RNA modifications and cancer

This paper introduces rPAL, a method for detecting native sialoglycoRNAs with significantly improved sensitivity compared to existing methods, demonstrating its application in human clinical samples.

The paper shows that Vitamin C and transferrin reduce m6A levels and promote pluripotency in mouse ESCs by affecting FTO and m6A regulation.

This study identifies m6A RNA methylation by Mettl3 as essential for developmental pausing in mice by maintaining transcriptional dormancy through mRNA destabilization and suppression of N-Myc.

This study shows that METTL3 regulates chromatin modifiers via m6A-dependent mRNA degradation, affecting epithelial homeostasis and causing cutaneous and oral phenotypes.

The paper discusses alternative conclusions about Ythdf2's role in maternal RNA clearance and zebrafish embryo development, citing previous studies and raising interpretive caveats.

The paper investigates how RNA modifications m6A and 5hmC regulate gene expression in monocytes and macrophages during differentiation and polarization, finding their roles in transcript stability and function.

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

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

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.

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

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.

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.

The paper identifies NAD+ capping in archaeal and mycobacterial organisms, showing its prevalence in stationary phase and involvement of specific promoter elements.

The study reveals that m6A RNA methylation stabilizes maternal RNAs in mouse oocytes and promotes the degradation of 2-cell specific RNAs during early embryonic development.

The paper investigates the role of SNORD13 in rRNA acetylation across eukaryotes, showing its requirement in human and zebrafish but not in yeast or C. elegans.

The paper develops a targeted Nanopore direct rRNA sequencing approach to assess disease-associated rRNA modifications in human cells and tissues.

The paper identifies UHRF1, NSUN2, and NEIL1 as potential clinical biomarkers in prostate adenocarcinoma linked to disease progression through analysis of m5C and hm5C pathway regulators.

This study identifies SRSF7 as a novel m6A regulator that promotes glioblastoma cell proliferation and migration through m6A methylation of specific target mRNAs.

The paper introduces a method called SLAP to quantitatively assess m6A modification frequency in RNA with single-nucleotide resolution, applied to viral and cellular long non-coding RNAs.

This study profiles m6A-RNA methylomes across oyster development, revealing dynamic epitranscriptome regulation linked to developmental stages and gene expression.

The paper introduces MePAIso-seq2, a method to study m6A, alternative splicing, and poly(A) tailing, finding m6A affects splicing but not polyadenylation site choice and is associated with longer poly(A) tails.

Yanocomp predicts m6A modifications in Nanopore direct RNA reads by modeling adjacent kmers and accounting for outliers, enabling stoichiometry measurement and correlation with RNA processing events.

This study investigates the prognostic value of m6A regulators and their associated pathways in breast invasive cancer using public datasets.

This study identifies METTL8 as the enzyme responsible for 3-methylcytosine modification in human mitochondrial tRNAs and shows its role in tRNA folding.