RNA modifications and cancer

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.

StackRAM is a cross-species method for identifying m6A sites using machine learning, achieving high accuracy in yeast, human, and Arabidopsis.

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 altered 2-O-methylation patterns in rRNA associated with senescence and quiescence in human fibroblasts using RiboMeth-seq.

The paper introduces NJU-seq and Nm-VAQ to quantify RNA 2'-O-methylation sites in mRNA, identifying thousands of new sites and validating their presence in human and mouse cell lines.

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

This study shows that the m6A reader Ythdf limits axonal growth in Drosophila by modulating Fmr1 target selection.

The paper develops a method to characterize the tRNA epitranscriptome of Escherichia coli by optimizing library preparation and deep sequencing to detect modifications without demethylation.

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 N6-methyladenosine in poly(A) tails of VSG transcripts in Trypanosoma brucei, showing it regulates mRNA stability through a cis-acting motif.

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.

The paper investigates the role of m6A methylation in prenatal skeletal muscle development in pigs using transcriptome-wide profiling and identifies its regulatory impact on myogenesis.

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 identifies a missense variant in TRMT1 causing intellectual disability by disrupting tRNA m2,2G modification.

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.

This study identifies a complex between METTL2 and DALRD3 that catalyzes 3-methylcytosine formation in specific arginine tRNA isoacceptors and shows DALRD3 deficiency leads to loss of this modification.

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.

The paper investigates m6A-RNA modifications in plant mitochondria, revealing their distribution across different RNA types and potential effects on gene expression.

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.

This study uses nanopore direct RNA sequencing to map the m6A epitranscriptome in Arabidopsis, revealing its role in mRNA processing and circadian rhythms.

SICM6A is a deep learning model that identifies m6A sites across species using a transposed GRU network and 3-mer encoding, achieving higher accuracy than existing methods.