RNA modifications and cancer

Limited effects of m6A modification on mRNA partitioning into stress granules

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

Exon-intron architecture determines mRNA stability by dictating m6A deposition

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.

The RNA demethylase FTO controls m6A marking on SARS-CoV-2 and classifies COVID-19 severity in patients

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

Conserved reduction of m6A marks during aging and neurodegeneration is linked to altered translation of synaptic transcripts

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.

Discovery of synapse-specific RNA N6-methyladenosine readers associated with the consolidation of fear extinction memory

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

Selective detection of m6A derived from mRNA using the Phospho-tag m6A assay

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

RNA modification mapping with JACUSA2

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.

Identification of a motif in Trm732 required for 2'-O-methylation of the tRNA anticodon loop by Trm7

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

Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling

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: a novel random forest-based algorithm for tRNA-derived fragment target prediction

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

Prediction of m6A and m5C at single-molecule resolution reveals a cooccurrence of RNA modifications across the transcriptome

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

CMTr cap-adjacent 2`-O-ribose mRNA methyltransferases are required for reward learning and mRNA localization to synapses

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

Epitranscriptomic reprogramming is required to prevent stress and damage from acetaminophen

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

The m6A reader YTHDF2 is a negative regulator for dendrite development and maintenance of retinal ganglion cells

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

Systematic mapping of rRNA 2'-O methylation during frog development and involvement of the methyltransferase Fibrillarin in eye and craniofacial development in Xenopus laevis

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.

Human tRNA methyltransferase ALKBH8 targets wider repertoire of tRNAs and non-coding RNAs

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.

DENA: training an authentic neural network model using Nanopore sequencing data of Arabidopsis transcripts for detection and quantification of N6-methyladenosine on RNA

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: A Machine Learning Framework for Transcriptome-Wide Single Molecule Mapping of 2{acute}-O-Methylation (Nm) Sites in Nanopore Direct RNA Sequencing Datasets

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.

NAD+ capping of RNA in Archaea and Mycobacteria

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

The dual role of N6-methyladenosine on mouse maternal RNAs and 2-cell specific RNAs revealed by ULI-MeRIP sequencing

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.

RNA modifications detection by comparative Nanopore direct RNA sequencing

The paper introduces Nanocompore, a method to detect RNA modifications using Nanopore direct RNA sequencing, validated on human polyA+ RNAs and non-coding RNAs.

Probing small ribosomal subunit RNA helix 45 acetylation across eukaryotic evolution

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.

Deep assessment of human disease-associated ribosomal RNA modifications using Nanopore direct RNA sequencing

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

UHRF1, NSUN2, and NEIL1 were Detected as Clinical Biomarker Candidates in Prostate Adenocarcinoma with Potential Roles in Disease Pathogenesis

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.

Direct RNA sequencing reveals SARS-CoV-2 m6A sites and possible differential DRACH motif methylation among variants

The paper uses direct RNA sequencing to identify m6A sites and analyze DRACH motif methylation differences in SARS-CoV-2 variants.

Serine/arginine-rich splicing factor 7 plays oncogenic roles through specific regulation of m6A RNA modification

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

The Arabidopsis m6A-binding proteins ECT2 and ECT3 bind largely overlapping mRNA target sets and influence target mRNA abundance, not alternative polyadenylation

The paper identifies overlapping mRNA targets of ECT2 and ECT3 using HyperTRIBE and shows they regulate target mRNA abundance, not alternative polyadenylation.

Principles of mRNA targeting via the Arabidopsism6A-binding protein ECT2

The paper identifies ECT2 binding sites in Arabidopsis m6A-containing mRNAs using iCLIP and HyperTRIBE, revealing sequence preferences and competition with other RNA-binding proteins.

Precise Regulation and Site-specifically Covalent Labeling of NSUN2 Enable by Genetic Encoding Expansion

The paper demonstrates the synthesis of modified lysines and their use in creating a system to specifically label NSUN2, enabling precise regulation and fluorescent labeling of the enzyme.

Determination of m6A frequency utilizing 4SedTTP-RT Ligation Assisted PCR (SLAP) in viral and cellular long non-coding RNAs

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.