RNA modifications and cancer

Single-base mapping of m6A in lncRNAs reveals a distinct landscape linked to transposable elements and RNA processing

The paper maps m6A modifications in lncRNAs at single-base resolution, revealing distinct patterns linked to transposable elements, RNA structure, and splicing.

Pho92 direct interaction with Not1 recruits the CCR4-NOT complex to m6A containing mRNAs to modulate meiosis in S. cerevisiae

This study shows Pho92 interacts with Not1 to recruit the CCR4-NOT complex to m6A-containing mRNAs, modulating meiosis in S. cerevisiae.

Metabolic stress reveals widespread accumulation of cap-unmethylated RNAs

The paper shows that under metabolic stress, many mRNAs lack cap methylation, yet they are still functional, suggesting cap methylation is a stress-responsive regulatory layer.

Nucleotide-resolution Mapping of RNA N6-Methyladenosine (m6A) modifications and comprehensive analysis of global polyadenylation events in mRNA 3' end processing in malaria pathogen Plasmodium falciparum

The paper maps m6A modifications and polyadenylation events in Plasmodium falciparum mRNAs, identifying stage-specific m6A sites and their potential role in 3' end processing.

Neuronal tRNA Modifications in Aplysia californica are Repatterned during Behavioral Habituation

The paper characterizes neuronal tRNA modifications during behavioral habituation in Aplysia californica, revealing a post-transcriptional mechanism of learning and memory.

The RNA m6A reader YTHDF2 depletion phenocopies high glucose induced-cellular stress response in diabetic kidney disease

This study shows that YTHDF2 depletion mimics high glucose-induced stress in diabetic kidney disease by altering RNA processing and increasing oxidative stress.

A maximum entropy model for m6A prediction: from human transcripts to influenza A viral segments

The paper introduces MEMAR, a Maximum Entropy model for predicting m6A methylation in human transcripts and influenza A viral segments, showing improved performance over existing methods.

METTL3-mediated m6A modification alleviates skeletal muscle atrophy in ALS by regulating ACSL1-dependent triglyceride metabolism

This study identifies METTL3-mediated m6A modification as a regulator of triglyceride metabolism in ALS skeletal muscle, alleviating atrophy through ACSL1 expression.

Cap-specific N6-adenosine methyltransferases and applications in m6A Cap-1 mRNA synthesis

This study identifies and characterizes PC04 and PC05, two cap-specific N6-adenosine methyltransferases, and demonstrates their use in synthesizing m6A Cap-1 mRNA in vitro.

Cytoplasmic localization of 5hmC reveals RNA hydroxymethylation in breast cancer

The paper identifies cytoplasmic 5hmC in breast cancer tissues and cell lines, linking it to TET3 expression and RNA processing, with implications for triple-negative breast cancer.

METTL1 gene dosage and catalytic activity define a targetable vulnerability in pediatric cancers

This study identifies METTL1 gene dosage and catalytic activity as therapeutic targets in pediatric cancers, showing that inhibiting METTL1 synergizes with BCL-xL inhibitors.

TGS1 mediates mRNA 5'-cap trimethylation to promote oxidative phosphorylation in acute myeloid leukaemia.

This study identifies TGS1 as a methyltransferase that modifies mRNAs encoding mitochondrial proteins in AML, promoting oxidative phosphorylation and cell survival, and shows its potential as a therapeutic target.

The m6A motif is an anti-3' splice site

The paper shows that the m6A writer spares canonical 3' splice sites from methylation, allowing efficient splicing despite cotranscriptional methylation.

Modulator Resolves Transcript-, Allele-, and Condition-associated RNA Modification Differences from Direct RNA Sequencing

Modulator processes nanopore direct-RNA sequencing data to differentiate transcript-, allele-, and condition-associated RNA modifications, improving the analysis of RNA modifications in single molecules.

SPEAR: Spatial Epitranscriptomic Analysis by Mass Spectrometry Reveals Localized RNA Modification Remodeling During Glioma Progression

SPEAR combines laser microdissection and LC-MS/MS to enable spatial epitranscriptomic profiling of FFPE tissue, revealing RNA modification changes in glioma progression.

Metabolically encoded cell-surface glycoRNA remodeling enhances antitumor immunity

This study shows that tumor cells remodel cell-surface glycoRNA through metabolic reprogramming, impairing immune responses and linking glycoRNA to antitumor immunity and tumor progression.

A ribosomal pseudouridine drives an oncogenic translation program

The paper shows that SNORA81-guided pseudouridylation at a specific 28S rRNA site influences selective translation and ovarian cancer cell proliferation.

Queuosine glycosylation occurs after anticodon loop methylations and protects against stress-induced tRNA fragmentation

The paper investigates the hierarchical modification pathways of tRNA anticodon loop modifications and shows that Q34 glycosylation protects tRNAAsp from stress-induced fragmentation.

METTL3 inhibition attenuates the macrophage type I interferon response

This study shows METTL3 inhibition reduces macrophage type I interferon response, increasing susceptibility to coronavirus infection.

Genome-wide landscape of m6A regulatory genes in Marchantia polymorpha: conservation, diversification, and expression dynamics

The paper identifies and characterizes m6A-related gene families in Marchantia polymorpha, revealing conservation, diversification, and expression dynamics across developmental stages and stress conditions.

A Ribosomal RNA modification regulates translation of PI3K/AKT activators in high-grade serous ovarian carcinoma

This study identifies a ribosomal RNA modification regulated by SNORA81 that affects translation of PI3K/AKT activators in high-grade serous ovarian carcinoma.

A direct RNA sequencing workflow for simultaneous profiling of tRNA abundance and modifications in mouse liver

This paper introduces a direct RNA sequencing workflow to profile tRNA abundance and modifications in mouse liver, identifying key modification sites and isotype-specific patterns.

Dynamic 2'-O-Me of rRNA regulates ribosome translation in Arabidopsis nucleolin1 mutants and during seed-to-seedling transition

This study shows that 2'-O-Me modifications on rRNA are dynamically regulated during seed-to-seedling transition in Arabidopsis and affect ribosome translation.

N6-methyladenosine (m6A) RNA modifications control the antiviral response to influenza A virus infection by limiting IFITM2/3 expression

This study shows that m6A RNA modifications regulate antiviral gene expression by limiting IFITM2/3 expression during influenza A virus infection.

m6A-Driven Intratumoral Cholesterol Biosynthesis Fuels Castration-Resistant Prostate Cancer Progression

This study identifies a functional cooperation between nuclear pore complexes and m6A signaling that promotes castration-resistant prostate cancer by linking mRNA export to cholesterol biosynthesis and androgen production.

Epitranscriptomic profiling of VSMC phenotypes reveals uridine modifications linked to post-transcriptional regulation

The paper identifies uridine modifications in VSMCs linked to post-transcriptional regulation during atherogenic transitions using epitranscriptomic profiling.

Sub-stoichiometric modifications of Aplysia californica tRNAs and tRNA fragments revealed by integrating intact and bottom-up mass spectrometry

The paper maps sub-stoichiometric tRNA modifications in Aplysia californica using integrated mass spectrometry, revealing tissue-specific variations and a novel eukaryotic modification.

Stoichiometric m6A regulation of YY1 orchestrates the metabolic switch during cardiac development

The paper identifies a bimodal m6A code in cardiac development, showing how m6A stoichiometry and context regulate metabolic switches and gene expression.

RNabel-A Standalone Software Tool for Annotating Tandem Mass Spectra of Modified Ribonucleic Acids

RNabel is a software tool for annotating tandem mass spectra of modified RNAs, supporting various modifications and formats, and providing quality metrics for spectral analysis.

Activity-based profiling of bacterial RNA-modifying enzymes reveals species-specific 5-methyluridine modification in Bacillus subtilis 23S rRNA

This study adapts RNABPP-PS to identify RNA-modifying enzymes in bacteria, revealing species-specific 5-methyluridine modification in B. subtilis 23S rRNA.