---
_id: '7147'
abstract:
- lang: eng
  text: "The expression of a gene is characterised by its transcription factors and
    the function processing them. If the transcription factors are not affected by
    gene products, the regulating function is often represented as a combinational
    logic circuit, where the outputs (product) are determined by current input values
    (transcription factors) only, and are hence independent on their relative arrival
    times. However, the simultaneous arrival of transcription factors (TFs) in genetic
    circuits is a strong assumption, given that the processes of transcription and
    translation of a gene into a protein introduce intrinsic time delays and that
    there is no global synchronisation among the arrival times of different molecular
    species at molecular targets.\r\n\r\nIn this paper, we construct an experimentally
    implementable genetic circuit with two inputs and a single output, such that,
    in presence of small delays in input arrival, the circuit exhibits qualitatively
    distinct observable phenotypes. In particular, these phenotypes are long lived
    transients: they all converge to a single value, but so slowly, that they seem
    stable for an extended time period, longer than typical experiment duration. We
    used rule-based language to prototype our circuit, and we implemented a search
    for finding the parameter combinations raising the phenotypes of interest.\r\n\r\nThe
    behaviour of our prototype circuit has wide implications. First, it suggests that
    GRNs can exploit event timing to create phenotypes. Second, it opens the possibility
    that GRNs are using event timing to react to stimuli and memorise events, without
    explicit feedback in regulation. From the modelling perspective, our prototype
    circuit demonstrates the critical importance of analysing the transient dynamics
    at the promoter binding sites of the DNA, before applying rapid equilibrium assumptions."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Claudia
  full_name: Igler, Claudia
  id: 46613666-F248-11E8-B48F-1D18A9856A87
  last_name: Igler
- first_name: Tatjana
  full_name: Petrov, Tatjana
  id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
  last_name: Petrov
  orcid: 0000-0002-9041-0905
- first_name: Ali
  full_name: Sezgin, Ali
  id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
  last_name: Sezgin
citation:
  ama: 'Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. Transient memory in gene
    regulation. In: <i>17th International Conference on Computational Methods in Systems
    Biology</i>. Vol 11773. Springer Nature; 2019:155-187. doi:<a href="https://doi.org/10.1007/978-3-030-31304-3_9">10.1007/978-3-030-31304-3_9</a>'
  apa: 'Guet, C. C., Henzinger, T. A., Igler, C., Petrov, T., &#38; Sezgin, A. (2019).
    Transient memory in gene regulation. In <i>17th International Conference on Computational
    Methods in Systems Biology</i> (Vol. 11773, pp. 155–187). Trieste, Italy: Springer
    Nature. <a href="https://doi.org/10.1007/978-3-030-31304-3_9">https://doi.org/10.1007/978-3-030-31304-3_9</a>'
  chicago: Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali
    Sezgin. “Transient Memory in Gene Regulation.” In <i>17th International Conference
    on Computational Methods in Systems Biology</i>, 11773:155–87. Springer Nature,
    2019. <a href="https://doi.org/10.1007/978-3-030-31304-3_9">https://doi.org/10.1007/978-3-030-31304-3_9</a>.
  ieee: C. C. Guet, T. A. Henzinger, C. Igler, T. Petrov, and A. Sezgin, “Transient
    memory in gene regulation,” in <i>17th International Conference on Computational
    Methods in Systems Biology</i>, Trieste, Italy, 2019, vol. 11773, pp. 155–187.
  ista: 'Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. 2019. Transient memory
    in gene regulation. 17th International Conference on Computational Methods in
    Systems Biology. CMSB: Computational Methods in Systems Biology, LNCS, vol. 11773,
    155–187.'
  mla: Guet, Calin C., et al. “Transient Memory in Gene Regulation.” <i>17th International
    Conference on Computational Methods in Systems Biology</i>, vol. 11773, Springer
    Nature, 2019, pp. 155–87, doi:<a href="https://doi.org/10.1007/978-3-030-31304-3_9">10.1007/978-3-030-31304-3_9</a>.
  short: C.C. Guet, T.A. Henzinger, C. Igler, T. Petrov, A. Sezgin, in:, 17th International
    Conference on Computational Methods in Systems Biology, Springer Nature, 2019,
    pp. 155–187.
conference:
  end_date: 2019-09-20
  location: Trieste, Italy
  name: 'CMSB: Computational Methods in Systems Biology'
  start_date: 2019-09-18
date_created: 2019-12-04T16:07:50Z
date_published: 2019-09-17T00:00:00Z
date_updated: 2023-09-06T11:18:08Z
day: '17'
department:
- _id: CaGu
- _id: ToHe
doi: 10.1007/978-3-030-31304-3_9
external_id:
  isi:
  - '000557875100009'
intvolume: '     11773'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
page: 155-187
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
- _id: 251EE76E-B435-11E9-9278-68D0E5697425
  grant_number: '24573'
  name: Design principles underlying genetic switch architecture
publication: 17th International Conference on Computational Methods in Systems Biology
publication_identifier:
  eissn:
  - 1611-3349
  isbn:
  - '9783030313036'
  - '9783030313043'
  issn:
  - 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transient memory in gene regulation
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11773
year: '2019'
...