RNA modifications and cancer

The paper identifies NOP58 as a reader and SIRT7 as an eraser of the RNA acetylation ac4C, showing SIRT7 can deacetylate RNA in vitro and affecting snoRNA function and pre-rRNA processing.

This study introduces PULSE, a deep learning model that predicts pseudouridylation sites and characterizes their sequence features using convolutional neural networks.

This paper shows that m6A methylation regulates HIV-1 RNA stability and alternative splicing through YTHDC1 and YTHDF2.

This paper reviews the role of m6A epitranscriptomic dysregulation in stress-induced psychiatric disorders using bioinformatic analysis of single-cell and bulk RNA-seq datasets.

The paper investigates the subcellular relocalization of TRMT1 and TRMT1L during neuronal activation and identifies their role in RNA modification dynamics and neuronal plasticity.

The paper investigates inosine RNA modifications in oocytes from Cnot6l-/- and Btg4-/- mice, finding depletion of inosine modifications in Cnot6l-/- oocytes, suggesting a novel mRNA clearance mechanism.

The paper identifies dyskerin's role in regulating mRNA expression and nuclear hormone receptor dependence through snoRNA-retaining transcripts in breast cancer.

The paper identifies m6A as an endogenous ligand for the A3 adenosine receptor, showing it has higher affinity than unmodified adenosine and plays a role in type I allergy.

The paper introduces an improved eCLIP method called m6A-eCLIP (meCLIP) that enables precise identification of m6A residues at single-nucleotide resolution with reliable confidence metrics.

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.

The paper shows that m6A methylation regulates APC translation, which is necessary for beta-actin mRNA transport and axon development in neurons.

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.

nanoDoc detects RNA modifications from Nanopore raw reads using deep one-class classification, achieving 0.96 AUC accuracy in E. coli and S. cerevisiae.

This study shows that pseudouridine is added co-transcriptionally to pre-mRNA and affects alternative splicing by modifying RNA structure and interactions.

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.

This study uses direct RNA sequencing to identify RNA modifications in SARS-CoV-2 isolated from human lung cells, revealing conserved modification patterns across isolates.

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 characterizes a new human H/ACA snoRNA, jouvence, showing it promotes cell proliferation and dedifferentiation while its knockdown reduces proliferation and ribosome biogenesis.

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 investigates functional compensation among Ythdf m6A readers in mouse gametogenesis and embryonic stem cells, revealing dosage-dependent redundancy and distinct roles.

The paper evaluates ML and DL models for predicting 2'O methylation sites, finding that embedding methods benefit ML but not DL, and identifies key nucleotides around 2'O sites.

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.