RNA modifications and cancer

This study identifies Tet-dependent 5-hydroxymethylcytosine (5hmrC) modifications on mRNAs in Drosophila and shows their role in regulating axon guidance genes.

The paper shows that tRNA modifications regulate the translational response to mitochondrial stress by altering codon decoding and pathway activity.

This study shows that Angiogenin regulates mitochondrial stress and function by generating tRNA-derived fragments and altering tRNA modifications.

magpie evaluates statistical power for differential RNA methylation analysis in m6A sequencing by simulating data and assessing factors like sample size and effect size.

The paper develops HDAMS, a method that improves differential m6A site analysis by incorporating antibody specificity predictions, leading to more accurate and functionally relevant results.

The paper introduces NanoPsiPy, a pipeline for detecting pseudouridylation sites using nanopore sequencing, and shows PUS7-dependent pseudouridylation affects m6A and m5C levels.

This paper introduces m6Aiso, a deep learning model that accurately detects m6A sites on single RNA molecules using endogenous labeling and DRS data, revealing new insights into m6A dynamics across RNA isoforms.

The paper shows that m1A methylation of ND5 mRNA, catalyzed by TRMT10C, leads to translation repression and mitochondrial dysfunction in Alzheimer's disease.

The paper identifies LOC339803 lncRNA as a mediator of intestinal inflammation through m6A methylation and YTHDC1 interaction, suggesting it as a potential therapeutic target for IBD.

The paper identifies NAT10's role in cancer through tRNA ac4C modification, showing RNPS1 stabilizes NAT10 and enhances translation efficiency via the AP-1 pathway.

This study shows that 5-FU treatment alters the export and base modifications of small RNAs in extracellular vesicles from colorectal cancer cells.

This study investigates how fumarate accumulation affects RNA methylation by targeting specific 2OGDD enzymes in HLRCC cell lines, revealing differential impacts on m6A, m1A, and f5C demethylases.

This study identifies RlmQ, a methyltransferase in Staphylococcus aureus responsible for a unique rRNA modification, and shows its impact on bacterial growth and virulence.

The paper identifies RluA as the main pseudouridine synthase in E. coli mRNAs, showing it modifies 31 of 44 high-confidence sites through a sequence and structural motif.

The paper identifies a specific role for Trm10-mediated m1G9 modification in tRNATrp quality control in yeast, showing it is essential for tRNATrp function and subject to a distinct quality control mechanism.

This paper shows that using high-accuracy nanopore RNA basecalling models improves detection of RNA modifications, read mappability, and basecalling accuracy.

This study shows that CTU1 is essential for zebrafish development and erythroid differentiation, as its knockdown impairs larval development and blocks erythroid cell differentiation.

This study identifies m1A as the prevalent mRNA modification in dinoflagellates, showing its role in post-transcriptional regulation of translation efficiency.

ModrRNA1 identifies potential rRNA modification sites and associated enzymes in bacteria using a curated database and sequence alignment, with a web interface and open-source code.

This study shows that CMTR1-mediated N1-2'O-methylation prevents antiviral recognition and regulates NVL2 mRNA splicing, affecting cell size, division, and ribosome biogenesis.

The paper shows that m6A methylation drives length-dependent mRNA enrichment in stress granules by enabling YTHDF-mediated mRNA interactions.

This study investigates how chronic morphine exposure and withdrawal alter tRNA cytosine methylation in the medial prefrontal cortex, linking these changes to reward-seeking behavior and opioid use disorder.

This study shows that Mettl1-dependent m7G tRNA modification is essential for spermatogenesis and fertility in Drosophila, as its loss leads to sterility and tRNA instability.

The paper tracks heritable methylation transmission in C. elegans and shows that parental starvation induces intergenerational hormesis via 18S rRNA methylation.

This study identifies Kar4 as a key component of the yeast mRNA methyltransferase complex required for both mating and meiosis, with distinct functional roles in these processes.

This study investigates the role of m6A methylation in early pancreatic β-cell differentiation in humans and mice, showing METTL14's essential role in this process.

The paper develops a method to detect m6A modifications at single-molecular resolution using direct-RNA sequencing by creating synthetic data and a bespoke algorithm.

This study shows that N6-adenosine methylation regulates insulin mRNA translation in D. melanogaster, leading to metabolic phenotypes and conserved m6A signatures in vertebrate insulin mRNAs.