RNA modifications and cancer

Rapid and sensitive detection of native glycoRNAs

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.

Vitamin C and Transferrin Reduce RNA Methylation in Mouse Embryonic Stem Cells

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

The importance of m6A topology in chicken embryo mRNA; a precise mapping of m6A at the conserved chicken β-actin zipcode

The paper maps and quantifies m6A sites in the chicken β-actin zipcode using MeRIPSeq and an antibody-independent assay, showing m6A's role in regulating ZBP1 binding and localized translation.

FUS modulates the level of ribosomal RNA modifications by regulating a subset of snoRNA expression

This study shows FUS regulates snoRNA expression, affecting rRNA modifications like 2-O-Me and pseudouridylation, which may contribute to ALS pathology.

The landscape of m1A modification and its posttranscriptional regulatory functions in primary neurons

The paper investigates m1A RNA modification in neurons under normal and OGD/R conditions, identifying its regulatory roles in noncoding RNAs and ceRNA mechanisms.

The ribose methylation enzyme FTSJ1 has a conserved role in neuron morphology and learning performance

The paper identifies a novel FTSJ1 pathogenic variant and shows its role in neuron morphology and learning performance through RiboMethSeq and transcriptome analysis in human and Drosophila models.

m6A RNA methylation orchestrates transcriptional dormancy during developmental pausing

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.

YTHDF2 in dentate gyrus is the m6A reader mediating m6A modification in hippocampus-dependent learning and memory

This study identifies YTHDF2 in the dentate gyrus as the m6A reader mediating hippocampus-dependent learning and memory by regulating mossy fiber development.

Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct and long-read sequencing

The paper develops a semi-quantitative method to detect pseudouridine modifications in human mRNAs using long-read nanopore sequencing and validates it with synthetic RNA controls.

Transcriptome-wide analysis of pseudouridylation in Drosophila melanogaster

The paper performs transcriptome-wide pseudouridylation analysis in Drosophila melanogaster, identifying thousands of Psi modifications across rRNAs, mRNAs, and non-coding RNAs, with implications for ribosome and mitochondrial function.

METTL3 maintains epithelial homeostasis through m6A-dependent regulation of chromatin modifiers

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

Global loss of cellular m6A RNA methylation following infection with different SARS-CoV-2 variants

The paper shows SARS-CoV-2 variants reduce m6A RNA methylation in host cells, affect METTL3 localization, and impair stress granules, with XPO1 inhibition reversing some effects.

ythdf2(ch200) and its role in development of the early zebrafish embryo

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

A single N6-methyladenosine site in lncRNA HOTAIR regulates its function in breast cancer cells

This study identifies an m6A modification in HOTAIR lncRNA that regulates its function in breast cancer by affecting chromatin localization and gene expression.

m6A epitranscriptomic modification regulates neural progenitor-to-glial cell transition in the retina

This study shows that m6A modification regulates the transition from retinal progenitor cells to glial cells, affecting retinal development and function.

Cerebrospinal fluid and blood profiles of transfer RNA fragments show age, sex and Parkinson's disease-related changes

The paper examines tRF levels in CSF and blood across age, sex, and Parkinson's disease, finding distinct patterns and suggesting their potential as biomarkers.

Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework

This paper introduces m6Anet, a Multiple Instance Learning framework for detecting m6A methylation from direct RNA sequencing data, achieving performance comparable to experimental methods without retraining.

RNA m6A and 5hmC regulate monocyte and macrophage gene expression programs

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.

7SK methylation Promotes Transcriptional Activity

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.

N6-Adenosine Methylation of a Single Site in SARS-CoV-2 5'-UTR Promotes Translation

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

Human NOP2/NSUN1 Regulates Ribosome Biogenesis Through Non-Catalytic Complex Formation with Box C/D snoRNPs.

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.

m6A-TSHub: unveiling the context-specific m6A methylation and m6A-affecting mutations in 23 human tissues

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.

Expression of m6A RNA methylation markers in the hypothalamus of Atlantic salmon

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.

m6A is required for resolving progenitor identity during planarian stem cell differentiation

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

The S. cerevisiae m6A-reader Pho92 impacts meiotic recombination by controlling key methylated transcripts

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.

Initiator tRNA lacking 1-methyladenosine is unexpectedly targeted by the rapid tRNA decay pathway in evolutionarily distant yeast species

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.

Understanding the source of METTL3-independent m6A in mRNA

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.

NMDAR mediated dynamic changes in m6A inversely correlates with neuronal translation

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

tRNA Analysis of eXpression (tRAX): A tool for integrating analysis of tRNAs, tRNA-derived small RNAs, and tRNA modifications

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

Penguin: A Tool for Predicting Pseudouridine Sites in Direct RNA Nanopore Sequencing Data

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.