Evidence map›Paper›PMID 25943345›Full record

ArticleMolecular systems biology2015

Orthogonal control of expression mean and variance by epigenetic features at different genomic loci.

Siddharth S Dey, Jonathan E Foley, Prajit Limsirichai, David V Schaffer, Adam P Arkin

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular systems biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.

0numbers the graph read from it
0cells of the map it votes in
65citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

65 citing papers in PubMed.

  1. Article
  2. Genome-Wide Landscape of Position Effect Variegation inJournal of fungi (Basel, Switzerland) · 2026
    Article
  3. What makes genes burst.Trends in cell biology · 2026
    Review
  4. Article
  5. Article
  6. Review
  7. Article
  8. Article
  9. Article
  10. Review
  11. Article
  12. Article
  13. Article
  14. Review
  15. Article
  16. Review
  17. Review
  18. Article
  19. Article
  20. Review

5 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Siddharth S DeyDepartment of Chemical and Biomolecular Engineering and the Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
Jonathan E FoleyDepartment of Bioengineering, University of California, Berkeley, CA, USA.
Prajit LimsirichaiDepartment of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
David V SchafferDepartment of Chemical and Biomolecular Engineering and the Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA Department of Bioengineering, University of California, Berkeley, CA, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA schaffer@berkeley.edu aparkin@lbl.gov.
Adam P ArkinDepartment of Bioengineering, University of California, Berkeley, CA, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA Virtual Institute of Microbial Stress and Survival, Lawrence Berkeley National Laboratory, Berkeley, CA, USA DOE, Joint BioEnergy Institute Lawrence Berkeley National Laboratory, Berkeley, CA, USA schaffer@berkeley.edu aparkin@lbl.gov.

Funding

Stochastic Gene Expression Effects in a Model RetrovirusR01GM073058 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI ARKIN, ADAM P, SCHAFFER, DAVID V · 2005 to 2014
$2.3M
NIGMS NIH HHS R01 GM073058NIGMS NIH HHS R01-GM073058
6 · The paper itself

Abstract

While gene expression noise has been shown to drive dramatic phenotypic variations, the molecular basis for this variability in mammalian systems is not well understood. Gene expression has been shown to be regulated by promoter architecture and the associated chromatin environment. However, the exact contribution of these two factors in regulating expression noise has not been explored. Using a dual-reporter lentiviral model system, we deconvolved the influence of the promoter sequence to systematically study the contribution of the chromatin environment at different genomic locations in regulating expression noise. By integrating a large-scale analysis to quantify mRNA levels by smFISH and protein levels by flow cytometry in single cells, we found that mean expression and noise are uncorrelated across genomic locations. Furthermore, we showed that this independence could be explained by the orthogonal control of mean expression by the transcript burst size and noise by the burst frequency. Finally, we showed that genomic locations displaying higher expression noise are associated with more repressed chromatin, thereby indicating the contribution of the chromatin environment in regulating expression noise.

Indexed as

Epigenesis, GeneticChromatinGenomicsHalf-LifeHEK293 CellsHumansJurkat CellsModels, GeneticPromoter Regions, GeneticProteinsRNA, MessengerChromatinProteinsRNA, Messengerchromatin environmentgene expression noisesingle‐cell biologysingle‐molecule RNA FISH

Identifiers

PMID25943345
PMCPMC4461400

What OpenQuestion holds

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Read underepoch 390

Registered trials

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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.