ArticleMolecular systems biology2011
Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli.
Article in Molecular systems biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers, 1 of them a synthesis that pooled it.
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Who cites it
90 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
- Gillespie-based simulation and inference for non-Markovian stochastic reaction networks.Briefings in bioinformatics · 2026Article
- VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.Nucleic acids research · 2026Article
- Transcriptional and functional profiles of muscarinic receptor-expressing neurons in primate lateral prefrontal and anterior cingulate cortices.Communications biology · 2026Article
- Coupling mechanisms coordinating mRNA translation with stages of the mRNA lifecycle.RNA biology · 2025Review
- Article
- Biophysical constraints on mRNA decay rates shape macroevolutionary divergence in steady-state abundances.bioRxiv : the preprint server for biology · 2025Article
- Quantifying Landscape and Flux from Single-Cell Omics: Unraveling the Physical Mechanisms of Cell Function.JACS Au · 2025Review
- Effective target genes for RNA interference-based management of the cabbage stem flea beetle.Insect molecular biology · 2025Article
- RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks.Bioinformatics (Oxford, England) · 2025Article
- Cell2fate infers RNA velocity modules to improve cell fate prediction.Nature methods · 2025Article
- Ribosome stalling-induced NIP5;1 mRNA decay triggers ARGONAUTE1-dependent transcription downregulation.Nucleic acids research · 2025Article
- DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes.Biostatistics (Oxford, England) · 2024Article
- Co-transcriptional gene regulation in eukaryotes and prokaryotes.Nature reviews. Molecular cell biology · 2024Review
- DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes.bioRxiv : the preprint server for biology · 2024Article
- Unveiling gene regulatory networks during cellular state transitions without linkage across time points.Scientific reports · 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
- Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells.Nature methods · 2024Article
- Pumping the brakes on RNA velocity by understanding and interpreting RNA velocity estimates.Genome biology · 2023Article
- SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle.Molecular systems biology · 2023Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Transcriptional responses to extracellular stimuli involve tuning the rates of transcript production and degradation. Here, we show that the time-dependent profiles of these rates can be inferred from simultaneous measurements of precursor mRNA (pre-mRNA) and mature mRNA profiles. Transcriptome-wide measurements demonstrate that genes with similar mRNA profiles often exhibit marked differences in the amplitude and onset of their production rate. The latter is characterized by a large dynamic range, with a group of genes exhibiting an unexpectedly strong transient production overshoot, thereby accelerating their induction and, when combined with time-dependent degradation, shaping transient responses with precise timing and amplitude.
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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.