ArticleMolecular systems biology2010
Quantitative analysis of the transcription control mechanism.
Article in Molecular systems biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Single gene analysis in yeast suggests nonequilibrium regulatory dynamics for transcription.Nature communications · 2024Article
- Transcriptional kinetic synergy: A complex landscape revealed by integrating modeling and synthetic biology.Cell systems · 2023Article
- Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses.Genetics · 2021Article
- Nucleosomal proofreading of activator-promoter interactions.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Feed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise.Nature communications · 2019Article
- Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies.Science (New York, N.Y.) · 2019Article
- An Optogenetic Platform for Real-Time, Single-Cell Interrogation of Stochastic Transcriptional Regulation.Molecular cell · 2018Article
- mRNA detection in budding yeast with single fluorophores.Nucleic acids research · 2017Article
- Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression.Scientific reports · 2016Article
- From Structural Variation of Gene Molecules to Chromatin Dynamics and Transcriptional Bursting.Genes · 2015Review
- Orthogonal control of expression mean and variance by epigenetic features at different genomic loci.Molecular systems biology · 2015Article
- Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism.PLoS computational biology · 2015Article
- Nucleosomal promoter variation generates gene expression noise.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Nucleosomes, transcription, and probability.Molecular biology of the cell · 2014Article
- Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Promoter-mediated transcriptional dynamics.Biophysical journal · 2014Article
- The yeast PHO5 promoter: from single locus to systems biology of a paradigm for gene regulation through chromatin.Nucleic acids research · 2014Review
- Mechanistic stochastic model of histone modification pattern formation.Epigenetics & chromatin · 2014Article
- Mapping the fine structure of a eukaryotic promoter input-output function.Nature genetics · 2013Article
- An effective method for computing the noise in biochemical networks.The Journal of chemical physics · 2013Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Gene transcription requires a sequence of promoter state transitions, including chromatin remodeling, assembly of the transcription machinery, and clearance of the promoter by RNA polymerase. The rate-limiting steps in this sequence are regulated by transcriptional activators that bind at specific promoter elements. As the transition kinetics of individual promoters cannot be observed, the identity of the activator-controlled steps has remained a matter of speculation. In this study, we investigated promoter chromatin structure, and the intrinsic noise of expression over a wide range of expression values for the PHO5 gene of yeast. Interpretation of our results with regard to a stochastic model of promoter chromatin remodeling and gene expression suggests that the regulatory architecture of the gene expression process is measurably reflected in its intrinsic noise profile. Our chromatin structure and noise analyses indicate that the activator of PHO5 transcription stimulates the rates of promoter nucleosome disassembly, and assembly of the transcription machinery after nucleosome removal, but no other rates of the expression process.
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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.