ArticleRNA (New York, N.Y.)2021
Mapping of pseudouridine residues on cellular and viral transcripts using a novel antibody-based technique.
Article in RNA (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 32 citations in OpenAlex.
- Ψ-Atlas: An Integrated Atlas for Pseudouridine Epitranscriptome.Genomics, proteomics & bioinformatics · 2026Article
- A nanopore-based HIV-1 reference epitranscriptome.Nucleic acids research · 2026Article
- Epitranscriptomic signatures of m5C, m6A, and pseudouridine in COVID-19 reveal host RNA modifications involved in viral pathogenesis.Microbiology spectrum · 2026Article
- Mechanistic insight into the pseudouridylation of RNA.RNA biology · 2025Review
- Pseudouridylation of 7SK by PUS7 regulates Pol II transcription elongation.Nature communications · 2025Article
- Pseudouridine prevalence in Kaposi's sarcoma-associated herpesvirus transcriptome reveals an essential mechanism for viral replication.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Resolving sequencing-based HIV-1 epitranscriptomics.Epigenomics · 2025Review
- RNA Through Time: From the Origin of Life to Therapeutic Frontiers in Transcriptomics and Epitranscriptional Medicine.International journal of molecular sciences · 2025Review
- Pseudouridine guides germline small RNA transport and epigenetic inheritance.Nature structural & molecular biology · 2025Article
- Role of the epitranscriptome in viral infections: beneficial or detrimental?Memorias do Instituto Oswaldo Cruz · 2025Review
- Past, Present, and Future of RNA Modifications in Infectious Disease Research.ACS infectious diseases · 2024Article
- Epitranscriptomic cytidine methylation of the hepatitis B viral RNA is essential for viral reverse transcription and particle production.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- New directions for Ψ and mRNA (New York, N.Y.) · 2024Article
- RNPS1 stabilizes NAT10 protein to facilitate translation in cancer via tRNA acInternational journal of oral science · 2024Article
- Advantages and challenges associated with bisulfite-assisted nanopore direct RNA sequencing for modifications.RSC chemical biology · 2023Article
- Control of protein synthesis through mRNA pseudouridylation by dyskerin.Science advances · 2023Article
- The regulation of antiviral innate immunity through non-mFrontiers in immunology · 2023Review
- The hidden RNA code: implications of the RNA epitranscriptome in the context of viral infections.Frontiers in genetics · 2023Review
- Role of Epitranscriptomic and Epigenetic Modifications during the Lytic and Latent Phases of Herpesvirus Infections.Microorganisms · 2022Review
- The plant epitranscriptome: revisiting pseudouridine and 2'-O-methyl RNA modifications.Plant biotechnology journal · 2022Review
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Pseudouridine (Ψ) is the most common noncanonical ribonucleoside present on mammalian noncoding RNAs (ncRNAs), including rRNAs, tRNAs, and snRNAs, where it contributes ∼7% of the total uridine level. However, Ψ constitutes only ∼0.1% of the uridines present on mRNAs and its effect on mRNA function remains unclear. Ψ residues have been shown to inhibit the detection of exogenous RNA transcripts by host innate immune factors, thus raising the possibility that viruses might have subverted the addition of Ψ residues to mRNAs by host pseudouridine synthase (PUS) enzymes as a way to inhibit antiviral responses in infected cells. Here, we describe and validate a novel antibody-based Ψ mapping technique called photo-crosslinking-assisted Ψ sequencing (PA-Ψ-seq) and use it to map Ψ residues on not only multiple cellular RNAs but also on the mRNAs and genomic RNA encoded by HIV-1. We describe 293T-derived cell lines in which human PUS enzymes previously reported to add Ψ residues to human mRNAs, specifically PUS1, PUS7, and TRUB1/PUS4, were inactivated by gene editing. Surprisingly, while this allowed us to assign several sites of Ψ addition on cellular mRNAs to each of these three PUS enzymes, Ψ sites present on HIV-1 transcripts remained unaffected. Moreover, loss of PUS1, PUS7, or TRUB1 function did not significantly reduce the level of Ψ residues detected on total human mRNA below the ∼0.1% level seen in wild-type cells, thus implying that the PUS enzyme(s) that adds the bulk of Ψ residues to human mRNAs remains to be defined.
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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 OpenQuestion graph.