ArticleGenome research2020
Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 1 of them a synthesis that pooled it.
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Who cites it
14 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The genetic and biochemical determinants of mRNA degradation rates in mammals.Genome biology · 2022Pooled it
- The Kinetic Intron Hypothesis.bioRxiv : the preprint server for biology · 2026Article
- Fragile X messenger ribonucleoprotein 1 (FMRP) regulates glycolytic gene expression under chronic hypoxia in HCT116 cells.Scientific reports · 2025Article
- Time-series transcriptomics reveals distinctive mRNA expression dynamics associated with gene ontology specificity and protein expression in skeletal muscle after electrical stimulation-induced resistance exercise.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2024Article
- Metabolic RNA Labeling and Translating Ribosome Affinity Purification for Measurement of Nascent RNA Translation.Bio-protocol · 2024Article
- Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens.Nature biotechnology · 2024Article
- Nanopore Direct RNA Sequencing for Modified Uridine Nucleotides Yields Signals Dependent on the Physical Properties of the Modified Base.Israel journal of chemistry · 2024Article
- Simultaneous measurement of nascent transcriptome and translatome using 4-thiouridine metabolic RNA labeling and translating ribosome affinity purification.Nucleic acids research · 2023Article
- Single-molecule imaging reveals translation-dependent destabilization of mRNAs.Molecular cell · 2023Article
- Synthesis of 4-thiouridines with prodrug functionalization for RNA metabolic labeling.RSC chemical biology · 2022Article
- Direct detection of RNA modifications and structure using single-molecule nanopore sequencing.Cell genomics · 2022Article
- Eukaryotic mRNA Decapping Activation.Frontiers in genetics · 2022Review
- Dynamics of transcriptional and post-transcriptional regulation.Briefings in bioinformatics · 2021Review
- Toward Mapping Spatiotemporally Resolved Transcriptomes and RNA-Protein Interactions.Wiley interdisciplinary reviews. RNAReview
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Authors and funding
8 authors.
Funding
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Abstract
Gene expression is determined by a balance between RNA synthesis and RNA degradation. To elucidate the underlying regulatory mechanisms and principles of this, simultaneous measurements of RNA synthesis and degradation are required. Here, we report the development of "Dyrec-seq," which uses 4-thiouridine and 5-bromouridine to simultaneously quantify RNA synthesis and degradation rates. Dyrec-seq enabled the quantification of RNA synthesis and degradation rates of 4702 genes in HeLa cells. Functional enrichment analysis showed that the RNA synthesis and degradation rates of genes are actually determined by the genes' biological functions. A comparison of theoretical and experimental analyses revealed that the amount of RNA is determined by the ratio of RNA synthesis to degradation rates, whereas the rapidity of responses to external stimuli is determined only by the degradation rate. This study emphasizes that not only RNA synthesis but also RNA degradation is important in shaping gene expression patterns.
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