ArticleProceedings of the National Academy of Sciences of the United States of America2014
Nucleosomal promoter variation generates gene expression noise.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed.
- Linking DNA-packing density distribution and TAD boundary locations.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genome-scale chromatin binding dynamics of RNA Polymerase II general transcription machinery components.The EMBO journal · 2024Article
- Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency.Nucleic acids research · 2023Article
- Quantifying stimulus-response specificity to probe the functional state of macrophages.Cell systems · 2023Article
- Interplay between genetic, epigenetic, and gene expression variability: Considering complexity in evolvability.Evolutionary applications · 2021Review
- Article
- Single-Molecule Techniques to Study Chromatin.Frontiers in cell and developmental biology · 2021Review
- Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell.International journal of molecular sciences · 2020Review
- Nucleosomal proofreading of activator-promoter interactions.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting.Cell · 2018Article
- CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness.Genome biology · 2018Article
- Toehold-enhanced LNA probes for selective pull down and single-molecule analysis of native chromatin.Scientific reports · 2017Article
- Fate-Regulating Circuits in Viruses: From Discovery to New Therapy Targets.Annual review of virology · 2017Review
- Effects of cell-cycle-dependent expression on random fluctuations in protein levels.Royal Society open science · 2016Article
- Transcription Dynamics in Living Cells.Annual review of biophysics · 2016Review
- 4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation?Genome biology · 2016Review
- Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression.Scientific reports · 2016Article
- Distinct promoter activation mechanisms modulate noise-driven HIV gene expression.Scientific reports · 2015Article
- Epigenomics and the structure of the living genome.Genome research · 2015Review
- A passive-flow microfluidic device for imaging latent HIV activation dynamics in single T cells.Integrative biology : quantitative biosciences from nano to macro · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene product molecule numbers fluctuate over time and between cells, confounding deterministic expectations. The molecular origins of this noise of gene expression remain unknown. Recent EM analysis of single PHO5 gene molecules of yeast indicated that promoter molecules stochastically assume alternative nucleosome configurations at steady state, including the fully nucleosomal and nucleosome-free configuration. Given that distinct configurations are unequally conducive to transcription, the nucleosomal variation of promoter molecules may constitute a source of gene expression noise. This notion, however, implies an untested conjecture, namely that the nucleosomal variation arises de novo or intrinsically (i.e., that it cannot be explained as the result of the promoter's deterministic response to variation in its molecular surroundings). Here, we show--by microscopically analyzing the nucleosome configurations of two juxtaposed physically linked PHO5 promoter copies--that the configurational variation, indeed, is intrinsically stochastic and thus, a cause of gene expression noise rather than its effect.
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.