---
_id: '1666'
abstract:
- lang: eng
text: Evolution of gene regulation is crucial for our understanding of the phenotypic
differences between species, populations and individuals. Sequence-specific binding
of transcription factors to the regulatory regions on the DNA is a key regulatory
mechanism that determines gene expression and hence heritable phenotypic variation.
We use a biophysical model for directional selection on gene expression to estimate
the rates of gain and loss of transcription factor binding sites (TFBS) in finite
populations under both point and insertion/deletion mutations. Our results show
that these rates are typically slow for a single TFBS in an isolated DNA region,
unless the selection is extremely strong. These rates decrease drastically with
increasing TFBS length or increasingly specific protein-DNA interactions, making
the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation
timescales. Similarly, evolution converges to the stationary distribution of binding
sequences very slowly, making the equilibrium assumption questionable. The availability
of longer regulatory sequences in which multiple binding sites can evolve simultaneously,
the presence of “pre-sites” or partially decayed old sites in the initial sequence,
and biophysical cooperativity between transcription factors, can all facilitate
gain of TFBS and reconcile theoretical calculations with timescales inferred from
comparative genomics.
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding
site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639
apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of
transcription factor binding site evolution. PLoS Genetics. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1005639
chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics
of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public
Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.
ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription
factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public
Library of Science, 2015.
ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor
binding site evolution. PLoS Genetics. 11(11).
mla: Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.”
PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.
short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).
date_created: 2018-12-11T11:53:21Z
date_published: 2015-11-06T00:00:00Z
date_updated: 2023-09-07T11:53:49Z
day: '06'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pgen.1005639
ec_funded: 1
file:
- access_level: open_access
checksum: a4e72fca5ccf40ddacf4d08c8e46b554
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:58Z
date_updated: 2020-07-14T12:45:10Z
file_id: '4657'
file_name: IST-2016-463-v1+1_journal.pgen.1005639.pdf
file_size: 2580778
relation: main_file
file_date_updated: 2020-07-14T12:45:10Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '5483'
pubrep_id: '463'
quality_controlled: '1'
related_material:
record:
- id: '9712'
relation: research_data
status: public
- id: '1131'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Dynamics of transcription factor binding site evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...