RNA modifications and cancer

The paper introduces a rapid UPLC-MS method for analyzing RNA modifications in complex samples, demonstrating its effectiveness across different organisms.

This study shows that m5C RNA modification in C. elegans affects translation efficiency and adaptation to heat stress by modulating leucine and proline decoding.

The paper uses direct RNA long-read sequencing to show m6A modifications on adenovirus RNA are necessary for efficient splicing.

The paper identifies NSUN6 as a methyltransferase that specifically targets mRNA 3UTR regions with the CTCCA motif, affecting translation termination but not essential for mouse development.

CIGAR-seq identifies mRNA modification regulators through CRISPR screening and RNA modification readout, revealing NSUN6 as a novel m5C methyltransferase.

The paper identifies NSUN6 as an mRNA methyltransferase targeting Type II m5C sites and reveals its structural specificity and functional relationship with translation efficiency.

The paper develops a bioinformatic pipeline to analyze tRNA fragments (tRFs) in Drosophila mutants, revealing how defects in tRNA biogenesis affect tRF and snoRNA populations.

This study identifies METTL4 as the methyltransferase responsible for m6Am modification in U2 snRNA, showing its role in regulating pre-mRNA splicing.

This study shows that Mettl3 and m6A modification influence liver metabolic disorders and insulin resistance in mice fed a high-fat diet.

The paper develops a combined tRNA sequencing protocol to measure expression and post-transcriptional modifications in plants, finding conserved and species-specific modification patterns in Arabidopsis thaliana.

The paper introduces MR-GAN, a GAN-based model for predicting epitranscriptome modification sites using unsupervised learning, showing significant improvement over one-hot encoding and SRAMP.

This study investigates how Alkbh1 affects tRNA cleavage and tiRNA generation under stress in rat cells, showing stress-specific impacts and differential tRNA cleavage.

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.