RNA modifications and cancer

This study uses time-resolved NMR to track tRNA maturation in yeast, revealing a sequential and hierarchically controlled modification process.

This study identifies that ADAR1-mediated A-to-I RNA editing in mouse oocytes preferentially targets the wobble position of codons, altering codon usage and potentially affecting mRNA stability and translation efficiency.

The paper identifies PCIF1 as the m6Am methyltransferase and develops a method to accurately map m6Am sites, revealing its role in mRNA stability.

This paper introduces an antibody-independent method for single-base m6A mapping, showing high reliability and conservation across species.

The paper identifies PCIF1 as the first human m6Am methyltransferase and shows it regulates gene expression by suppressing cap-dependent translation through m6Am methylation.

This study shows that a mutation in ADAT3, linked to intellectual disability, disrupts tRNA wobble inosine formation and ADAT2/ADAT3 complex function.

This paper introduces MASTER-seq, a method to quantitatively profile m6A sites at single-nucleotide resolution, revealing a predictable code that determines m6A stoichiometry and dynamics.

The paper identifies NSUN2 as a methyltransferase that introduces 5-methylcytidine into mitochondrial tRNAs in mice and humans.

The paper analyzes tRNA fragments (tRFs) across 32 cancer types, identifying disease-specific patterns and associations with mRNAs and repeat elements.

This study shows FTO demethylates m2-snRNA to regulate splicing by controlling reversible methylation of snRNAs.

This paper introduces Deep-m6A, a deep learning model for predicting m6A sites and identifies 709 functionally significant m6A-regulated genes and nine subnetworks associated with cancer and other diseases.

This paper reconciles conflicting findings on m1A modification in cytosolic mRNAs by reanalyzing data, revealing most sites are artifacts and only 53 are genuine internal modifications, primarily catalyzed by TRMT6/TRMT61A at low levels.

This study shows that METTL14 is essential for mouse post-implantation development by promoting epiblast maturation from naive to primed state.

The paper identifies a single m1A modification in rRNA that affects ribosome structure and translation of metabolic enzymes in yeast and humans.

The paper identifies m6A methylation in the 5' vicinity of transcripts as a mechanism for directing mRNAs to stress granules via YTHDF3 recognition during oxidative stress.

This paper investigates how m6A RNA methylation in the brain is regulated by stress and shows its role in fear memory, transcriptome response, and synaptic plasticity, with implications for stress-related disorders.

The paper identifies the synaptic m6A epitranscriptome in mouse forebrain and shows its role in synaptic function and disease-related pathways.

The paper investigates the role of m6A in splicing efficiency by analyzing nascent RNA transcripts and shows that early m6A deposition accelerates splicing.

PEA is an R toolkit for plant epitranscriptome analysis, offering CMR calling, prediction, and annotation with high accuracy for m6A modifications in Arabidopsis thaliana.

The paper analyzes 110 C/D box sRNA families in six Pyrobaculum species, revealing their genomic organization, evolutionary patterns, and functional features through computational and genomic methods.

SPORTS1.0 annotates and profiles non-coding RNAs, including rRNA- and tRNA-derived sRNAs, and identifies RNA modification sites from sRNA-seq data.

This study identifies snoRNA expression changes in cartilage ageing and osteoarthritis, showing their impact on chondrogenic and hypertrophic gene expression.

This paper introduces a method using gamma-toxin endonuclease to detect mcm5s2U modification in eukaryotic tRNAs and shows its conservation across species.

The paper develops a computational method to accurately call methylation in whole-transcriptome bisulfite sequencing data, revealing new methylation patterns in mouse RNAs.

The paper quantifies changes in mitochondrial RNA processing in cancers using genomic data from 1226 samples, finding altered methylation rates and associations with survival outcomes.

The paper identifies regulatory RNPs (regRNPs) formed from processed scaRNAs that influence rRNA modifications, contributing to ribosome heterogeneity.