---
_id: '1242'
abstract:
- lang: eng
text: A crucial step in the regulation of gene expression is binding of transcription
factor (TF) proteins to regulatory sites along the DNA. But transcription factors
act at nanomolar concentrations, and noise due to random arrival of these molecules
at their binding sites can severely limit the precision of regulation. Recent
work on the optimization of information flow through regulatory networks indicates
that the lower end of the dynamic range of concentrations is simply inaccessible,
overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain
proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest
a scheme in which transcription factors also act as indirect translational regulators,
binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule
acts as an independent sensor of the input concentration, and averaging over these
multiple sensors reduces the noise. We analyze information flow through this scheme
and identify conditions under which it outperforms direct transcriptional regulation.
Our results suggest that the dual role of homeodomain proteins is not just a historical
accident, but a solution to a crucial physics problem in the regulation of gene
expression.
acknowledgement: "We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions.
This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370
from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W.
acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561.
G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S."
article_number: '022404'
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Aleksandra
full_name: Walczak, Aleksandra
last_name: Walczak
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of
transcription factor action by translational regulation. Physical Review E
Statistical Nonlinear and Soft Matter Physics. 2016;93(2). doi:10.1103/PhysRevE.93.022404
apa: Sokolowski, T. R., Walczak, A., Bialek, W., & Tkačik, G. (2016). Extending
the dynamic range of transcription factor action by translational regulation.
Physical Review E Statistical Nonlinear and Soft Matter Physics. American
Institute of Physics. https://doi.org/10.1103/PhysRevE.93.022404
chicago: Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik.
“Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.”
Physical Review E Statistical Nonlinear and Soft Matter Physics. American
Institute of Physics, 2016. https://doi.org/10.1103/PhysRevE.93.022404.
ieee: T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic
range of transcription factor action by translational regulation,” Physical
Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2. American
Institute of Physics, 2016.
ista: Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic
range of transcription factor action by translational regulation. Physical Review
E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404.
mla: Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription
Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 93, no. 2, 022404, American Institute of Physics,
2016, doi:10.1103/PhysRevE.93.022404.
short: T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical
Nonlinear and Soft Matter Physics 93 (2016).
date_created: 2018-12-11T11:50:54Z
date_published: 2016-02-04T00:00:00Z
date_updated: 2021-01-12T06:49:20Z
day: '04'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.93.022404
intvolume: ' 93'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.02562
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '6088'
quality_controlled: '1'
scopus_import: 1
status: public
title: Extending the dynamic range of transcription factor action by translational
regulation
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2016'
...