution of Three tRNA Modification Enzymes to Proteus mirabilis Fitness and Catheter-Associated Urinary Tract Infection

This study investigates the role of DusA, DusB, and DusC enzymes in Proteus mirabilis, showing DusB is critical for fitness, biofilm formation, and virulence in urinary tract infections.

IGF2BP2 links m6A-modified HMGA1 mRNA stability to mitochondrial metabolism and cell proliferation

This study shows IGF2BP2 enhances recombinant protein yield in CHO cells by stabilizing HMGA1 mRNA and improving mitochondrial metabolism and cell proliferation.

Long-term stability of RNA nucleoside standards for accurate LC-MS quantification

This study evaluates the long-term stability of RNA nucleoside standards under different storage conditions and proposes guidelines for their preparation and quality control.

Benchmarking Tools for Identification of rRNA Modifications in Escherichia coli using Oxford Nanopore Direct RNA Sequencing

This paper benchmarks RNA modification detection tools on bacterial rRNA using Oxford Nanopore DRS, finding that no single tool recovers all sites and that combining tools improves performance.

Fine-tuning m6A and METTL3 levels have profound impact on cellular proliferation and protein synthesis

The paper shows that altering m6A and METTL3 levels affects cellular proliferation and protein synthesis in TNBC cells.

YTHDF1 mediates translational control by m6A mRNA methylation in adaptation to environmental challenges

This study shows that YTHDF1 mediates m6A mRNA methylation in neuronal adaptation to environmental challenges, with distinct roles in D1 and D2 neurons.

Loss of host factor-mediated m6Am methylation of the viral RNA cap impairs SARS CoV-2 replication

This study identifies PCIF1 as a host factor that methylates the SARS-CoV-2 RNA cap, enhancing viral replication and reducing disease severity in mice.

Investigation of TRMT61B methyltransferase activity on mRNA and its effects on translation

This study identifies TRMT61B as an m1A methyltransferase active on cytosolic mRNAs and shows context-dependent effects of m1A on translation and ribosome recruitment.

Cap-adjacent 2'-O-ribose methylation of RNA in C. elegans is required for postembryonic growth and germline development in the presence of the decapping exonuclease EOL-1

The paper investigates the role of cap-adjacent 2'-O-ribose methylation (cOMe) in C. elegans, showing it protects transcripts from decapping exonuclease EOL-1 and is essential for growth and germline development.