---
_id: '1576'
abstract:
- lang: eng
  text: 'Gene expression is controlled primarily by interactions between transcription
    factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured
    well by thermodynamic models of regulation. These models, however, neglect regulatory
    crosstalk: the possibility that noncognate TFs could initiate transcription, with
    potentially disastrous effects for the cell. Here, we estimate the importance
    of crosstalk, suggest that its avoidance strongly constrains equilibrium models
    of TF binding, and propose an alternative nonequilibrium scheme that implements
    kinetic proofreading to suppress erroneous initiation. This proposal is consistent
    with the observed covalent modifications of the transcriptional apparatus and
    predicts increased noise in gene expression as a trade-off for improved specificity.
    Using information theory, we quantify this trade-off to find when optimal proofreading
    architectures are favored over their equilibrium counterparts. Such architectures
    exhibit significant super-Poisson noise at low expression in steady state.'
article_number: '248101'
article_processing_charge: No
arxiv: 1
author:
- first_name: Sarah A
  full_name: Cepeda Humerez, Sarah A
  id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
  last_name: Cepeda Humerez
- first_name: Georg
  full_name: Rieckh, Georg
  id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
  last_name: Rieckh
- first_name: Gasper
  full_name: Tkacik, Gasper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkacik
  orcid: 0000-0002-6699-1455
citation:
  ama: Cepeda Humerez SA, Rieckh G, Tkačik G. Stochastic proofreading mechanism alleviates
    crosstalk in transcriptional regulation. <i>Physical Review Letters</i>. 2015;115(24).
    doi:<a href="https://doi.org/10.1103/PhysRevLett.115.248101">10.1103/PhysRevLett.115.248101</a>
  apa: Cepeda Humerez, S. A., Rieckh, G., &#38; Tkačik, G. (2015). Stochastic proofreading
    mechanism alleviates crosstalk in transcriptional regulation. <i>Physical Review
    Letters</i>. American Physical Society. <a href="https://doi.org/10.1103/PhysRevLett.115.248101">https://doi.org/10.1103/PhysRevLett.115.248101</a>
  chicago: Cepeda Humerez, Sarah A, Georg Rieckh, and Gašper Tkačik. “Stochastic Proofreading
    Mechanism Alleviates Crosstalk in Transcriptional Regulation.” <i>Physical Review
    Letters</i>. American Physical Society, 2015. <a href="https://doi.org/10.1103/PhysRevLett.115.248101">https://doi.org/10.1103/PhysRevLett.115.248101</a>.
  ieee: S. A. Cepeda Humerez, G. Rieckh, and G. Tkačik, “Stochastic proofreading mechanism
    alleviates crosstalk in transcriptional regulation,” <i>Physical Review Letters</i>,
    vol. 115, no. 24. American Physical Society, 2015.
  ista: Cepeda Humerez SA, Rieckh G, Tkačik G. 2015. Stochastic proofreading mechanism
    alleviates crosstalk in transcriptional regulation. Physical Review Letters. 115(24),
    248101.
  mla: Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates
    Crosstalk in Transcriptional Regulation.” <i>Physical Review Letters</i>, vol.
    115, no. 24, 248101, American Physical Society, 2015, doi:<a href="https://doi.org/10.1103/PhysRevLett.115.248101">10.1103/PhysRevLett.115.248101</a>.
  short: S.A. Cepeda Humerez, G. Rieckh, G. Tkačik, Physical Review Letters 115 (2015).
corr_author: '1'
date_created: 2018-12-11T11:52:49Z
date_published: 2015-12-08T00:00:00Z
date_updated: 2026-04-08T13:55:46Z
day: '08'
department:
- _id: GaTk
doi: 10.1103/PhysRevLett.115.248101
ec_funded: 1
external_id:
  arxiv:
  - '1504.05716'
  isi:
  - '000366106700014'
intvolume: '       115'
isi: 1
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1504.05716
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '250152'
  name: Limits to selection in biology and in evolutionary computation
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5595'
quality_controlled: '1'
related_material:
  record:
  - id: '6473'
    relation: part_of_dissertation
    status: public
scopus_import: '1'
status: public
title: Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 115
year: '2015'
...