RNA modifications and cancer

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

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

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

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.

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.

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

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.

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

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

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.

The paper quantifies variation in mitochondrial RNA modification levels across multiple tissues and identifies nuclear genetic variants associated with these modifications and disease phenotypes.

The paper shows that m6A and m1A regulators, YTHDF2 and ALKBH3, co-regulate transgene expression in mammalian cells.

This study examines m6A dynamics during early vertebrate embryogenesis, finding increased m6A in polyadenylated mRNA and its association with translational efficiency and RNA degradation.

The paper investigates how gut microbiota influences m6A RNA modifications in different host tissues, finding significant effects in the cecum and liver, with Akkermansia muciniphila showing specific impacts.

The paper develops ELIGOS, a bioinformatic tool to detect RNA modifications and secondary structures using native RNA sequencing data from E. coli, yeast, and human cells.

The paper identifies 2′-O-methyl ribose (Nm) as a prevalent mRNA modification in yeast, showing that Spb1 methylates ribosomal protein mRNAs and that its expression is required for normal levels of target mRNAs.

The paper identifies and functionally characterizes tRNA-derived small RNAs (tsRNAs) in cell state transitions, showing their role in regulating translation and stem cell states.

The paper identifies and characterizes m6A methylated circular RNAs, showing cell-type specificity and cross-talk with m6A-mRNAs through YTHDF2.