RNA modifications and cancer

Profiling of N6-methyladenosine dynamics indicates regulation of oyster development by m6A-RNA epitranscriptomes

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

Interactions between RNA m6A modification, alternative splicing, and poly(A) tail revealed by MePAIso-seq2

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.

SnoRNA guide activities-real and ambiguous

The paper tests guide RNA activities for snoRNAs and scaRNAs in yeast and vertebrates, finding that some guide RNAs induce modifications in artificial substrates but not endogenous RNAs.

Mapping of pseudouridine residues on cellular and viral transcripts using a novel antibody-based technique

The paper introduces PA-{Psi}-seq, a technique to map pseudouridine residues on cellular and viral transcripts, and shows that HIV-1 transcripts are not affected by PUS enzyme inactivation.

Acute depletion of METTL3 identifies a role for N6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome

The paper shows that m6A modification affects alternative intron/exon inclusion in nascent RNA by disrupting splicing when METTL3 is depleted.

m6A RNA methylation regulates promoter proximal pausing of RNA Polymerase II

This study shows that m6A RNA methylation regulates RNAP II promoter-proximal pausing, affecting gene expression and transcription.

Detection of differential RNA modifications from direct RNA sequencing of human cell lines

This paper introduces xPore, a method to detect differential RNA modifications from direct RNA sequencing, showing it identifies m6A sites with single base resolution and quantifies modification rate differences across cell lines.

Methyltransferase-like 3 modulates severe acute respiratory syndrome coronavirus-2 RNA N6-methyladenosine modification and replication

This study shows that SARS-CoV-2 RNA undergoes N6-methyladenosine modification, and host METTL3 interacts with viral RdRp to modulate viral replication.

The m6A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication.

The paper maps m6A modifications on PAN RNA during KSHV infection and identifies regulators of these modifications.

Yanocomp: robust prediction of m6A modifications in individual nanopore direct RNA reads.

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.

Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning

The paper improves m6A RNA modification detection using miCLIP2 and m6Aboost, identifying thousands of high-confidence sites in human and mouse cells without requiring Mettl3 depletion.

A comprehensive investigation of m6A regulators prognostic value and associated molecular pathways in breast invasive cancer

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

Epitranscriptomic editing of the RNA N6-methyladenosine modification by dCasRx conjugated methyltransferase and demethylase

This study develops a dCasRx-based platform to edit m6A RNA modifications and demonstrates its use in studying m6A-binding protein functions.

Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships

The paper quantifies snoRNA abundance across seven human tissues and identifies two distinct abundance classes with different host gene relationships and regulatory features.

N6-methyladenosine RNA modification regulates strawberry fruit ripening in an ABA-dependent manner

This study shows that N6-methyladenosine (m6A) RNA modification regulates strawberry fruit ripening through the ABA pathway, differing from its role in climacteric tomato fruit.

Quantitative profiling of native RNA modifications and their dynamics using nanopore sequencing

The paper introduces a method to quantify RNA modifications using nanopore sequencing, revealing novel modification sites and dynamics in yeast under environmental stress.

METTL8 is required for 3-methylcytosine modification in human mitochondrial tRNAs

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

Small-molecule inhibitors of the RNA m6A demethylase FTO potently support the survival of dopamine neurons

This study develops small-molecule FTO inhibitors that enhance dopamine neuron survival and show BBB penetration, with greater potency than existing AlkBH5 inhibitors.

Nuclear RNA-acetylation can be erased by the deacetylase SIRT7

The paper identifies NOP58 as a reader and SIRT7 as an eraser of the RNA acetylation ac4C, showing SIRT7 can deacetylate RNA in vitro and affecting snoRNA function and pre-rRNA processing.

Characterizing RNA Pseudouridylation By Convolutional Neural Networks

This study introduces PULSE, a deep learning model that predicts pseudouridylation sites and characterizes their sequence features using convolutional neural networks.

Epitranscriptomic addition of m6A regulates HIV-1 RNA stability and alternative splicing

This paper shows that m6A methylation regulates HIV-1 RNA stability and alternative splicing through YTHDC1 and YTHDF2.

Epitranscriptomic Dysregulation in Stress-induced Psychopathologies

This paper reviews the role of m6A epitranscriptomic dysregulation in stress-induced psychiatric disorders using bioinformatic analysis of single-cell and bulk RNA-seq datasets.

Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation

The paper investigates the subcellular relocalization of TRMT1 and TRMT1L during neuronal activation and identifies their role in RNA modification dynamics and neuronal plasticity.

Loss of Cnot6l impairs inosine RNA modifications in mouse oocytes

The paper investigates inosine RNA modifications in oocytes from Cnot6l-/- and Btg4-/- mice, finding depletion of inosine modifications in Cnot6l-/- oocytes, suggesting a novel mRNA clearance mechanism.

The pseudouridine synthase dyskerin binds to cytoplasmic H/ACA-box snoRNA retaining transcripts affecting nuclear hormone receptor dependence

The paper identifies dyskerin's role in regulating mRNA expression and nuclear hormone receptor dependence through snoRNA-retaining transcripts in breast cancer.

N6-methyladenosine (m6A) is an endogenous A3 adenosine receptor ligand

The paper identifies m6A as an endogenous ligand for the A3 adenosine receptor, showing it has higher affinity than unmodified adenosine and plays a role in type I allergy.

Identification of m6A residues at single-nucleotide resolution using eCLIP and an accessible custom analysis pipeline

The paper introduces an improved eCLIP method called m6A-eCLIP (meCLIP) that enables precise identification of m6A residues at single-nucleotide resolution with reliable confidence metrics.

Broad-range RNA modification analysis of complex biological samples using rapid C18-UPLC-MS

The paper introduces a rapid UPLC-MS method for analyzing RNA modifications in complex samples, demonstrating its effectiveness across different organisms.

Translational adaptation to heat stress is mediated by 5-methylcytosine RNA modification in Caenorhabditis elegans

This study shows that m5C RNA modification in C. elegans affects translation efficiency and adaptation to heat stress by modulating leucine and proline decoding.

Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing

The paper uses direct RNA long-read sequencing to show m6A modifications on adenovirus RNA are necessary for efficient splicing.