Welcome to the Berkeley Drosophila Transcription Network Project, a multidisciplinary team centered at Lawrence Berkeley National Laboratory,and UC Berkeley, with additional members at UC Davis, UC Irvine and the University of Washington, Seattle.

Our goal is to decipher the transcriptional information contained in the extensive cis-acting DNA sequences that direct the patterns of gene expression that underlie animal development. Using the early blastoderm embryo of the fruitfly Drosophila melanogaster as our principal model, we are developing experimental and computational methods to systematically characterize and dissect the complex expression patterns and regulatory interactions already present prior to gastrulation. We have identified 37 principal regulatory factors within this network for initial analysis together with their target genes. In addition, we perform selected analysis in embryos at later stages of development to help test the generality of our models and examine dynamics during specification and differentiation.

Components of this effort include:
3D gene expression: we are developing advanced image analysis methods to capture the expression patterns of hundreds of genes in 3D at cellular resolution
In vivo DNA binding: we are using in vivo crosslinking and either ChIP/chip or ChIP/seq to measure binding of endogenous factors to DNA elements in living embryos
In vitro DNA binding: we are measuring the in vitro DNA binding specificities of transcription factors active in the early embryo using purified, over-expressed proteins and a modified binding site selection (SELEX) protocol
Transgenic promoter analysis: we are testing and characterizing the ability of a large number of predicted potential cis regulatory sequences to drive reporter-gene expression in the early embryo
Chromatin Accessibility: we are measuring the degree to which different genomic regions are accessible to enzyme digestion in isolated embryo nuclei using DNase-seq
Automation/engineering: we are building devices to automate our data collection methods, including an automated Drosophila embryo injector and a fly handling robot
Bioinformatic modeling: we are developing methods to utilize the above data and Drosophila genome sequences to model crucial aspects of the transcriptional network and to decode the cis-regulatory information in non-coding DNA.
This project is chiefly funded by grants from NIGMS and NHGRI to Mark Biggin, Sue Celniker, Michael Eisen and David Knowles, as well as additional funding to and Bernd Hamann, Claire Tomlin, Michael Jordan and Peter Bickel, and HHMI funding to Micheal Eisen.