ArticleBriefings in bioinformatics2021
A comparison of metabolic labeling and statistical methods to infer genome-wide dynamics of RNA turnover.
Article in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- STAR Suite: Integrating transcriptomics through AI software engineering in the NIH MorPhiC consortium.bioRxiv : the preprint server for biology · 2026Article
- RNA stability: a novel perspective on gene regulatory networks in bovine mastitis.BMC genomics · 2025Article
- RNADecayCafe, a uniformly processed atlas of RNA half-life estimates across multiple human cell lines.bioRxiv : the preprint server for biology · 2025Article
- Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite.PLoS computational biology · 2025Article
- Article
- Assessment of mRNA Decay and Calculation of Codon Occurrence to mRNA Stability Correlation Coefficients after 5-EU Metabolic Labeling.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics.NAR genomics and bioinformatics · 2024Article
- Transcription bodies regulate gene expression by sequestering CDK9.Nature cell biology · 2024Article
- Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics.bioRxiv : the preprint server for biology · 2023Article
- Synergising single-cell resolution and 4sU labelling boosts inference of transcriptional bursting.Genome biology · 2023Article
- grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis.Nature communications · 2023Article
- Improving the study of RNA dynamics through advances in RNA-seq with metabolic labeling and nucleotide-recoding chemistry.bioRxiv : the preprint server for biology · 2023Article
- Buffering of transcription rate by mRNA half-life is a conserved feature of Rett syndrome models.Nature communications · 2023Article
- Determining RNA Natural Modifications and Nucleoside Analog-Labeled Sites by a Chemical/Enzyme-Induced Base Mutation Principle.Molecules (Basel, Switzerland) · 2023Review
- Functional RNA Dynamics Are Progressively Governed by RNA Destabilization during the Adaptation to Chronic Hypoxia.International journal of molecular sciences · 2022Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabolic labeling of newly transcribed RNAs coupled with RNA-seq is being increasingly used for genome-wide analysis of RNA dynamics. Methods including standard biochemical enrichment and recent nucleotide conversion protocols each require special experimental and computational treatment. Despite their immediate relevance, these technologies have not yet been assessed and benchmarked, and no data are currently available to advance reproducible research and the development of better inference tools. Here, we present a systematic evaluation and comparison of four RNA labeling protocols: 4sU-tagging biochemical enrichment, including spike-in RNA controls, SLAM-seq, TimeLapse-seq and TUC-seq. All protocols are evaluated based on practical considerations, conversion efficiency and wet lab requirements to handle hazardous substances. We also compute decay rate estimates and confidence intervals for each protocol using two alternative statistical frameworks, pulseR and GRAND-SLAM, for over 11 600 human genes and evaluate the underlying computational workflows for their robustness and ease of use. Overall, we demonstrate a high inter-method reliability across eight use case scenarios. Our results and data will facilitate reproducible research and serve as a resource contributing to a fuller understanding of RNA biology.
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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.