RNA modifications and cancer

Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6

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.

m6A RNA methylation-dependent APC translation is required for local translation of beta-actin and axon 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, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators

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

Sequence- and structure-selective mRNA m5C methylation by NSUN6 in animals

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

tRNA fragments (tRFs) populations analysis in mutants affecting tRNAs processing and tRNA methylation

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: RNA modification detection using Nanopore raw reads with Deep One-Class Classification

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

Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect splicing

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

METTL4 catalyzes m6Am methylation in U2 snRNA to regulate pre-mRNA splicing

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

m6A Regulates Liver Metabolic Disorders and Hepatogenous Diabetes

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

Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification

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 landscape of SARS-CoV-2 RNA modifications

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.

Predicting sites of epitranscriptome modifications using unsupervised representation learning based on generative adversarial networks

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.

jouvence, a new human H/ACA snoRNA involves in the control of cell proliferation and differentiation

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 stress specific impact of ALKBH1 on tRNA cleavage and tiRNA generation

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

Context-dependent functional compensation between Ythdf m6A readers

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

Machine Learning and Deep Learning challenges for building 2'O site prediction

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.

Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

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.

The human mitochondrial 12S rRNA m4C methyltransferase METTL15 is required for proper mitochondrial function

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: A database for exploring N6-methyladenosine methylome

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: a cross-species method for identifying RNA N6-methyladenosine sites based on stacked ensemble

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

Limits in the detection of m6A changes using MeRIP/m6A-seq

This study evaluates the reproducibility of m6A peak detection and changes using MeRIP-seq and finds limited consistency across studies.

Multiple links between 5-methylcytosine content of mRNA and translation

The paper investigates the relationship between m5C modification in mRNA and translation by analyzing polysome profiles and validating m5C sites across different cell lines.

Cellular senescence and quiescence are associated with altered ribosomal RNA methylation and processing

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

A novel platform of RNA 2'-O-methylation high-throughput and site-specific quantification tools revealed its broad distribution on mRNA

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.

5’ tRNA halves are highly expressed in the primate hippocampus and sequence-specifically regulate gene expression

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

The m6A reader Ythdf restricts axonal growth in Drosophila through target selection modulation of the Fragile X mental retardation protein

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

Highly reproducible characterization of Escherichia coli tRNA epitranscriptome with a simple method of library preparation for deep sequencing

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.

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry

The paper introduces NASE, a database search engine for RNA mass spectrometry data, demonstrating its ability to identify modified RNA sequences in three datasets.

N6-methyladenosine in poly(A) tails stabilize VSG transcripts

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.

TRMT2B is responsible for both tRNA and rRNA m5U-methylation in human mitochondria

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.