RNA modifications and cancer

The paper shows that m6A methylation of 7SK RNA promotes transcriptional activity in response to growth factor stimulation by releasing the HEXIM1/P-TEFb complex.

The paper shows that a single m6A modification in SARS-CoV-2 5'-UTR enhances translation by destabilizing a stem loop and increasing accessibility.

The paper identifies NOP2/NSUN1's role in ribosome biogenesis by showing it deposits m5C on 28S rRNA and forms non-catalytic complexes with box C/D snoRNAs, which is not essential for rRNA processing.

The paper introduces m6A-TSHub, a platform that provides m6A methylation sites and mutations across 23 human tissues and 25 tumor conditions, enabling tissue-specific analysis of m6A regulation.

The paper investigates m6A RNA methylation gene expression in Atlantic salmon hypothalamus, finding differential expression of m6A reader and eraser genes associated with sexual maturation timing.

This study shows that m6A modification is essential for planarian stem cell differentiation and tissue regeneration by regulating histone variant transcription and chromatin modifications.

This study shows that the m6A-reader Pho92 in S. cerevisiae promotes meiotic progression by accelerating the down-regulation of specific mRNAs during meiotic recombination.

The paper shows that the rapid tRNA decay pathway is involved in degrading tRNAiMet(CAU) lacking m1A58 in both S. pombe and S. cerevisiae, challenging previous assumptions about tRNA decay mechanisms.

The paper investigates the source of METTL3-independent m6A in mRNA, finding that most m6A is due to METTL3 and that apparent knockouts often have altered but functional METTL3 isoforms.

The paper shows that NMDAR stimulation increases m6A levels and inhibits translation, linking m6A dynamics to neuronal translation regulation.

tRAX is a tool for analyzing tRNAs and tRNA-derived small RNAs, demonstrating its effectiveness in characterizing these transcriptomes in mouse tissues.

Penguin is a tool that uses machine learning to predict pseudouridine sites in direct RNA nanopore sequencing data, achieving high accuracy compared to existing methods.

The paper investigates the role of m6A modification in mRNA partitioning into stress granules and finds that m6A has limited effects on this process.

The paper shows that m6A methylation is excluded near exon-intron junctions and is determined by m6A motifs and exon-intron architecture, linking mRNA stability to splicing memory.

This study shows that FTO affects m6A marking on SARS-CoV-2 RNA and correlates with COVID-19 severity in patients.

The paper examines m6A RNA methylation changes in mouse and human brains during aging and Alzheimer's disease, finding reduced m6A levels in synaptic transcripts and impaired synaptic protein synthesis.

The paper identifies synapse-specific m6A RNA readers and their role in fear extinction memory consolidation through RNA immunoprecipitation and sequencing in mice.

The paper introduces a method to specifically detect m6A in mRNA from total RNA samples, addressing biases from mRNA purification protocols.

The paper introduces JACUSA2, a software framework for analyzing RNA modification data from multiple sequencing platforms and experimental conditions, demonstrating its use on m6A detection datasets.

The paper identifies a conserved motif in Trm732 essential for tRNA 2'-O-methylation by Trm7 in yeast and its human homolog THADA.

The paper develops a method to profile single-molecule RNA modifications in yeast rRNA, revealing concerted modifications at functional centers and subpopulation changes in ribosome biogenesis.

tRForest improves tRNA fragment target prediction using random forest, validated in cell lines and showing enrichment in neuronal function.

CHEUI predicts m6A and m5C modifications at single-molecule resolution, revealing co-occurrence of these modifications in mRNAs across cell lines and tissues.

This study identifies CMTr1 and CMTr2 as cap-adjacent 2'-O-ribose methyltransferases essential for reward learning and synaptic mRNA localization in Drosophila.

This study shows that acetaminophen induces epitranscriptomic reprogramming, and Alkbh8 is critical for regulating selenoprotein production and mitigating APAP toxicity.

This study shows YTHDF2 negatively regulates RGC dendrite development and maintenance, with its knockout improving visual acuity and protecting against glaucoma in mice.

This study investigates the role of fibrillarin in ribosome biogenesis and its impact on neural crest cell development in Xenopus laevis, revealing developmental defects and hypomethylation patterns in rRNA.

The paper identifies new RNA targets of ALKBH8, including additional tRNAs and non-coding RNAs, through transcriptome-wide analysis using HITS-CLIP-seq and RIP-seq.

The paper introduces DENA, a neural network model trained on Nanopore sequencing data to detect and quantify N6-methyladenosine (m6A) in RNA, showing high accuracy in Arabidopsis and consistency with human data.

Nm-Nano predicts Nm sites in Nanopore RNA sequencing data with high accuracy, identifying frequently modified genes in human cell lines and their biological roles.