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PXD007892

DataSet Summary

  • HostingRepository: jPOST
  • AnnounceDate: 2018-04-13
  • AnnouncementXML: Submission_2018-09-19_00:38:51.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Michael Sweredoski
  • Title: A systematic and scalable approach for dissecting the molecular 2 mechanisms of transcriptional regulation in bacteria
  • Description: Gene regulation is one of the most ubiquitous processes in biology. And yet, while the catalogue of 15 bacterial genomes continues to expand rapidly, we remain ignorant about how almost all of the genes in 16 these genomes are regulated. Characterizing the molecular mechanisms by which regulatory sequences 17 operate still requires focused efforts using low-throughput methods. Here we show how a combination of 18 massively parallel reporter assays, mass spectrometry, and information-theoretic modeling can be used 19 to dissect bacterial promoters in a systematic and scalable way. We demonstrate this method on both 20 well-studied and previously uncharacterized promoters in the enteric bacterium Escherichia coli. In all 21 cases we recover nucleotide-resolution models of promoter mechanism. For some promoters, including 22 previously unannotated ones, we can further extract quantitative biophysical models describing 23 input-output relationships. This method opens up the possibility of exhaustively dissecting the 24 mechanisms of promoter function in E. coli and a wide range of other bacteria.
  • SpeciesList: scientific name: Escherichia coli; NCBI TaxID: 562;
  • ModificationList: S-carboxamidomethyl-L-cysteine; Label:13C(6)15N(2); alpha-amino acetylated residue; L-methionine sulfoxide
  • Instrument: LTQ Orbitrap Elite

Dataset History

VersionDatetimeStatusChangeLog Entry
02017-10-02 11:56:14ID requested
12018-04-13 15:10:30announced
22018-05-11 08:54:56announcedUpdated PubMed.
32018-09-19 00:38:52announcedUpdated CV, FTP location and Modification list.

Publication List

  1. Belliveau NM, Barnes SL, Ireland WT, Jones DL, Sweredoski MJ, Moradian A, Hess S, Kinney JB, Phillips R, Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria. Proc Natl Acad Sci U S A, 115(21):E4796-E4805(2018) [pubmed]

Keyword List

  1. submitter keyword: e coli, SILAC, DNA affinity, transcription factors

Contact List

    Rob Phillips
    • lab head:
    Michael Sweredoski
    • contact affiliation: California Institute of Technology
    • dataset submitter:

Full Dataset Link List

  1. jPOST dataset URI
  2. Dataset FTP location
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