ArticlePloS one2014
SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 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.
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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
36 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
- Endothelial transcriptomic, epigenomic and proteomic data challenge the proposed role for TSAd in vascular permeability.Angiogenesis · 2025Article
- The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes.Nucleic acids research · 2024Article
- Activating transcription factor 4 plays a major role in shaping the transcriptional response to isoginkgetin in HCT116 cells.Scientific reports · 2024Article
- Bulking up to shed light on leaky transcription in endothelium.Nature cardiovascular research · 2024Article
- The BulkECexplorer compiles endothelial bulk transcriptomes to predict functional versus leaky transcription.Nature cardiovascular research · 2024Article
- Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation.The Plant journal : for cell and molecular biology · 2024Article
- Article
- Longitudinal intronic RNA-Seq analysis of Parkinson's disease patients reveals disease-specific nascent transcription.Experimental biology and medicine (Maywood, N.J.) · 2022Article
- Extended intergenic DNA contributes to neuron-specific expression of neighboring genes in the mammalian nervous system.Nature communications · 2022Article
- Genetic variants associated mRNA stability in lung.BMC genomics · 2022Article
- Review
- Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages.Genome research · 2022Article
- Therapeutic Targeting of Alternative Splicing: A New Frontier in Cancer Treatment.Frontiers in oncology · 2022Review
- Dynamics of transcriptional and post-transcriptional regulation.Briefings in bioinformatics · 2021Review
- Preprocessing choices affect RNA velocity results for droplet scRNA-seq data.PLoS computational biology · 2021Article
- Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling.Genome research · 2020Article
- MeCP2 Represses Enhancers through Chromosome Topology-Associated DNA Methylation.Molecular cell · 2020Article
- INSPEcT-GUI Reveals the Impact of the Kinetic Rates of RNA Synthesis, Processing, and Degradation, on Premature and Mature RNA Species.Frontiers in genetics · 2020Article
- The spliceosome inhibitors isoginkgetin and pladienolide B induce ATF3-dependent cell death.PloS one · 2020Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
mRNA synthesis, processing, and destruction involve a complex series of molecular steps that are incompletely understood. Because the RNA intermediates in each of these steps have finite lifetimes, extensive mechanistic and dynamical information is encoded in total cellular RNA. Here we report the development of SnapShot-Seq, a set of computational methods that allow the determination of in vivo rates of pre-mRNA synthesis, splicing, intron degradation, and mRNA decay from a single RNA-Seq snapshot of total cellular RNA. SnapShot-Seq can detect in vivo changes in the rates of specific steps of splicing, and it provides genome-wide estimates of pre-mRNA synthesis rates comparable to those obtained via labeling of newly synthesized RNA. We used SnapShot-Seq to investigate the origins of the intrinsic bimodality of metazoan gene expression levels, and our results suggest that this bimodality is partly due to spillover of transcriptional activation from highly expressed genes to their poorly expressed neighbors. SnapShot-Seq dramatically expands the information obtainable from a standard RNA-Seq experiment.
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