---
_id: '5861'
abstract:
- lang: eng
  text: In zebrafish larvae, it is the cell type that determines how the cell responds
    to a chemokine signal.
article_number: e37888
article_processing_charge: No
article_type: original
author:
- first_name: Jonna H
  full_name: Alanko, Jonna H
  id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87
  last_name: Alanko
  orcid: 0000-0002-7698-3061
- first_name: Michael K
  full_name: Sixt, Michael K
  id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
  last_name: Sixt
  orcid: 0000-0002-6620-9179
citation:
  ama: Alanko JH, Sixt MK. The cell sets the tone. <i>eLife</i>. 2018;7. doi:<a href="https://doi.org/10.7554/eLife.37888">10.7554/eLife.37888</a>
  apa: Alanko, J. H., &#38; Sixt, M. K. (2018). The cell sets the tone. <i>ELife</i>.
    eLife Sciences Publications. <a href="https://doi.org/10.7554/eLife.37888">https://doi.org/10.7554/eLife.37888</a>
  chicago: Alanko, Jonna H, and Michael K Sixt. “The Cell Sets the Tone.” <i>ELife</i>.
    eLife Sciences Publications, 2018. <a href="https://doi.org/10.7554/eLife.37888">https://doi.org/10.7554/eLife.37888</a>.
  ieee: J. H. Alanko and M. K. Sixt, “The cell sets the tone,” <i>eLife</i>, vol.
    7. eLife Sciences Publications, 2018.
  ista: Alanko JH, Sixt MK. 2018. The cell sets the tone. eLife. 7, e37888.
  mla: Alanko, Jonna H., and Michael K. Sixt. “The Cell Sets the Tone.” <i>ELife</i>,
    vol. 7, e37888, eLife Sciences Publications, 2018, doi:<a href="https://doi.org/10.7554/eLife.37888">10.7554/eLife.37888</a>.
  short: J.H. Alanko, M.K. Sixt, ELife 7 (2018).
date_created: 2019-01-20T22:59:19Z
date_published: 2018-06-06T00:00:00Z
date_updated: 2023-09-19T10:01:39Z
day: '06'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.7554/eLife.37888
external_id:
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  file_name: 2018_eLife_Alanko.pdf
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month: '06'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
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publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: The cell sets the tone
tmp:
  image: /images/cc_by.png
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  short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2018'
...
---
_id: '704'
abstract:
- lang: eng
  text: 'How the organization of genes on a chromosome shapes adaptation is essential
    for understanding evolutionary paths. Here, we investigate how adaptation to rapidly
    increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance
    gene inserted at different positions of the Escherichia coli chromosome. Using
    a dual-fluorescence reporter that allows us to distinguish gene amplifications
    from other up-mutations, we track in real-time adaptive changes in expression
    of the drug-resistance gene. We find that the relative contribution of several
    mutation types differs systematically between loci due to properties of neighboring
    genes: essentiality, expression, orientation, termination, and presence of duplicates.
    These properties determine rate and fitness effects of gene amplification, deletions,
    and mutations compromising transcriptional termination. Thus, the adaptive potential
    of a gene under selection is a system-property with a complex genetic basis that
    is specific for each chromosomal locus, and it can be inferred from detailed functional
    and genomic data.'
article_number: e25100
author:
- first_name: Magdalena
  full_name: Steinrück, Magdalena
  id: 2C023F40-F248-11E8-B48F-1D18A9856A87
  last_name: Steinrück
  orcid: 0000-0003-1229-9719
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
citation:
  ama: Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the
    adaptive potential of a gene under selection. <i>eLife</i>. 2017;6. doi:<a href="https://doi.org/10.7554/eLife.25100">10.7554/eLife.25100</a>
  apa: Steinrück, M., &#38; Guet, C. C. (2017). Complex chromosomal neighborhood effects
    determine the adaptive potential of a gene under selection. <i>ELife</i>. eLife
    Sciences Publications. <a href="https://doi.org/10.7554/eLife.25100">https://doi.org/10.7554/eLife.25100</a>
  chicago: Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood
    Effects Determine the Adaptive Potential of a Gene under Selection.” <i>ELife</i>.
    eLife Sciences Publications, 2017. <a href="https://doi.org/10.7554/eLife.25100">https://doi.org/10.7554/eLife.25100</a>.
  ieee: M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine
    the adaptive potential of a gene under selection,” <i>eLife</i>, vol. 6. eLife
    Sciences Publications, 2017.
  ista: Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine
    the adaptive potential of a gene under selection. eLife. 6, e25100.
  mla: Steinrück, Magdalena, and Calin C. Guet. “Complex Chromosomal Neighborhood
    Effects Determine the Adaptive Potential of a Gene under Selection.” <i>ELife</i>,
    vol. 6, e25100, eLife Sciences Publications, 2017, doi:<a href="https://doi.org/10.7554/eLife.25100">10.7554/eLife.25100</a>.
  short: M. Steinrück, C.C. Guet, ELife 6 (2017).
date_created: 2018-12-11T11:48:01Z
date_published: 2017-07-25T00:00:00Z
date_updated: 2024-03-25T23:30:14Z
day: '25'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.7554/eLife.25100
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language:
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month: '07'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
  issn:
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publication_status: published
publisher: eLife Sciences Publications
publist_id: '6990'
pubrep_id: '890'
quality_controlled: '1'
related_material:
  record:
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    relation: popular_science
    status: public
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    relation: dissertation_contains
    status: public
scopus_import: 1
status: public
title: Complex chromosomal neighborhood effects determine the adaptive potential of
  a gene under selection
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: 6
year: '2017'
...
---
_id: '713'
abstract:
- lang: eng
  text: To determine the dynamics of allelic-specific expression during mouse development,
    we analyzed RNA-seq data from 23 F1 tissues from different developmental stages,
    including 19 female tissues allowing X chromosome inactivation (XCI) escapers
    to also be detected. We demonstrate that allelic expression arising from genetic
    or epigenetic differences is highly tissue-specific. We find that tissue-specific
    strain-biased gene expression may be regulated by tissue-specific enhancers or
    by post-transcriptional differences in stability between the alleles. We also
    find that escape from X-inactivation is tissue-specific, with leg muscle showing
    an unexpectedly high rate of XCI escapers. By surveying a range of tissues during
    development, and performing extensive validation, we are able to provide a high
    confidence list of mouse imprinted genes including 18 novel genes. This shows
    that cluster size varies dynamically during development and can be substantially
    larger than previously thought, with the Igf2r cluster extending over 10 Mb in
    placenta.
article_number: e25125
author:
- first_name: Daniel
  full_name: Andergassen, Daniel
  last_name: Andergassen
- first_name: Christoph
  full_name: Dotter, Christoph
  id: 4C66542E-F248-11E8-B48F-1D18A9856A87
  last_name: Dotter
- first_name: Dyniel
  full_name: Wenzel, Dyniel
  last_name: Wenzel
- first_name: Verena
  full_name: Sigl, Verena
  last_name: Sigl
- first_name: Philipp
  full_name: Bammer, Philipp
  last_name: Bammer
- first_name: Markus
  full_name: Muckenhuber, Markus
  last_name: Muckenhuber
- first_name: Daniela
  full_name: Mayer, Daniela
  last_name: Mayer
- first_name: Tomasz
  full_name: Kulinski, Tomasz
  last_name: Kulinski
- first_name: Hans
  full_name: Theussl, Hans
  last_name: Theussl
- first_name: Josef
  full_name: Penninger, Josef
  last_name: Penninger
- first_name: Christoph
  full_name: Bock, Christoph
  last_name: Bock
- first_name: Denise
  full_name: Barlow, Denise
  last_name: Barlow
- first_name: Florian
  full_name: Pauler, Florian
  id: 48EA0138-F248-11E8-B48F-1D18A9856A87
  last_name: Pauler
- first_name: Quanah
  full_name: Hudson, Quanah
  last_name: Hudson
citation:
  ama: Andergassen D, Dotter C, Wenzel D, et al. Mapping the mouse Allelome reveals
    tissue specific regulation of allelic expression. <i>eLife</i>. 2017;6. doi:<a
    href="https://doi.org/10.7554/eLife.25125">10.7554/eLife.25125</a>
  apa: Andergassen, D., Dotter, C., Wenzel, D., Sigl, V., Bammer, P., Muckenhuber,
    M., … Hudson, Q. (2017). Mapping the mouse Allelome reveals tissue specific regulation
    of allelic expression. <i>ELife</i>. eLife Sciences Publications. <a href="https://doi.org/10.7554/eLife.25125">https://doi.org/10.7554/eLife.25125</a>
  chicago: Andergassen, Daniel, Christoph Dotter, Dyniel Wenzel, Verena Sigl, Philipp
    Bammer, Markus Muckenhuber, Daniela Mayer, et al. “Mapping the Mouse Allelome
    Reveals Tissue Specific Regulation of Allelic Expression.” <i>ELife</i>. eLife
    Sciences Publications, 2017. <a href="https://doi.org/10.7554/eLife.25125">https://doi.org/10.7554/eLife.25125</a>.
  ieee: D. Andergassen <i>et al.</i>, “Mapping the mouse Allelome reveals tissue specific
    regulation of allelic expression,” <i>eLife</i>, vol. 6. eLife Sciences Publications,
    2017.
  ista: Andergassen D, Dotter C, Wenzel D, Sigl V, Bammer P, Muckenhuber M, Mayer
    D, Kulinski T, Theussl H, Penninger J, Bock C, Barlow D, Pauler F, Hudson Q. 2017.
    Mapping the mouse Allelome reveals tissue specific regulation of allelic expression.
    eLife. 6, e25125.
  mla: Andergassen, Daniel, et al. “Mapping the Mouse Allelome Reveals Tissue Specific
    Regulation of Allelic Expression.” <i>ELife</i>, vol. 6, e25125, eLife Sciences
    Publications, 2017, doi:<a href="https://doi.org/10.7554/eLife.25125">10.7554/eLife.25125</a>.
  short: D. Andergassen, C. Dotter, D. Wenzel, V. Sigl, P. Bammer, M. Muckenhuber,
    D. Mayer, T. Kulinski, H. Theussl, J. Penninger, C. Bock, D. Barlow, F. Pauler,
    Q. Hudson, ELife 6 (2017).
date_created: 2018-12-11T11:48:05Z
date_published: 2017-08-14T00:00:00Z
date_updated: 2021-01-12T08:11:57Z
day: '14'
ddc:
- '576'
department:
- _id: GaNo
- _id: SiHi
doi: 10.7554/eLife.25125
file:
- access_level: open_access
  checksum: 1ace3462e64a971b9ead896091829549
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:13:36Z
  date_updated: 2020-07-14T12:47:50Z
  file_id: '5020'
  file_name: IST-2017-885-v1+1_elife-25125-figures-v2.pdf
  file_size: 6399510
  relation: main_file
- access_level: open_access
  checksum: 6241dc31eeb87b03facadec3a53a6827
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:13:36Z
  date_updated: 2020-07-14T12:47:50Z
  file_id: '5021'
  file_name: IST-2017-885-v1+2_elife-25125-v2.pdf
  file_size: 4264398
  relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
intvolume: '         6'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P27201-B22
  name: Revealing the mechanisms underlying drug interactions
publication: eLife
publication_identifier:
  issn:
  - 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6971'
pubrep_id: '885'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mapping the mouse Allelome reveals tissue specific regulation of allelic expression
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: 6
year: '2017'
...
---
_id: '569'
abstract:
- lang: eng
  text: The actomyosin ring generates force to ingress the cytokinetic cleavage furrow
    in animal cells, yet its filament organization and the mechanism of contractility
    is not well understood. We quantified actin filament order in human cells using
    fluorescence polarization microscopy and found that cleavage furrow ingression
    initiates by contraction of an equatorial actin network with randomly oriented
    filaments. The network subsequently gradually reoriented actin filaments along
    the cell equator. This strictly depended on myosin II activity, suggesting local
    network reorganization by mechanical forces. Cortical laser microsurgery revealed
    that during cytokinesis progression, mechanical tension increased substantially
    along the direction of the cell equator, while the network contracted laterally
    along the pole-to-pole axis without a detectable increase in tension. Our data
    suggest that an asymmetric increase in cortical tension promotes filament reorientation
    along the cytokinetic cleavage furrow, which might have implications for diverse
    other biological processes involving actomyosin rings.
article_number: e30867
author:
- first_name: Felix
  full_name: Spira, Felix
  last_name: Spira
- first_name: Sara
  full_name: Cuylen Haering, Sara
  last_name: Cuylen Haering
- first_name: Shalin
  full_name: Mehta, Shalin
  last_name: Mehta
- first_name: Matthias
  full_name: Samwer, Matthias
  last_name: Samwer
- first_name: Anne
  full_name: Reversat, Anne
  id: 35B76592-F248-11E8-B48F-1D18A9856A87
  last_name: Reversat
  orcid: 0000-0003-0666-8928
- first_name: Amitabh
  full_name: Verma, Amitabh
  last_name: Verma
- first_name: Rudolf
  full_name: Oldenbourg, Rudolf
  last_name: Oldenbourg
- first_name: Michael K
  full_name: Sixt, Michael K
  id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
  last_name: Sixt
  orcid: 0000-0002-6620-9179
- first_name: Daniel
  full_name: Gerlich, Daniel
  last_name: Gerlich
citation:
  ama: Spira F, Cuylen Haering S, Mehta S, et al. Cytokinesis in vertebrate cells
    initiates by contraction of an equatorial actomyosin network composed of randomly
    oriented filaments. <i>eLife</i>. 2017;6. doi:<a href="https://doi.org/10.7554/eLife.30867">10.7554/eLife.30867</a>
  apa: Spira, F., Cuylen Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma,
    A., … Gerlich, D. (2017). Cytokinesis in vertebrate cells initiates by contraction
    of an equatorial actomyosin network composed of randomly oriented filaments. <i>ELife</i>.
    eLife Sciences Publications. <a href="https://doi.org/10.7554/eLife.30867">https://doi.org/10.7554/eLife.30867</a>
  chicago: Spira, Felix, Sara Cuylen Haering, Shalin Mehta, Matthias Samwer, Anne
    Reversat, Amitabh Verma, Rudolf Oldenbourg, Michael K Sixt, and Daniel Gerlich.
    “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin
    Network Composed of Randomly Oriented Filaments.” <i>ELife</i>. eLife Sciences
    Publications, 2017. <a href="https://doi.org/10.7554/eLife.30867">https://doi.org/10.7554/eLife.30867</a>.
  ieee: F. Spira <i>et al.</i>, “Cytokinesis in vertebrate cells initiates by contraction
    of an equatorial actomyosin network composed of randomly oriented filaments,”
    <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.
  ista: Spira F, Cuylen Haering S, Mehta S, Samwer M, Reversat A, Verma A, Oldenbourg
    R, Sixt MK, Gerlich D. 2017. Cytokinesis in vertebrate cells initiates by contraction
    of an equatorial actomyosin network composed of randomly oriented filaments. eLife.
    6, e30867.
  mla: Spira, Felix, et al. “Cytokinesis in Vertebrate Cells Initiates by Contraction
    of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.”
    <i>ELife</i>, vol. 6, e30867, eLife Sciences Publications, 2017, doi:<a href="https://doi.org/10.7554/eLife.30867">10.7554/eLife.30867</a>.
  short: F. Spira, S. Cuylen Haering, S. Mehta, M. Samwer, A. Reversat, A. Verma,
    R. Oldenbourg, M.K. Sixt, D. Gerlich, ELife 6 (2017).
date_created: 2018-12-11T11:47:14Z
date_published: 2017-11-06T00:00:00Z
date_updated: 2023-02-23T12:30:29Z
day: '06'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.7554/eLife.30867
file:
- access_level: open_access
  checksum: ba09c1451153d39e4f4b7cee013e314c
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:10:40Z
  date_updated: 2020-07-14T12:47:10Z
  file_id: '4829'
  file_name: IST-2017-919-v1+1_elife-30867-figures-v1.pdf
  file_size: 9666973
  relation: main_file
- access_level: open_access
  checksum: 01eb51f1d6ad679947415a51c988e137
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:10:41Z
  date_updated: 2020-07-14T12:47:10Z
  file_id: '4830'
  file_name: IST-2017-919-v1+2_elife-30867-v1.pdf
  file_size: 5951246
  relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: '         6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
  issn:
  - 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7245'
pubrep_id: '919'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin
  network composed of randomly oriented filaments
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: 6
year: '2017'
...
---
_id: '570'
abstract:
- lang: eng
  text: 'Most phenotypes are determined by molecular systems composed of specifically
    interacting molecules. However, unlike for individual components, little is known
    about the distributions of mutational effects of molecular systems as a whole.
    We ask how the distribution of mutational effects of a transcriptional regulatory
    system differs from the distributions of its components, by first independently,
    and then simultaneously, mutating a transcription factor and the associated promoter
    it represses. We find that the system distribution exhibits increased phenotypic
    variation compared to individual component distributions - an effect arising from
    intermolecular epistasis between the transcription factor and its DNA-binding
    site. In large part, this epistasis can be qualitatively attributed to the structure
    of the transcriptional regulatory system and could therefore be a common feature
    in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the
    constraints of individual components, thereby increasing phenotypic variation
    that selection could act on and facilitating adaptive evolution. '
article_number: e28921
author:
- first_name: Mato
  full_name: Lagator, Mato
  id: 345D25EC-F248-11E8-B48F-1D18A9856A87
  last_name: Lagator
- first_name: Srdjan
  full_name: Sarikas, Srdjan
  id: 35F0286E-F248-11E8-B48F-1D18A9856A87
  last_name: Sarikas
- first_name: Hande
  full_name: Acar, Hande
  id: 2DDF136A-F248-11E8-B48F-1D18A9856A87
  last_name: Acar
  orcid: 0000-0003-1986-9753
- first_name: Jonathan P
  full_name: Bollback, Jonathan P
  id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
  last_name: Bollback
  orcid: 0000-0002-4624-4612
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
citation:
  ama: Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure
    determines patterns of intermolecular epistasis. <i>eLife</i>. 2017;6. doi:<a
    href="https://doi.org/10.7554/eLife.28921">10.7554/eLife.28921</a>
  apa: Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., &#38; Guet, C. C. (2017).
    Regulatory network structure determines patterns of intermolecular epistasis.
    <i>ELife</i>. eLife Sciences Publications. <a href="https://doi.org/10.7554/eLife.28921">https://doi.org/10.7554/eLife.28921</a>
  chicago: Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin
    C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.”
    <i>ELife</i>. eLife Sciences Publications, 2017. <a href="https://doi.org/10.7554/eLife.28921">https://doi.org/10.7554/eLife.28921</a>.
  ieee: M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory
    network structure determines patterns of intermolecular epistasis,” <i>eLife</i>,
    vol. 6. eLife Sciences Publications, 2017.
  ista: Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network
    structure determines patterns of intermolecular epistasis. eLife. 6, e28921.
  mla: Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of
    Intermolecular Epistasis.” <i>ELife</i>, vol. 6, e28921, eLife Sciences Publications,
    2017, doi:<a href="https://doi.org/10.7554/eLife.28921">10.7554/eLife.28921</a>.
  short: M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).
date_created: 2018-12-11T11:47:14Z
date_published: 2017-11-13T00:00:00Z
date_updated: 2021-01-12T08:03:15Z
day: '13'
ddc:
- '576'
department:
- _id: CaGu
- _id: JoBo
- _id: NiBa
doi: 10.7554/eLife.28921
ec_funded: 1
file:
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file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: '         6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
- _id: 2578D616-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '648440'
  name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
  issn:
  - 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7244'
pubrep_id: '918'
quality_controlled: '1'
scopus_import: 1
status: public
title: Regulatory network structure determines patterns of intermolecular epistasis
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: 6
year: '2017'
...
---
_id: '655'
abstract:
- lang: eng
  text: 'The bacterial flagellum is a self-assembling nanomachine. The external flagellar
    filament, several times longer than a bacterial cell body, is made of a few tens
    of thousands subunits of a single protein: flagellin. A fundamental problem concerns
    the molecular mechanism of how the flagellum grows outside the cell, where no
    discernible energy source is available. Here, we monitored the dynamic assembly
    of individual flagella using in situ labelling and real-time immunostaining of
    elongating flagellar filaments. We report that the rate of flagellum growth, initially
    ~1,700 amino acids per second, decreases with length and that the previously proposed
    chain mechanism does not contribute to the filament elongation dynamics. Inhibition
    of the proton motive force-dependent export apparatus revealed a major contribution
    of substrate injection in driving filament elongation. The combination of experimental
    and mathematical evidence demonstrates that a simple, injection-diffusion mechanism
    controls bacterial flagella growth outside the cell.'
article_number: e23136
author:
- first_name: Thibaud
  full_name: Renault, Thibaud
  last_name: Renault
- first_name: Anthony
  full_name: Abraham, Anthony
  last_name: Abraham
- first_name: Tobias
  full_name: Bergmiller, Tobias
  id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
  last_name: Bergmiller
  orcid: 0000-0001-5396-4346
- first_name: Guillaume
  full_name: Paradis, Guillaume
  last_name: Paradis
- first_name: Simon
  full_name: Rainville, Simon
  last_name: Rainville
- first_name: Emmanuelle
  full_name: Charpentier, Emmanuelle
  last_name: Charpentier
- 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: Yuhai
  full_name: Tu, Yuhai
  last_name: Tu
- first_name: Keiichi
  full_name: Namba, Keiichi
  last_name: Namba
- first_name: James
  full_name: Keener, James
  last_name: Keener
- first_name: Tohru
  full_name: Minamino, Tohru
  last_name: Minamino
- first_name: Marc
  full_name: Erhardt, Marc
  last_name: Erhardt
citation:
  ama: Renault T, Abraham A, Bergmiller T, et al. Bacterial flagella grow through
    an injection diffusion mechanism. <i>eLife</i>. 2017;6. doi:<a href="https://doi.org/10.7554/eLife.23136">10.7554/eLife.23136</a>
  apa: Renault, T., Abraham, A., Bergmiller, T., Paradis, G., Rainville, S., Charpentier,
    E., … Erhardt, M. (2017). Bacterial flagella grow through an injection diffusion
    mechanism. <i>ELife</i>. eLife Sciences Publications. <a href="https://doi.org/10.7554/eLife.23136">https://doi.org/10.7554/eLife.23136</a>
  chicago: Renault, Thibaud, Anthony Abraham, Tobias Bergmiller, Guillaume Paradis,
    Simon Rainville, Emmanuelle Charpentier, Calin C Guet, et al. “Bacterial Flagella
    Grow through an Injection Diffusion Mechanism.” <i>ELife</i>. eLife Sciences Publications,
    2017. <a href="https://doi.org/10.7554/eLife.23136">https://doi.org/10.7554/eLife.23136</a>.
  ieee: T. Renault <i>et al.</i>, “Bacterial flagella grow through an injection diffusion
    mechanism,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.
  ista: Renault T, Abraham A, Bergmiller T, Paradis G, Rainville S, Charpentier E,
    Guet CC, Tu Y, Namba K, Keener J, Minamino T, Erhardt M. 2017. Bacterial flagella
    grow through an injection diffusion mechanism. eLife. 6, e23136.
  mla: Renault, Thibaud, et al. “Bacterial Flagella Grow through an Injection Diffusion
    Mechanism.” <i>ELife</i>, vol. 6, e23136, eLife Sciences Publications, 2017, doi:<a
    href="https://doi.org/10.7554/eLife.23136">10.7554/eLife.23136</a>.
  short: T. Renault, A. Abraham, T. Bergmiller, G. Paradis, S. Rainville, E. Charpentier,
    C.C. Guet, Y. Tu, K. Namba, J. Keener, T. Minamino, M. Erhardt, ELife 6 (2017).
date_created: 2018-12-11T11:47:44Z
date_published: 2017-03-06T00:00:00Z
date_updated: 2021-01-12T08:07:55Z
day: '06'
ddc:
- '579'
department:
- _id: CaGu
doi: 10.7554/eLife.23136
file:
- access_level: open_access
  checksum: 39e1c3e82ddac83a30422fa72fa1a383
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:08:53Z
  date_updated: 2020-07-14T12:47:33Z
  file_id: '4716'
  file_name: IST-2017-904-v1+1_elife-23136-v2.pdf
  file_size: 5520359
  relation: main_file
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  checksum: a6d542253028f52e00aa29739ddffe8f
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:08:54Z
  date_updated: 2020-07-14T12:47:33Z
  file_id: '4717'
  file_name: IST-2017-904-v1+2_elife-23136-figures-v2.pdf
  file_size: 11242920
  relation: main_file
file_date_updated: 2020-07-14T12:47:33Z
has_accepted_license: '1'
intvolume: '         6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
  issn:
  - 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7082'
pubrep_id: '904'
quality_controlled: '1'
scopus_import: 1
status: public
title: Bacterial flagella grow through an injection diffusion mechanism
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: 6
year: '2017'
...
---
_id: '954'
abstract:
- lang: eng
  text: Understanding the relation between genotype and phenotype remains a major
    challenge. The difficulty of predicting individual mutation effects, and particularly
    the interactions between them, has prevented the development of a comprehensive
    theory that links genotypic changes to their phenotypic effects. We show that
    a general thermodynamic framework for gene regulation, based on a biophysical
    understanding of protein-DNA binding, accurately predicts the sign of epistasis
    in a canonical cis-regulatory element consisting of overlapping RNA polymerase
    and repressor binding sites. Sign and magnitude of individual mutation effects
    are sufficient to predict the sign of epistasis and its environmental dependence.
    Thus, the thermodynamic model offers the correct null prediction for epistasis
    between mutations across DNA-binding sites. Our results indicate that a predictive
    theory for the effects of cis-regulatory mutations is possible from first principles,
    as long as the essential molecular mechanisms and the constraints these impose
    on a biological system are accounted for.
article_number: e25192
article_processing_charge: Yes
author:
- first_name: Mato
  full_name: Lagator, Mato
  id: 345D25EC-F248-11E8-B48F-1D18A9856A87
  last_name: Lagator
- 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: Jonathan P
  full_name: Bollback, Jonathan P
  id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
  last_name: Bollback
  orcid: 0000-0002-4624-4612
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
citation:
  ama: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature
    of epistasis in a canonical cis-regulatory element. <i>eLife</i>. 2017;6. doi:<a
    href="https://doi.org/10.7554/eLife.25192">10.7554/eLife.25192</a>
  apa: Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., &#38; Guet, C. C.
    (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element.
    <i>ELife</i>. eLife Sciences Publications. <a href="https://doi.org/10.7554/eLife.25192">https://doi.org/10.7554/eLife.25192</a>
  chicago: Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and
    Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory
    Element.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href="https://doi.org/10.7554/eLife.25192">https://doi.org/10.7554/eLife.25192</a>.
  ieee: M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the
    mechanistic nature of epistasis in a canonical cis-regulatory element,” <i>eLife</i>,
    vol. 6. eLife Sciences Publications, 2017.
  ista: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic
    nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.
  mla: Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical
    Cis-Regulatory Element.” <i>ELife</i>, vol. 6, e25192, eLife Sciences Publications,
    2017, doi:<a href="https://doi.org/10.7554/eLife.25192">10.7554/eLife.25192</a>.
  short: M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-05-18T00:00:00Z
date_updated: 2023-09-22T10:01:17Z
day: '18'
ddc:
- '576'
department:
- _id: CaGu
- _id: NiBa
- _id: JoBo
doi: 10.7554/eLife.25192
ec_funded: 1
external_id:
  isi:
  - '000404024800001'
file:
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  checksum: 59cdd4400fb41280122d414fea971546
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:17:49Z
  date_updated: 2020-07-14T12:48:16Z
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  file_size: 2441529
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  date_created: 2018-12-12T10:17:50Z
  date_updated: 2020-07-14T12:48:16Z
  file_id: '5307'
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  file_size: 3752660
  relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: '         6'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '618091'
  name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
- _id: 2578D616-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '648440'
  name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
  issn:
  - 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6460'
pubrep_id: '841'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the mechanistic nature of epistasis in a canonical cis-regulatory element
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 6
year: '2017'
...