ArticleCell reports2016
Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development.
Article in Cell reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 121 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
121 citing papers in PubMed, 208 citations in OpenAlex.
- Review
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- Escaping Constraints to Innovate: Maternal Neofunctionalization in a HoxB4 Duplicate.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2026Article
- In-Cell Proteomics Enables High-Resolution Spatial and Temporal Mapping of Early Xenopus tropicalis Embryos.Molecular & cellular proteomics : MCP · 2026Article
- Ric-8A controls Cited2 subcellular localization and transcriptional programs during neural crest development.Frontiers in cell and developmental biology · 2026Article
- Xenbase: A Guide to the Xenopus Genetics and Genomics Knowledgebase.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Pre-marking chromatin with H3K4 methylation is required for accurate zygotic genome activation and development.Nature communications · 2025Article
- Cell-type-specific DNA methylation dynamics in the prenatal and postnatal human cortex.Cell genomics · 2025Article
- CANTAC-seq analysis reveals E2f1 and Otx1 coordinate zygotic genome activation in Xenopus tropicalis.Nature communications · 2025Article
- Foxi2 and Sox3 are master transcription regulators that control ectoderm germ layer specification in Xenopus.PLoS biology · 2025Article
- Foxh1 is a locus-specific PRC2 recruiter governing germ layer silencing.bioRxiv : the preprint server for biology · 2025Article
- Article
- Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos.Nucleic acids research · 2025Article
- Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.Communications medicine · 2025Article
- The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus.Nature reviews. Genetics · 2025Review
- TheBiomolecules · 2025Review
- An Integrated Database for Exploring Alternative Promoters in Animals.Scientific data · 2025Article
- Maternal and zygotic contributions to H3K4me1 chromatin marking during germ layer formation.Developmental biology · 2025Article
- Nup107 contributes to the maternal-to-zygotic transition by preventing the premature nuclear export of pri-miR427.Development (Cambridge, England) · 2025Article
- A case for absolute gene expression estimates in microbiome studies using metatranscriptomics.The ISME journal · 2025Article
61 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack a comprehensive understanding of transcript kinetics, which limits quantitative biology. This is an acute challenge in embryonic development, where rapid changes in gene expression dictate cell fate decisions. By ultra-high-frequency sampling of Xenopus embryos and absolute normalization of sequence reads, we present smooth gene expression trajectories in absolute transcript numbers. During a developmental period approximating the first 8 weeks of human gestation, transcript kinetics vary by eight orders of magnitude. Ordering genes by expression dynamics, we find that "temporal synexpression" predicts common gene function. Remarkably, a single parameter, the characteristic timescale, can classify transcript kinetics globally and distinguish genes regulating development from those involved in cellular metabolism. Overall, our analysis provides unprecedented insight into the reorganization of maternal and embryonic transcripts and redefines our ability to perform quantitative biology.
Indexed as
Identifiers
What OpenQuestion holds
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.