ReviewNature protocols2024
BID-seq for transcriptome-wide quantitative sequencing of mRNA pseudouridine at base resolution.
Review in Nature protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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.
The trial behind it
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
27 citing papers in PubMed, 36 citations in OpenAlex.
- Comprehensive post-transcriptional modification profiles in individual Staphylococcus aureus tRNA species.Nucleic acids research · 2026Article
- High-throughput Profiling of Pseudouridines in Microbiome-derived Bacterial RNA.Current protocols · 2026Article
- Article
- Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples.Nature biotechnology · 2026Article
- Cytoplasmic localization of pseudouridine synthase 7 facilitates a pseudouridine-dependent enhancement of cellular stress tolerance.Nature communications · 2026Article
- RNA modification-mediated multidimensional crosstalk: a novel perspective on gene expression regulation.Genome biology · 2026Review
- Ribosome Molecular Aging Shapes Translation Dynamics.bioRxiv : the preprint server for biology · 2026Article
- Quantitative mapping of pseudouridines in bacterial RNA.Nature communications · 2026Article
- Decoding human tRNA modifications and crosstalk by enhanced single-read analysis.Genome biology · 2026Article
- Seven wonders of RNA modification biology.RNA (New York, N.Y.) · 2026Review
- Molecular Insights into Widespread Pseudouridine RNA Modifications: Implications for Women's Health and Disease.Biology · 2026Review
- RNA modifications in cancer: from biological insights to therapeutic targets.Bioorganic & medicinal chemistry · 2026Review
- Pseudouridine increases ribosome stability in a thermophilic eukaryote.Nucleic acids research · 2025Article
- Uli-epic: profiling RNA modifications from ultra-low input samples.Genome biology · 2025Article
- Quantitative CRACI reveals transcriptome-wide distribution of RNA dihydrouridine at base resolution.Nature communications · 2025Article
- The tRNA epitranscriptomic landscape and RNA modification enzymes in Vibrio cholerae.PLoS genetics · 2025Article
- Cytoplasmic localization of PUS7 facilitates a pseudouridine-dependent enhancement of cellular stress tolerance.bioRxiv : the preprint server for biology · 2025Article
- Review
- Review
- RNA modifications in the tumor microenvironment: insights into the cancer-immunity cycle and beyond.Experimental hematology & oncology · 2025Review
Corrections and comments
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Authors and funding
10 authors at 1 institution in 2 countries.
Funding
Abstract
Pseudouridine (Ψ) is an abundant RNA modification that is present in and affects the functions of diverse non-coding RNA species, including rRNA, tRNA and small nuclear RNA. Ψ also exists in mammalian mRNA and probably exhibits functional roles; however, functional investigations of mRNA Ψ modifications in mammals have been hampered by the lack of a quantitative method that detects Ψ at base precision. We have recently developed bisulfite-induced deletion sequencing (BID-seq), which provides the community with a quantitative method to map RNA Ψ distribution transcriptome-wide at single-base resolution. Here, we describe an optimized BID-seq protocol for mapping Ψ distribution across cellular mRNAs, which includes fast steps in both library preparation and data analysis. This protocol generates highly reproducible results by inducing high deletion ratios at Ψ modification within diverse sequence contexts, and meanwhile displayed almost zero background deletions at unmodified uridines. When used for transcriptome-wide Ψ profiling in mouse embryonic stem cells, the current protocol uncovered 8,407 Ψ sites from as little as 10 ng of polyA
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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.