RNA modifications and cancer

RNA m6A Methylation Control Salt Response by Affecting Photosynthesis Capacity

This study shows that m6A methylation affects photosynthesis capacity and salt tolerance in Arabidopsis by altering gene expression and chloroplast function under salt stress.

Temporal and spatial profiling of ALKBH5 activity through NAIL-MS and compartmentalized RNA Isolation

This study uses NAIL-MS to investigate ALKBH5's role in m6A demethylation in vivo, finding no significant effect on m6A dynamics or spatial distribution in HEK 293T cells.

Isoform-level profiling of m6A epitranscriptomic signatures in human brain

The paper uses Oxford Nanopore DRS to profile m6A modifications at the isoform level in human brain regions, identifying thousands of m6A sites and region-specific patterns.

CRISPR RiPCA for Investigating eIF4E-m7GpppX Capped mRNA Interactions

This paper introduces CRISPR RiPCA, a platform combining CRISPR and live-cell RNA-protein interaction assays to measure inhibitor activity against eIF4E-m7GpppX interactions relevant to cancer drug discovery.

DNA-encoded Library Screening Uncovers Potent DNMT2 Inhibitors Targeting a Cryptic Allosteric Binding Site

This study identifies potent DNMT2 inhibitors through DNA-encoded library screening, revealing a cryptic allosteric binding site and optimizing an inhibitor with low nanomolar affinity.

Accurate detection and quantification of single-base m6A RNA modification using nanopore signals with multi-view deep learning

MultiNano uses multi-view deep learning to accurately detect and quantify m6A RNA modifications from Nanopore DRS signals, achieving state-of-the-art performance in multiple tasks.

MoDorado: Enhanced detection of tRNA modifications in nanopore sequencing by off-label use of modification callers

The paper introduces MoDorado, an algorithm that detects tRNA modifications beyond those trained in existing models, identifying seven new modifications in S. pombe.

Epitranscriptome analysis of HeLa-expressed HPV18 early transcripts

The paper identifies candidate m6A modification sites on HPV18 early transcripts in HeLa cells using RNA sequencing and perturbation experiments.

RNA Methylation dynamics regulates cancer stemness through modulation of cell migration and cell proliferation in the spheroidal model of TNBC

This study investigates the role of m6A regulators WTAP and FTO in TNBC cell proliferation, migration, and stemness using 2D and 3D cultures, finding m6A modulates cell cycle and EMT markers and CSC markers.

No phenotypes in Ttc22 knockout mice

This paper investigates the effects of Ttc22 knockout in mice and finds no significant phenotypes in development, fertility, or colon cancer induction.

tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa

The paper profiles tRNA modifications in Pseudomonas aeruginosa to uncover regulatory networks and validate gene annotations.

ModiDeC: a multi-RNA modification classifier for direct nanopore sequencing

ModiDeC is a deep-learning classifier that identifies multiple RNA modifications from direct nanopore sequencing, validated on synthetic data and biological samples.

The knockdown of the snoRNA-jouvence blocks the cell proliferation and leads to cell death of human primary cancerous glioblastoma cells

This study shows that knocking down snoRNA-jouvence in human glioblastoma cells reduces proliferation and induces apoptosis, suggesting it as a potential therapeutic target.

Direct RNA Oxford Nanopore sequencing distinguishes between modifications in tRNA at the U34 position

The paper develops methods to distinguish tRNA modifications at the U34 position using Oxford Nanopore sequencing, showing its potential for accurate modification detection.

A transfer RNA methyltransferase with an unusual domain composition catalyzes 2'-O-methylation at position 6 in tRNA

This paper identifies TrmTS as a tRNA methyltransferase that catalyzes 2'-O-methylation at position 6 in tRNA, extending knowledge of tRNA methyltransferase architecture.

Single-nucleotide Resolution Epitranscriptomic Profiling Uncovers Dynamic m6A Regulation in Bovine Preimplantation Development

This study uses SAC-seq to map m6A modifications at single-nucleotide resolution in bovine preimplantation embryos, identifying a critical m6A site in RPL12 that regulates translation and development.

O-GlcNAcylation-Ubiquitin Crosstalk of METTL1 Drives m7G Epitranscriptomic Collapse and Lipid Metabolic Reprogramming in Diabetic Cardiomyopathy

This study identifies METTL1 O-GlcNAcylation and ubiquitination as key regulators of m7G modification and lipid metabolism in diabetic cardiomyopathy, with a drug targeting this pathway showing therapeutic potential.

IGF2BP3 Promotes Autophagy-Mediated TNBC Metastasis via M6A-Dependent, Cap-Independent c-Met Translation

This study identifies IGF2BP3's role in promoting TNBC metastasis through m6A-dependent, cap-independent c-Met translation via autophagy.

A Comparative Evaluation of Computational Models for RNA modification detection using Nanopore sequencing with RNA004 Chemistry

This study compares two RNA modification detection models, Dorado and m6Anet, using RNA004 sequencing data, finding Dorado has higher recall but both have high false discovery rates for m6A and pseudouridine.

Passive shaping of intra- and intercellular m6A dynamics via mRNA metabolism

The paper introduces a differential model m6ADyn to predict m6A dynamics by integrating mRNA metabolism and validates its predictions through experimental confirmation.

Recognition and catalytic mechanism of tRNA m3C methyltransferase METTL6

This study defines the mechanism by which METTL6 and SerRS cooperatively recognize and catalyze tRNA m3C methylation using simulations and in vitro experiments.

Gut Commensal Bacteria-Derived Methionine is Required for Host Reproduction by Modulating RNA m6A Methylation of the Insulin Receptor

This study shows that gut bacteria provide methionine, which modulates RNA m6A methylation of the insulin receptor, thereby promoting host reproduction in Bactrocera dorsalis.

Post-transcriptional Modifications of the Large Ribosome Subunit Assembly Intermediates in E. coli Expressing Helicase-Inactive DbpA Variant

The paper develops a method to detect RNA post-transcriptional modifications in E. coli ribosomal RNA without chemical treatment, identifying modification incorporation times in ribosome assembly intermediates.

Selective Biogenesis and Structural Diversity Shape tRNA-Derived Fragment Landscapes across Mouse Organs

The paper analyzes tDRs across seven mouse tissues, identifying tissue-specific enrichment, diversity, and structural features of tDRs.

Direct RNA nanopore sequencing reveals rapid RNA modification changes following glucose stimulation of human pancreatic beta-cell lines

The paper uses direct RNA nanopore sequencing to identify RNA modification changes in human pancreatic beta-cells after glucose stimulation, finding 1,697 differentially modified sites linked to type 2 diabetes genes.

Loss of Ythdf3 causes Danon disease-like features

This study shows that loss of Ythdf3 in mice causes Danon disease-like features due to impaired Sox9 mRNA decay, and targeted therapy with AAV-shRNA against Sox9 improves disease outcomes.

Depletion of rRNA Methyltranferase METTL5 Enhances Anti-Tumor Immune Response via Neoantigen Generated from Cryptic Translation

This study shows that inhibiting METTL5 increases neoantigen production and enhances anti-tumor immunity through non-canonical translation in murine models.

Differential requirement of m6A reader proteins, IGF2BP2 and HNRNPA2B1 for the processing of N6-methyladenosine modified H19 lncRNA: Stability versus miR-675 biogenesis

This study shows that m6A reader proteins IGF2BP2 and HNRNPA2B1 differentially regulate H19 lncRNA processing, with IGF2BP2 enhancing stability and HNRNPA2B1 promoting miR-675 biogenesis, which drives glioma cell migration.

HAMRLNC: A Comprehensive Pipeline for High-throughput Analysis of Modified Ribonucleotides and Long Non-Coding Ribonucleic Acids

HAMRLNC is a computational pipeline for analyzing RNA-seq data to quantify transcript abundance, infer RNA modifications, and annotate lncRNAs, producing labeled figures for visualization.

RBM15-MKL1 fusion protein promotes leukemia via m6A methylation and WNT pathway activation

This study shows that the RBM15-MKL1 fusion protein drives leukemia through m6A methylation and WNT pathway activation, with METTL3 inhibition reducing tumor growth.