RNA modifications and cancer

The paper investigates how RNA modifications affect protein-RNA interactions and introduces an algorithm to predict these effects.

This study investigates how METTL3 regulates RNGTT expression and activity, finding that METTL3 knockdown destabilizes RNGTT mRNA and reduces protein expression, with downstream effects on ribosomal protein capping and mTOR pathway disruption.

This study shows METTL3 reduces blood pressure by stabilizing RUNX1b mRNA via m6A modification, increasing eNOS expression in endothelial cells.

This study shows that RNA methylation, specifically m6A, regulates stress granule formation and function during erythropoiesis by modulating ATXN2 expression and RNA translation.

This paper shows YTHDF2 upregulation and nuclear relocation enhance CD8 T cell polyfunctionality and tumor immunity by regulating gene transcription and mitochondrial fitness.

The paper introduces Xron, a semi-supervised basecaller for detecting m6A methylation from nanopore sequencing by combining synthetic and experimental data.

This study shows that altering m6A regulators in glioma cells changes RNA biology, affecting gene expression, splicing, and signaling pathways.

This study identifies YTHDF proteins as key regulators of Alzheimer's disease brain gene signatures through m6A-dependent and independent mechanisms.

This study develops a timing-controllable m6A demethylation tool with reduced off-target effects by combining PUF RNA-binding proteins with m6A-erasers and a rapamycin-based switch.

The paper introduces an IVT-based method with dRNA-seq to detect RNA modifications across the transcriptome, identifying 26,619 modification sites and revealing non-random co-occurrence and isoform-specific patterns.

This study investigates RNA modification changes in HEK293T cells under 5-fluorouracil treatment using NAIL-MS, revealing dynamic modifications in tRNA and rRNA.

The paper shows that N1-methylation at position 9 of mt-Leu(UAA) stabilizes wild-type mt-tRNA but destabilizes pathogenic variants, suggesting methylation control could be therapeutic.

This study investigates whether METTL3-METTL14 or m6A modifications enhance Drosha-DGCR8-mediated microRNA processing, finding no general promotion effect.

This study identifies PDE1A as a promoter of NSCLC metastasis through interaction with YTHDF2 and activation of the STAT3 pathway.

This study examines the effects of CHMA1004, a METTL3/METTL14 activator, on anxiety, depression, and striatal gene expression in rats, finding increased locomotor activity and anxiolytic-like effects.

This paper introduces EpiPlex, a method for simultaneous mapping of multiple RNA modifications, demonstrating its application in analyzing m6A and inosine levels in HEK293T cells.

This study identifies YTHDF paralogs and VIRMA as major tumor drivers among m6A core genes through a pan-cancer analysis of 10,000 samples.

This paper introduces BACS, a method for single-base resolution pseudouridine quantification, and identifies {Psi} sites in human RNA and viral transcripts.

This paper reviews Oxford Nanopore Sequencing datasets for RNA modifications, finding that methylated data have lower mapping success rates and quality compared to non-methylated data, with artificial reference sequences performing better.

GenoM7GNet is a deep learning model for predicting N7-methylguanosine sites using a nucleotide language model, achieving high accuracy and outperforming existing methods.

This study identifies ZBTB48 as a regulator of FTO's substrate selectivity by facilitating its binding to m6A/m6Am-containing RNAs, affecting RNA decay and cancer cell growth.

This study identifies YTHDF1 as a driver of lung adenocarcinoma progression by promoting EEF1G translation through m6A-dependent mechanisms.

This study investigates the role of m6A RNA modification in synaptic function and ageing using a mouse model of synucleinopathy, finding age-related changes in m6A methylation of synaptic genes.

This study identifies peptide regions outside the YTH domain of ECT2 that regulate its m6A-RNA binding and shows structural elements enhance this interaction.

m6AConquer provides a unified framework for quantifying and integrating m6A detection techniques, improving data consistency and biological relevance across methods.

The paper identifies pseudouridine as a marker for germline small RNAs in plants and mammals, showing its role in epigenetic inheritance through nuclear transport.

This paper adapts nanopore sequencing basecalling models for modification detection using incremental learning and anomaly detection, achieving single-molecule and single-nucleotide resolution across multiple species and modification types.

This study shows that ALKBH5 and FTO promote ATF4 mRNA translation in sorafenib-treated hepatocarcinoma cells, contributing to chemoresistance.

This study shows YTHDF2 regulates inflammatory signaling in astrocytes during neurotoxic stress by modulating SEK1-JNK-cJUN pathway activation.