On chaotic dynamics in transcription factors and the associated effects in differential gene regulation View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-12

AUTHORS

Mathias L. Heltberg, Sandeep Krishna, Mogens H. Jensen

ABSTRACT

The control of proteins by a transcription factor with periodically varying concentration exhibits intriguing dynamical behaviour. Even though it is accepted that transcription factors vary their dynamics in response to different situations, insight into how this affects downstream genes is lacking. Here, we investigate how oscillations and chaotic dynamics in the transcription factor NF-κB can affect downstream protein production. We describe how it is possible to control the effective dynamics of the transcription factor by stimulating it with an oscillating ligand. We find that chaotic dynamics modulates gene expression and up-regulates certain families of low-affinity genes, even in the presence of extrinsic and intrinsic noise. Furthermore, this leads to an increase in the production of protein complexes and the efficiency of their assembly. Finally, we show how chaotic dynamics creates a heterogeneous population of cell states, and describe how this can be beneficial in multi-toxic environments. More... »

PAGES

71

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41467-018-07932-1

DOI

http://dx.doi.org/10.1038/s41467-018-07932-1

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1111061194

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30622249


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Regulation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Ligands", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Models, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "NF-kappa B", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Nonlinear Dynamics", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100, Copenhagen, Denmark"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Heltberg", 
        "givenName": "Mathias L.", 
        "id": "sg:person.013175336345.00", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013175336345.00"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Agricultural Sciences, Bangalore", 
          "id": "https://www.grid.ac/institutes/grid.413008.e", 
          "name": [
            "Simons Centre for the Study of Living Machines, National Centre for Biological Sciences-TIFR, GKVK Campus, Bellary Road, 560065, Bangalore, India"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Krishna", 
        "givenName": "Sandeep", 
        "id": "sg:person.01207433430.52", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01207433430.52"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100, Copenhagen, Denmark"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Jensen", 
        "givenName": "Mogens H.", 
        "id": "sg:person.01152213267.83", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01152213267.83"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1103/physrevlett.92.094101", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000730260"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1103/physrevlett.92.094101", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000730260"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0032678", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001079469"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1600-065x.2011.01092.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003710085"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.molcel.2008.01.021", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004335148"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0604085103", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004687556"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cels.2016.11.014", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005899878"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.febslet.2012.04.044", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006661448"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1742-2094-2-26", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007631791", 
          "https://doi.org/10.1186/1742-2094-2-26"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-94-010-0217-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009134840", 
          "https://doi.org/10.1007/978-94-010-0217-2"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-94-010-0217-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009134840", 
          "https://doi.org/10.1007/978-94-010-0217-2"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1239999", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009701548"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1046/j.1365-2249.2000.01339.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011734855"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1164860", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012072615"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1103/physreve.76.061909", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013313981"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1103/physreve.76.061909", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013313981"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1071914", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018025859"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0375-9601(85)90651-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018995564"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0375-9601(85)90651-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018995564"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.022628299", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019107802"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1752-0509-5-115", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023471183", 
          "https://doi.org/10.1186/1752-0509-5-115"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.celrep.2016.09.060", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025869315"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1293", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028461027", 
          "https://doi.org/10.1038/ng1293"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1293", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028461027", 
          "https://doi.org/10.1038/ng1293"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1205369", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029524766"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1600-065x.2007.00501.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030150509"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature01259", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031369938", 
          "https://doi.org/10.1038/nature01259"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature01259", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031369938", 
          "https://doi.org/10.1038/nature01259"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature01259", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031369938", 
          "https://doi.org/10.1038/nature01259"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.biophys.093008.131241", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032896418"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1098/rspb.1999.0911", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035607975"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0906361106", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036466201"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1175/1520-0469(1963)020<0130:dnf>2.0.co;2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037677363"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1156951", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048646284"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.gde.2010.08.008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050332485"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2015.01.013", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050775486"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/j100540a008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055672411"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1049/iet-syb.2009.0070", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1056838963"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1049/iet-syb.2009.0070", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1056838963"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1103/physreva.30.1960", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060472678"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1103/physreva.30.1960", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060472678"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1103/physrevlett.50.1637", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060788526"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1103/physrevlett.50.1637", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060788526"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1103/physrevlett.52.2277", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060790050"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1103/physrevlett.52.2277", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060790050"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1103/physrevlett.55.2798", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060792508"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1103/physrevlett.55.2798", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060792508"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1103/physrevlett.55.596", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060792670"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1103/physrevlett.55.596", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060792670"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1103/physrevlett.57.1060", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060793672"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1103/physrevlett.57.1060", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060793672"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1099962", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062449802"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1078462314", 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s10955-017-1750-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1084028221", 
          "https://doi.org/10.1007/s10955-017-1750-x"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s10955-017-1750-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1084028221", 
          "https://doi.org/10.1007/s10955-017-1750-x"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1039/c7lc00531h", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1085567172"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/acs.analchem.8b00312", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1105900137"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/acs.analchem.8b00312", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1105900137"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2019-12", 
    "datePublishedReg": "2019-12-01", 
    "description": "The control of proteins by a transcription factor with periodically varying concentration exhibits intriguing dynamical behaviour. Even though it is accepted that transcription factors vary their dynamics in response to different situations, insight into how this affects downstream genes is lacking. Here, we investigate how oscillations and chaotic dynamics in the transcription factor NF-\u03baB can affect downstream protein production. We describe how it is possible to control the effective dynamics of the transcription factor by stimulating it with an oscillating ligand. We find that chaotic dynamics modulates gene expression and up-regulates certain families of low-affinity genes, even in the presence of extrinsic and intrinsic noise. Furthermore, this leads to an increase in the production of protein complexes and the efficiency of their assembly. Finally, we show how chaotic dynamics creates a heterogeneous population of cell states, and describe how this can be beneficial in multi-toxic environments.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/s41467-018-07932-1", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1043282", 
        "issn": [
          "2041-1723"
        ], 
        "name": "Nature Communications", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "10"
      }
    ], 
    "name": "On chaotic dynamics in transcription factors and the associated effects in differential gene regulation", 
    "pagination": "71", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "1d747b23e999df077beb521629d2b26fa6bcc92b9b46a722a30af0ab08845c63"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "30622249"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101528555"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/s41467-018-07932-1"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1111061194"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/s41467-018-07932-1", 
      "https://app.dimensions.ai/details/publication/pub.1111061194"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T12:45", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000363_0000000363/records_70068_00000003.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://www.nature.com/articles/s41467-018-07932-1"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/s41467-018-07932-1'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41467-018-07932-1'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41467-018-07932-1'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41467-018-07932-1'


 

This table displays all metadata directly associated to this object as RDF triples.

236 TRIPLES      21 PREDICATES      76 URIs      26 LITERALS      14 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/s41467-018-07932-1 schema:about N5d8d613603514379afa665c04501edb5
2 N77d78950d1c740108347de399178bb28
3 N9af35a86c2f04c61bbf764e01f57beaf
4 Nb889ad0cef184b088341565fba8d7f8d
5 Nbf6b60d5dd4c4af0be222f959f023959
6 anzsrc-for:06
7 anzsrc-for:0604
8 schema:author N7c348bf56c844529b5466a726b51aa52
9 schema:citation sg:pub.10.1007/978-94-010-0217-2
10 sg:pub.10.1007/s10955-017-1750-x
11 sg:pub.10.1038/nature01259
12 sg:pub.10.1038/ng1293
13 sg:pub.10.1186/1742-2094-2-26
14 sg:pub.10.1186/1752-0509-5-115
15 https://app.dimensions.ai/details/publication/pub.1078462314
16 https://doi.org/10.1016/0375-9601(85)90651-6
17 https://doi.org/10.1016/j.cell.2015.01.013
18 https://doi.org/10.1016/j.celrep.2016.09.060
19 https://doi.org/10.1016/j.cels.2016.11.014
20 https://doi.org/10.1016/j.febslet.2012.04.044
21 https://doi.org/10.1016/j.gde.2010.08.008
22 https://doi.org/10.1016/j.molcel.2008.01.021
23 https://doi.org/10.1021/acs.analchem.8b00312
24 https://doi.org/10.1021/j100540a008
25 https://doi.org/10.1039/c7lc00531h
26 https://doi.org/10.1046/j.1365-2249.2000.01339.x
27 https://doi.org/10.1049/iet-syb.2009.0070
28 https://doi.org/10.1073/pnas.022628299
29 https://doi.org/10.1073/pnas.0604085103
30 https://doi.org/10.1073/pnas.0906361106
31 https://doi.org/10.1098/rspb.1999.0911
32 https://doi.org/10.1103/physreva.30.1960
33 https://doi.org/10.1103/physreve.76.061909
34 https://doi.org/10.1103/physrevlett.50.1637
35 https://doi.org/10.1103/physrevlett.52.2277
36 https://doi.org/10.1103/physrevlett.55.2798
37 https://doi.org/10.1103/physrevlett.55.596
38 https://doi.org/10.1103/physrevlett.57.1060
39 https://doi.org/10.1103/physrevlett.92.094101
40 https://doi.org/10.1111/j.1600-065x.2007.00501.x
41 https://doi.org/10.1111/j.1600-065x.2011.01092.x
42 https://doi.org/10.1126/science.1071914
43 https://doi.org/10.1126/science.1099962
44 https://doi.org/10.1126/science.1156951
45 https://doi.org/10.1126/science.1164860
46 https://doi.org/10.1126/science.1205369
47 https://doi.org/10.1126/science.1239999
48 https://doi.org/10.1146/annurev.biophys.093008.131241
49 https://doi.org/10.1175/1520-0469(1963)020<0130:dnf>2.0.co;2
50 https://doi.org/10.1371/journal.pone.0032678
51 schema:datePublished 2019-12
52 schema:datePublishedReg 2019-12-01
53 schema:description The control of proteins by a transcription factor with periodically varying concentration exhibits intriguing dynamical behaviour. Even though it is accepted that transcription factors vary their dynamics in response to different situations, insight into how this affects downstream genes is lacking. Here, we investigate how oscillations and chaotic dynamics in the transcription factor NF-κB can affect downstream protein production. We describe how it is possible to control the effective dynamics of the transcription factor by stimulating it with an oscillating ligand. We find that chaotic dynamics modulates gene expression and up-regulates certain families of low-affinity genes, even in the presence of extrinsic and intrinsic noise. Furthermore, this leads to an increase in the production of protein complexes and the efficiency of their assembly. Finally, we show how chaotic dynamics creates a heterogeneous population of cell states, and describe how this can be beneficial in multi-toxic environments.
54 schema:genre research_article
55 schema:inLanguage en
56 schema:isAccessibleForFree true
57 schema:isPartOf N731bf362b406452cb299c74e5dccf72d
58 Na0a2a75881a74123b26a1f082e30e7b4
59 sg:journal.1043282
60 schema:name On chaotic dynamics in transcription factors and the associated effects in differential gene regulation
61 schema:pagination 71
62 schema:productId N0d120b3908744d0aaa521400664befee
63 N157ab3f02a58416f82d493b7f4692ff5
64 N2d604732447843eca8c8a3473e493a61
65 N3b7d868a67f94857bf4776cba0b29c24
66 Ne3024fb21dcb4917b08dd15bde7fb378
67 schema:sameAs https://app.dimensions.ai/details/publication/pub.1111061194
68 https://doi.org/10.1038/s41467-018-07932-1
69 schema:sdDatePublished 2019-04-11T12:45
70 schema:sdLicense https://scigraph.springernature.com/explorer/license/
71 schema:sdPublisher N359f05d730134eba9dfc86a9284071a1
72 schema:url https://www.nature.com/articles/s41467-018-07932-1
73 sgo:license sg:explorer/license/
74 sgo:sdDataset articles
75 rdf:type schema:ScholarlyArticle
76 N054f540464324581b6c2e34ab03a22b1 rdf:first sg:person.01152213267.83
77 rdf:rest rdf:nil
78 N0d120b3908744d0aaa521400664befee schema:name readcube_id
79 schema:value 1d747b23e999df077beb521629d2b26fa6bcc92b9b46a722a30af0ab08845c63
80 rdf:type schema:PropertyValue
81 N157ab3f02a58416f82d493b7f4692ff5 schema:name nlm_unique_id
82 schema:value 101528555
83 rdf:type schema:PropertyValue
84 N2d604732447843eca8c8a3473e493a61 schema:name doi
85 schema:value 10.1038/s41467-018-07932-1
86 rdf:type schema:PropertyValue
87 N359f05d730134eba9dfc86a9284071a1 schema:name Springer Nature - SN SciGraph project
88 rdf:type schema:Organization
89 N3b7d868a67f94857bf4776cba0b29c24 schema:name dimensions_id
90 schema:value pub.1111061194
91 rdf:type schema:PropertyValue
92 N5d8d613603514379afa665c04501edb5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
93 schema:name NF-kappa B
94 rdf:type schema:DefinedTerm
95 N731bf362b406452cb299c74e5dccf72d schema:issueNumber 1
96 rdf:type schema:PublicationIssue
97 N77d78950d1c740108347de399178bb28 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
98 schema:name Gene Expression Regulation
99 rdf:type schema:DefinedTerm
100 N7c348bf56c844529b5466a726b51aa52 rdf:first sg:person.013175336345.00
101 rdf:rest Nc47a9097d4a84c529f0ca33cda99c2e0
102 N9af35a86c2f04c61bbf764e01f57beaf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
103 schema:name Models, Genetic
104 rdf:type schema:DefinedTerm
105 Na0a2a75881a74123b26a1f082e30e7b4 schema:volumeNumber 10
106 rdf:type schema:PublicationVolume
107 Nb889ad0cef184b088341565fba8d7f8d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
108 schema:name Nonlinear Dynamics
109 rdf:type schema:DefinedTerm
110 Nbf6b60d5dd4c4af0be222f959f023959 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
111 schema:name Ligands
112 rdf:type schema:DefinedTerm
113 Nc47a9097d4a84c529f0ca33cda99c2e0 rdf:first sg:person.01207433430.52
114 rdf:rest N054f540464324581b6c2e34ab03a22b1
115 Ne3024fb21dcb4917b08dd15bde7fb378 schema:name pubmed_id
116 schema:value 30622249
117 rdf:type schema:PropertyValue
118 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
119 schema:name Biological Sciences
120 rdf:type schema:DefinedTerm
121 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
122 schema:name Genetics
123 rdf:type schema:DefinedTerm
124 sg:journal.1043282 schema:issn 2041-1723
125 schema:name Nature Communications
126 rdf:type schema:Periodical
127 sg:person.01152213267.83 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
128 schema:familyName Jensen
129 schema:givenName Mogens H.
130 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01152213267.83
131 rdf:type schema:Person
132 sg:person.01207433430.52 schema:affiliation https://www.grid.ac/institutes/grid.413008.e
133 schema:familyName Krishna
134 schema:givenName Sandeep
135 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01207433430.52
136 rdf:type schema:Person
137 sg:person.013175336345.00 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
138 schema:familyName Heltberg
139 schema:givenName Mathias L.
140 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013175336345.00
141 rdf:type schema:Person
142 sg:pub.10.1007/978-94-010-0217-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009134840
143 https://doi.org/10.1007/978-94-010-0217-2
144 rdf:type schema:CreativeWork
145 sg:pub.10.1007/s10955-017-1750-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1084028221
146 https://doi.org/10.1007/s10955-017-1750-x
147 rdf:type schema:CreativeWork
148 sg:pub.10.1038/nature01259 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031369938
149 https://doi.org/10.1038/nature01259
150 rdf:type schema:CreativeWork
151 sg:pub.10.1038/ng1293 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028461027
152 https://doi.org/10.1038/ng1293
153 rdf:type schema:CreativeWork
154 sg:pub.10.1186/1742-2094-2-26 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007631791
155 https://doi.org/10.1186/1742-2094-2-26
156 rdf:type schema:CreativeWork
157 sg:pub.10.1186/1752-0509-5-115 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023471183
158 https://doi.org/10.1186/1752-0509-5-115
159 rdf:type schema:CreativeWork
160 https://app.dimensions.ai/details/publication/pub.1078462314 schema:CreativeWork
161 https://doi.org/10.1016/0375-9601(85)90651-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018995564
162 rdf:type schema:CreativeWork
163 https://doi.org/10.1016/j.cell.2015.01.013 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050775486
164 rdf:type schema:CreativeWork
165 https://doi.org/10.1016/j.celrep.2016.09.060 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025869315
166 rdf:type schema:CreativeWork
167 https://doi.org/10.1016/j.cels.2016.11.014 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005899878
168 rdf:type schema:CreativeWork
169 https://doi.org/10.1016/j.febslet.2012.04.044 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006661448
170 rdf:type schema:CreativeWork
171 https://doi.org/10.1016/j.gde.2010.08.008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050332485
172 rdf:type schema:CreativeWork
173 https://doi.org/10.1016/j.molcel.2008.01.021 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004335148
174 rdf:type schema:CreativeWork
175 https://doi.org/10.1021/acs.analchem.8b00312 schema:sameAs https://app.dimensions.ai/details/publication/pub.1105900137
176 rdf:type schema:CreativeWork
177 https://doi.org/10.1021/j100540a008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1055672411
178 rdf:type schema:CreativeWork
179 https://doi.org/10.1039/c7lc00531h schema:sameAs https://app.dimensions.ai/details/publication/pub.1085567172
180 rdf:type schema:CreativeWork
181 https://doi.org/10.1046/j.1365-2249.2000.01339.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1011734855
182 rdf:type schema:CreativeWork
183 https://doi.org/10.1049/iet-syb.2009.0070 schema:sameAs https://app.dimensions.ai/details/publication/pub.1056838963
184 rdf:type schema:CreativeWork
185 https://doi.org/10.1073/pnas.022628299 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019107802
186 rdf:type schema:CreativeWork
187 https://doi.org/10.1073/pnas.0604085103 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004687556
188 rdf:type schema:CreativeWork
189 https://doi.org/10.1073/pnas.0906361106 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036466201
190 rdf:type schema:CreativeWork
191 https://doi.org/10.1098/rspb.1999.0911 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035607975
192 rdf:type schema:CreativeWork
193 https://doi.org/10.1103/physreva.30.1960 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060472678
194 rdf:type schema:CreativeWork
195 https://doi.org/10.1103/physreve.76.061909 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013313981
196 rdf:type schema:CreativeWork
197 https://doi.org/10.1103/physrevlett.50.1637 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060788526
198 rdf:type schema:CreativeWork
199 https://doi.org/10.1103/physrevlett.52.2277 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060790050
200 rdf:type schema:CreativeWork
201 https://doi.org/10.1103/physrevlett.55.2798 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060792508
202 rdf:type schema:CreativeWork
203 https://doi.org/10.1103/physrevlett.55.596 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060792670
204 rdf:type schema:CreativeWork
205 https://doi.org/10.1103/physrevlett.57.1060 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060793672
206 rdf:type schema:CreativeWork
207 https://doi.org/10.1103/physrevlett.92.094101 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000730260
208 rdf:type schema:CreativeWork
209 https://doi.org/10.1111/j.1600-065x.2007.00501.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1030150509
210 rdf:type schema:CreativeWork
211 https://doi.org/10.1111/j.1600-065x.2011.01092.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1003710085
212 rdf:type schema:CreativeWork
213 https://doi.org/10.1126/science.1071914 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018025859
214 rdf:type schema:CreativeWork
215 https://doi.org/10.1126/science.1099962 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062449802
216 rdf:type schema:CreativeWork
217 https://doi.org/10.1126/science.1156951 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048646284
218 rdf:type schema:CreativeWork
219 https://doi.org/10.1126/science.1164860 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012072615
220 rdf:type schema:CreativeWork
221 https://doi.org/10.1126/science.1205369 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029524766
222 rdf:type schema:CreativeWork
223 https://doi.org/10.1126/science.1239999 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009701548
224 rdf:type schema:CreativeWork
225 https://doi.org/10.1146/annurev.biophys.093008.131241 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032896418
226 rdf:type schema:CreativeWork
227 https://doi.org/10.1175/1520-0469(1963)020<0130:dnf>2.0.co;2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037677363
228 rdf:type schema:CreativeWork
229 https://doi.org/10.1371/journal.pone.0032678 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001079469
230 rdf:type schema:CreativeWork
231 https://www.grid.ac/institutes/grid.413008.e schema:alternateName University of Agricultural Sciences, Bangalore
232 schema:name Simons Centre for the Study of Living Machines, National Centre for Biological Sciences-TIFR, GKVK Campus, Bellary Road, 560065, Bangalore, India
233 rdf:type schema:Organization
234 https://www.grid.ac/institutes/grid.5254.6 schema:alternateName University of Copenhagen
235 schema:name Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100, Copenhagen, Denmark
236 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...