RNA modifications and cancer

Single residues within the YTHDF intrinsically disordered region control m6A-dependent mRNA decay

This study identifies specific residues in the YTHDF2 IDR that regulate m6A-dependent mRNA decay using base-editor screens.

Pseudouridylation landscape across 42 nuclear-encoded S. cerevisiae tRNAs

The paper identifies 21 novel pseudouridine sites in S. cerevisiae tRNAs using DRS and BACS, and maps their modifying enzymes.

The RNA modification N6-methyladenosine restrains SIRPα to license myeloid efferocytosis in atherosclerosis

This study identifies the m6A-SIRP axis as a regulator of efferocytosis in atherosclerosis, showing myeloid m6A loss increases plaque instability.

Interrogating the Escherichia coli epitranscriptome via CRISPR interference and Nanopore native RNA sequencing

This study uses CRISPR interference and Nanopore sequencing to investigate RNA modifications in E. coli, revealing their impact on growth and protein pathways.

METTL3 promotes human coronavirus replication through an interferon-independent mechanism

This study shows METTL3 promotes human coronavirus replication without requiring interferon signaling.

LARP1-DM15/Sgt is a reader for cap-adjacent 2`-O-ribose methylation in TOP ribosomal protein mRNAs required for localization to synapses

RNA demethylase FTO uses conserved aromatic residues to recognize the mRNA 5' cap and promote efficient m6Am demethylation

This study identifies conserved aromatic residues in FTO that recognize the mRNA 5' cap and enhance m6Am demethylation, providing structural insights into FTO's selectivity for m6Am over m6A.

N6-methyladenosine promotes temozolomide resistance through non-canonical regulation of mRNA stability in glioblastoma cells

This study shows that m6A methylation stabilizes genes involved in temozolomide resistance in glioblastoma, and inhibiting METTL3 can restore drug sensitivity.

Single-molecule nanopore sequencing reveals spatial coordination of rRNA modifications in human ribosomes

This study uses single-molecule nanopore sequencing to analyze rRNA modifications in human cells, revealing local coordination of modifications and their response to drug treatment.

The m6A methyltransferase complex protein VIRMA engages hepatitis C virus RNA through a WTAP-independent mechanism

This study identifies VIRMA as an HCV RNA-targeting factor that recruits the m6A-MTC to the viral genome through a WTAP-independent mechanism.

Characterization of the N7 RNA cap methyltransferase from Trichomonas vaginalis and inhibitor discovery

The paper functionally and structurally characterizes RNA cap methyltransferases from Trichomonas vaginalis and identifies inhibitors targeting these enzymes.

Atlas of stress-induced changes in yeast tRNA modification levels

This study maps stress-induced changes in yeast tRNA modifications, revealing stress-specific reprogramming and introducing a metric to separate modification changes from tRNA abundance.

mBACS enhances pseudouridine profiling through efficient and robust chemical conversion

mBACS improves pseudouridine profiling with higher conversion efficiency and lower false positives, revealing new sites and functional insights into tRNA modifications.

Orphan C/D box snoRNAs modulate fear-related memory processes in mice

The paper identifies C/D box snoRNAs, including orphans, that are involved in fear-related memory processes in mice by modulating mRNA methylation and synaptic function.

Hakai links m6A RNA methylation to immune regulation in colorectal cancer

This study shows Hakai regulates m6A RNA methylation and immune response in colorectal cancer by interacting with VIRMA and affecting METTL3 localization.

Molecular basis of tRNA substrate recognition and modification by the atypical SPOUT methyltransferase Trm10

This study determines the structural basis of Trm10's specific tRNA methylation by capturing its post-catalytic states using cryo-EM and MD simulations.

N6-methyladenosine regulates Influenza A virus mRNA stability yet is rarely found on genomic RNA

This study shows that N6-methyladenosine (m6A) is abundant on IAV mRNAs but rare on genomic RNA, and m6A promotes mRNA stability and viral replication.

Temozolomide Induces Aberrant RNA Alkylation and Widespread Translational Repression

This study shows temozolomide causes RNA alkylation and widespread translational repression in glioblastoma cells by targeting guanine-rich transcripts.

A virus co-opts vector's m⁶A machinery for adaptive compensation

The paper shows TYLCV co-opts its vector's m6A machinery to enhance reproductive fitness in resistant whiteflies, revealing a mechanism for adaptive virus-vector interactions.

Modtector: Ultra-Fast Modification Signal Mining on Mapped Sequencing Reads

Modtector efficiently extracts RNA modification signals from sequencing data, outperforming existing tools on large datasets.

snoCLASH Reveals Extensive snoRNA-mRNA Interaction Networks

The paper introduces snoCLASH, a method to identify snoRNA-mRNA interactions, revealing thousands of interactions and validating a target with functional effects on protein expression.

ERFMTDA: Predicting tsRNA-disease associations using an enhanced rotative factorization machine

ERFMTDA predicts tsRNA-disease associations by modeling complex feature interactions and using a biologically informed negative sampling strategy, outperforming existing methods.

Structural and functional basis of the non-canonical human Dicer-tRNA complex

The paper reveals the structural basis of hDicer-tRNA complex formation and shows that m5C modification facilitates tRNA cleavage by hDicer.

Direct RNA sequencing reveals selective remodeling of the host m6A epitranscriptome during Leishmania infection

This study uses direct RNA sequencing to show that Leishmania infection remodels the host m6A epitranscriptome, affecting immune and metabolic transcripts.

TriTower-m6Am: a triple-tower heterogeneous deep learning architecture integrating semantic, sequential, and structural information for N6,2-O-dimethyladenosine site prediction

TriTower-m6Am improves m6Am site prediction by integrating semantic, sequential, and structural RNA features, achieving higher sensitivity than existing methods.

Reversible m6Am methylation of snRNA by FTO controls morphine reward and tolerance without altering analgesia

This study shows that FTO regulates morphine reward and tolerance through m6Am methylation of snRNA, without affecting analgesia.

Integrated sequencing approach to probe rRNA modification landscape during human embryonic stem cell differentiation

The paper identifies dynamic changes in rRNA modifications during human embryonic stem cell differentiation using Nanopore sequencing and snoRNA profiling.

Dual-site specificity of the archaeal tRNA m2G methyltransferase Trm14

This study shows that the archaeal Trm14 methyltransferase modifies both m2G6 and m2G67 in tRNAs and that these modifications are important for growth at high temperatures.

Mechanosensitive Endothelial METTL7A Regulates Internal m7G mRNA Methylation and Protects Against Atherosclerosis

This study identifies METTL7A as a mechanosensitive methyltransferase that regulates internal m7G methylation in endothelial cells, protecting against atherosclerosis through stabilization of anti-inflammatory transcripts.

RNA m6A demethylase ALKBH4 governs whitefly development

This study identifies ALKBH4 as an m6A demethylase in whiteflies, showing its role in reversing mRNA methylation and regulating development.