RNA modifications and cancer

The paper identifies tissue- and cancer-specific RNA modification machinery (RMP) expression patterns and dysregulation across 32 tissues, 10 species, and 13,358 tumor-normal samples.

This study identifies METTL15 as the enzyme responsible for m4C839 methylation in human 12S mt-rRNA and shows its critical role in mitochondrial function.

REPIC compiles and provides access to m6A methylation data from 672 samples across 11 organisms, integrating it with histone and chromatin data for comprehensive analysis.

This study evaluates the reproducibility of m6A peak detection and changes using MeRIP-seq and finds limited consistency across studies.

The paper investigates the relationship between m5C modification in mRNA and translation by analyzing polysome profiles and validating m5C sites across different cell lines.

The paper identifies high expression of 5' tRNA halves in primate hippocampus and shows they regulate gene expression through sequence-specific mechanisms.

The paper introduces NASE, a database search engine for RNA mass spectrometry data, demonstrating its ability to identify modified RNA sequences in three datasets.

The paper identifies TRMT2B as the enzyme responsible for m5U modification in both mitochondrial tRNAs and rRNAs in human cells, showing it is not essential for viability.

This study identifies two tRNA methyltransferases in Drosophila that modulate small RNA silencing and lifespan by modifying specific tRNAs.

This study shows that Flaviviridae viruses alter m6A modification of specific host transcripts, affecting viral infection through changes in translation and splicing.

This study identifies AtTrm5 as a bifunctional tRNA methyltransferase in Arabidopsis, showing its role in tRNA modifications and plant growth.

This study identifies 8 differentially expressed tRNA-derived fragments in SAMP8 mouse brains, suggesting their potential role in age-related neurological diseases.

The paper shows that m1A is only present in the mitochondrial MT-ND5 transcript, and previous findings of m1A in 5 UTRs were due to antibody cross-reactivity with m7G caps.

The paper profiles m6A and m6Am methylomes across 42 human and 16 mouse tissues, revealing tissue-specific patterns and cross-species conservation.

This study shows that m6A RNA binding enables YTHDF2 and other m6A readers to undergo phase separation, which may regulate their localization in cells.

This paper demonstrates the detection of m6A RNA modifications in native RNA sequences using Oxford Nanopore Technologies with high accuracy.

The paper introduces CapQuant, a mass spectrometry-based method to analyze RNA caps, revealing new cap structures and variations in humans and mice.

This study identifies m6A mRNA methylation dynamics in Plasmodium falciparum during blood-stage development, showing its role in regulating gene expression and mRNA stability.

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.