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Reference
Citation
Zinzen, R.P., Girardot, C., Gagneur, J., Braun, M., Furlong, E.E. (2009). Combinatorial binding predicts spatio-temporal cis-regulatory activity.  Nature 462(7269): 65--70.
FlyBase ID
FBrf0209262
Publication Type
Research paper
Abstract

Development requires the establishment of precise patterns of gene expression, which are primarily controlled by transcription factors binding to cis-regulatory modules. Although transcription factor occupancy can now be identified at genome-wide scales, decoding this regulatory landscape remains a daunting challenge. Here we used a novel approach to predict spatio-temporal cis-regulatory activity based only on in vivo transcription factor binding and enhancer activity data. We generated a high-resolution atlas of cis-regulatory modules describing their temporal and combinatorial occupancy during Drosophila mesoderm development. The binding profiles of cis-regulatory modules with characterized expression were used to train support vector machines to predict five spatio-temporal expression patterns. In vivo transgenic reporter assays demonstrate the high accuracy of these predictions and reveal an unanticipated plasticity in transcription factor binding leading to similar expression. This data-driven approach does not require previous knowledge of transcription factor sequence affinity, function or expression, making it widely applicable.

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Personal communication to FlyBase

Furlong Lab EMBL TFBS contribution.
Monfort and Furlong, 2015.1.15, Furlong Lab EMBL TFBS contribution. [FBrf0227761]

Note

ChIPs and regulatory bits.
He and Sinha, 2010, Nat. Biotechnol. 28(2): 142--143 [FBrf0214969]

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Secondary IDs
    Language of Publication
    English
    Additional Languages of Abstract
    Parent Publication
    Publication Type
    Journal
    Abbreviation
    Nature
    Title
    Nature
    Publication Year
    1869-
    ISBN/ISSN
    0028-0836
    Data From Reference
    Alleles (14)
    Genes (10)
    Datasets (46)
    Sequence Features (78)
    Natural transposons (1)
    Experimental Tools (1)
    Transgenic Constructs (14)
    Transcripts (12)