ArticleNature communications2024
Single-cell total-RNA profiling unveils regulatory hubs of transcription factors.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Lack of evidence for transcription-to-RNA maturation lags across G1-to-G2-phase boundary in fibroblasts.Life science alliance · 2026Article
- Selective RNA sequestration in biomolecular condensates directs cell fate transitions.Nature biotechnology · 2026Article
- Scalable single-cell total RNA sequencing unifies coding and noncoding transcriptomics.Nature biotechnology · 2026Article
- To jump or not to jump: comparing effects of phenotypic plasticity on the visual responses and escape behavior of locusts and grasshoppers.Journal of neurophysiology · 2026Article
- Enhanced MiRISC expression noise reduction by self-feedback regulation of mRNA degradation.Computational and structural biotechnology journal · 2026Article
- Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapes.bioRxiv : the preprint server for biology · 2025Article
- Cell-cycle dynamics of nascent transcription and mature RNA accumulation are concordant in normal fibroblasts.bioRxiv : the preprint server for biology · 2025Article
- Investigating Gene Expression Noise Reduction by MicroRNAs and MiRISC Reinforcement by Self-Feedback Regulation of mRNA Degradation.bioRxiv : the preprint server for biology · 2025Article
- Scalable single-cell total RNA-seq reveals non-coding programs in immunity, infection, and brain development.Research square · 2025Article
- Efficient profiling of total RNA in single cells with STORM-seq.bioRxiv : the preprint server for biology · 2025Article
- Single-cell total-RNA profiling unveils regulatory hubs of transcription factors.Nature communications · 2024Article
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Authors and funding
3 authors.
Funding
Abstract
Recent development of RNA velocity uses master equations to establish the kinetics of the life cycle of RNAs from unspliced RNA to spliced RNA (i.e., mature RNA) to degradation. To feed this kinetic analysis, simultaneous measurement of unspliced RNA and spliced RNA in single cells is greatly desired. However, the majority of single-cell RNA-seq chemistry primarily captures mature RNA species to measure gene expressions. Here, we develop a one-step total-RNA chemistry-based single-cell RNA-seq method: snapTotal-seq. We benchmark this method with multiple single-cell RNA-seq assays in their performance in kinetic analysis of cell cycle by RNA velocity. Next, with LASSO regression between transcription factors, we identify the critical regulatory hubs mediating the cell cycle dynamics. We also apply snapTotal-seq to profile the oncogene-induced senescence and identify the key regulatory hubs governing the entry of senescence. Furthermore, from the comparative analysis of unspliced RNA and spliced RNA, we identify a significant portion of genes whose expression changes occur in spliced RNA but not to the same degree in unspliced RNA, indicating these gene expression changes are mainly controlled by post-transcriptional regulation. Overall, we demonstrate that snapTotal-seq can provide enriched information about gene regulation, especially during the transition between cell states.
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