RNA modifications and cancer

Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods

This paper introduces Deep-m6A, a deep learning model for predicting m6A sites and identifies 709 functionally significant m6A-regulated genes and nine subnetworks associated with cancer and other diseases.

A role for gut microbiota in m6A epitranscriptomic mRNA modifications in different host tissues

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.

Decoding the Epitranscriptional Landscape from Native RNA Sequences

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.

M1A within cytoplasmic mRNAs at single nucleotide resolution: A reconciled transcriptome-wide map

This paper reconciles conflicting findings on m1A modification in cytosolic mRNAs by reanalyzing data, revealing most sites are artifacts and only 53 are genuine internal modifications, primarily catalyzed by TRMT6/TRMT61A at low levels.

Mettl14 is required for mouse post-implantation development by facilitating epiblast maturation

This study shows that METTL14 is essential for mouse post-implantation development by promoting epiblast maturation from naive to primed state.

A single N1-methyladenosine on the large ribosomal subunit rRNA impacts locally its structure and the translation of key metabolic enzymes

The paper identifies a single m1A modification in rRNA that affects ribosome structure and translation of metabolic enzymes in yeast and humans.

Dynamic m6A methylation facilitates mRNA triaging to stress granules

The paper identifies m6A methylation in the 5' vicinity of transcripts as a mechanism for directing mRNAs to stress granules via YTHDF3 recognition during oxidative stress.

The role of m6A-RNA methylation in stress response regulation

This paper investigates how m6A RNA methylation in the brain is regulated by stress and shows its role in fear memory, transcriptome response, and synaptic plasticity, with implications for stress-related disorders.

Synaptic m6A Epitranscriptome Reveals Functional Partitioning of Localized Transcripts for Dynamic Tripartite Synapse Modulation

The paper identifies the synaptic m6A epitranscriptome in mouse forebrain and shows its role in synaptic function and disease-related pathways.

Transient N-6-methyladensosine Transcriptome sequencing reveals a regulatory role of m6A in splicing efficiency

The paper investigates the role of m6A in splicing efficiency by analyzing nascent RNA transcripts and shows that early m6A deposition accelerates splicing.

PEA: an integrated R toolkit for plant epitranscriptome analysis

PEA is an R toolkit for plant epitranscriptome analysis, offering CMR calling, prediction, and annotation with high accuracy for m6A modifications in Arabidopsis thaliana.

Methylation guide RNA evolution in archaea: structure, function, and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species

The paper analyzes 110 C/D box sRNA families in six Pyrobaculum species, revealing their genomic organization, evolutionary patterns, and functional features through computational and genomic methods.

SPORTS1.0: a tool for annotating and profiling non-coding RNAs optimized for rRNA- and tRNA- derived small RNAs

SPORTS1.0 annotates and profiles non-coding RNAs, including rRNA- and tRNA-derived sRNAs, and identifies RNA modification sites from sRNA-seq data.

SnoRNA signatures in cartilage ageing and osteoarthritis

This study identifies snoRNA expression changes in cartilage ageing and osteoarthritis, showing their impact on chondrogenic and hypertrophic gene expression.

Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose

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.

Monitoring the 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification in eukaryotic tRNAs via the gamma-toxin endonuclease

This paper introduces a method using gamma-toxin endonuclease to detect mcm5s2U modification in eukaryotic tRNAs and shows its conservation across species.

Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs

The paper develops a computational method to accurately call methylation in whole-transcriptome bisulfite sequencing data, revealing new methylation patterns in mouse RNAs.

Dynamic expression of tRNA-derived small RNAs define cellular states

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.

Integrated Genomic Analysis of Mitochondrial RNA Processing in Human Cancers

The paper quantifies changes in mitochondrial RNA processing in cancers using genomic data from 1226 samples, finding altered methylation rates and associations with survival outcomes.

Identification and characterization of m6A circular RNA epitranscriptomes

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

Regulatory RNPs: A novel class of ribonucleoproteins that contribute to ribosome heterogeneity

The paper identifies regulatory RNPs (regRNPs) formed from processed scaRNAs that influence rRNA modifications, contributing to ribosome heterogeneity.

RNAModR: Functional analysis of mRNA modifications in R

RNAModR provides a framework for analyzing mRNA modifications, enabling statistical evaluation of their distribution and functional insights.