One of the greatest challenges in animal biology is to learn how genomic sequence information is read by transcription factors to produce patterns of gene expression within the context of regulatory networks in developing embryos. This proposed Program Project will integrate computational modeling and wet laboratory methods to address this challenge in the belief that only quantitative, predictive mathematical models that have been validated experimentally can provide the rigorous understanding required. The proposal builds on a set of complementary, quantitative datasets that we have established for the Drosophila early embryo regulatory network, together with initial computational models for the targeting of factors to DNA and for the subsequent generation of specific patterns of transcriptional output. These preliminary experiments illustrate that factors show a shockingly broad, quantitative continuum of binding and function to highly overlapping genomic regions in vivo and suggest the molecular mechanism chiefly responsible for driving DNA binding in vivo. Our proposal is organized into four interdependent Research Projects and one Shared Resource Core. These will map at a new, much higher resolution the binding of transcription factors to their specific recognition sites in embryos;test the predictions of our computational models by extensively measuring the effect of point mutations in factor recognition sites on both in vivo factor occupancy and spatial and temporal transcriptional outputs;establish image analysis methods to measure relative rates of nuclear transcription cell by cell;and develop an ordered series of computational models that link input and output datasets to establish the key molecular interactions within a transcription network and grammar rules for the organization of functional factor recognition sites. Our project will provide uniquely detailed datasets and modeling strategies for studying the developmental control of transcription, including extensive experimental testing and validation of the models predictions.

Public Health Relevance

Many genetic diseases, including cancer, result from mutational changes in genome sequence that cause transcriptional miss regulation. Most normal changes in physiology and development involve the coordinated modulation of transcription via changes in the activity of sequence specific transcription factors. By establishing how to read transcriptional information in animal genomes, we will greatly aid both the development of therapeutics for genetic diseases and the understanding of animal development.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Program Projects (P01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-GGG-H (40))
Program Officer
Sledjeski, Darren D
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Lawrence Berkeley National Laboratory
Organized Research Units
United States
Zip Code
Li, Jingyi Jessica; Chew, Guo-Liang; Biggin, Mark D (2017) Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them. Nucleic Acids Res 45:11821-11836
Li, Jingyi Jessica; Bickel, Peter J; Biggin, Mark D (2014) System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ 2:e270
Knowles, David W; Biggin, Mark D (2013) Building quantitative, three-dimensional atlases of gene expression and morphology at cellular resolution. Wiley Interdiscip Rev Dev Biol 2:767-79
Fisher, William W; Li, Jingyi Jessica; Hammonds, Ann S et al. (2012) DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proc Natl Acad Sci U S A 109:21330-5