ArticleMethods in enzymology2015
Pseudo-Seq: Genome-Wide Detection of Pseudouridine Modifications in RNA.
Article in Methods in enzymology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 70 citations in OpenAlex.
- Post-transcriptional regulatory networks: The dynamic interplay of RNA-binding proteins.The FEBS journal · 2026Review
- Hidden in plain sight: illuminating the tRNA landscape by sequencing.Genome biology · 2026Review
- Investigating RNA dynamics from single molecule transcriptomes.Trends in genetics : TIG · 2025Review
- YModPred: an interpretable prediction method for multi-type RNA modification sites in S. cerevisiae based on deep learning.BMC biology · 2025Article
- Review
- Epitranscriptomic alterations induced by environmental toxins: implications for RNA modifications and disease.Genes and environment : the official journal of the Japanese Environmental Mutagen Society · 2025Review
- ModiDeC: a multi-RNA modification classifier for direct nanopore sequencing.Nucleic acids research · 2025Article
- tRNA pseudouridine synthase D (TruD) fromRNA (New York, N.Y.) · 2025Article
- The RMaP challenge of predicting RNA modifications by nanopore sequencing.Communications chemistry · 2025Article
- High-throughput approaches for the identification of ribosome heterogeneity.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Full-length direct RNA sequencing reveals extensive remodeling of RNA expression, processing and modification in aging Caenorhabditis elegans.Nucleic acids research · 2024Article
- A hybrid residue based sequential encoding mechanism with XGBoost improved ensemble model for identifying 5-hydroxymethylcytosine modifications.Scientific reports · 2024Article
- Article
- Full-length direct RNA sequencing reveals extensive remodeling of RNA expression, processing and modification in agingbioRxiv : the preprint server for biology · 2024Article
- Transfer learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing.Nature communications · 2024Article
- scaRNA20 promotes pseudouridylatory modification of small nuclear snRNA U12 and improves cardiomyogenesis.Experimental cell research · 2024Article
- Advances in brain epitranscriptomics research and translational opportunities.Molecular psychiatry · 2024Review
- Heterogeneity of chemical modifications on RNA.Biophysical reviews · 2024Review
- Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression.Nature cell biology · 2023Article
- The expanding role of RNA modifications in plant RNA polymerase II transcripts: highlights and perspectives.Journal of experimental botany · 2023Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
RNA molecules contain a variety of chemically diverse, posttranscriptionally modified bases. The most abundant modified base found in cellular RNAs, pseudouridine (Ψ), has recently been mapped to hundreds of sites in mRNAs, many of which are dynamically regulated. Though the pseudouridine landscape has been determined in only a few cell types and growth conditions, the enzymes responsible for mRNA pseudouridylation are universally conserved, suggesting many novel pseudouridylated sites remain to be discovered. Here, we present Pseudo-seq, a technique that allows the identification of sites of pseudouridylation genome-wide with single-nucleotide resolution. In this chapter, we provide a detailed description of Pseudo-seq. We include protocols for RNA isolation from Saccharomyces cerevisiae, Pseudo-seq library preparation, and data analysis, including descriptions of processing and mapping of sequencing reads, computational identification of sites of pseudouridylation, and assignment of sites to specific pseudouridine synthases. The approach presented here is readily adaptable to any cell or tissue type from which high-quality mRNA can be isolated. Identification of novel pseudouridylation sites is an important first step in elucidating the regulation and functions of these modifications.
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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.