ArticleCell systems2025
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line.
Article in Cell systems, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed.
- Reduced sensitivity to RNA structural differences distinguishes eukaryotic Pus4 from bacterial TruB.RNA (New York, N.Y.) · 2026Article
- Epigenetic landscapes of classical psychedelics and ketamine: molecular mechanisms of long-lasting neuromodulation.Molecular psychiatry · 2026Review
- NanoCortex: A Unified Agentic System for Nanopore Sequencing Analysis.bioRxiv : the preprint server for biology · 2026Article
- Assessment of nanopore RNA modification calling in human cell lines and synthetic systems.Genome biology · 2026Article
- Multimodal profiling reveals cell type-specific pseudouridine modification and density-dependent translational regulation.Nucleic acids research · 2026Article
- The new era of single-molecule RNA modification detection through nanopore base-calling models.Nature reviews. Molecular cell biology · 2026Review
- Nano-Mod-Amp reveals RNA sequence, structural and cell type specific features of pseudouridylation by PUS7.bioRxiv : the preprint server for biology · 2025Article
- Pseudouridine reprogramming in the human T-cell epitranscriptome: from primary to immortalized states.RNA (New York, N.Y.) · 2025Article
- mRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Chemical modifications in mRNAs, such as pseudouridine (psi), can control gene expression. Yet, we know little about how they are regulated, especially in neurons. We applied nanopore direct RNA sequencing to investigate psi dynamics in SH-SY5Y cells in response to two perturbations that model a natural and unnatural cellular state: retinoic-acid-mediated differentiation (healthy) and exposure to the neurotoxicant lead (unhealthy). We discovered that the expression of some psi writers changes significantly in response to physiological conditions. We also found that globally, lead-treated cells have more psi sites but lower relative occupancy than untreated cells and differentiated cells. Examples of highly plastic sites were accompanied by constant expression for psi writers, suggesting trans-regulation. Many positions were static throughout all three cellular states, suggestive of a "housekeeping" function. This study enables investigations into mechanisms that control psi modifications in neurons and their possible protective effects in response to cellular stress.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.