Communication between cells is essential for normal development. Instructive signals between cells ensure their proper position and identity throughout embryogenesis. Our research is focused on understanding how such cell signaling interactions and their accompanying genomic regulatory networks coordinate development. We combine mouse genetics with genomic and computational studies to define and experimentally test regulatory network structure and dynamics. Our genetic studies focus on specific components of evolutionarily conserved signaling pathways. One such factor, Sprouty2 (Spry2) acts as a modulator of the FGF signaling pathway. We have generated a collection of Spry2 mutant mice that constitute an allelic series ranging from reduced expression to complete loss of Spry2 function. We are using these mice to examine how cross-talk between conserved pathways, such as FGF, BMP and SHH, guides dosage sensitive cellular interactions that shape developing structures. We have focused on the head and face, the branched architecture of the respiratory tree and the collecting ducts of the kidney.

As developmental signals are received by cells they must be transformed into morphogenic responses. Genomic regulatory networks, consisting of signaling pathway-dependent and cell type-specific transcription factors and their binding sites, are designed to convert cellular signals into changes in gene expression. At the genomic level, target loci are controlled by combinatorial regulatory modules. We have constructed a computational pipeline to search for patterns based on positional relationships between genes and putative regulatory modules. This provides a view for studying how the genome is organized to coordinate gene expression during development. Our tool can also identify novel conserved sequence motifs and predict genes in the network. Experimental validation of predicted genes combined with additional modeling allows us to evolve the structure of genomic regulatory networks that guide morphogenesis.

We also use genetic screens to identify genes that are essential for mouse development. Much of our work has grown from our early studies using a classic genetic resource in the mouse, the piebald deletion complex. We used this set of overlapping chromosomal deficiencies to reveal a developmental role for genes such as Spry2. We have also taken advantage of the piebald coat color marker and the deletions to perform an ENU mutagenesis screen as part of our effort to functionally annotate this ~40 Mb region of mouse chromosome 14. We continue to perform genetic screens focusing on specific chromosomal regions. Here, we are adding some technical twists that include chemical mutagenesis of ES cells and GFP marked mice. These new approaches should permit even more efficient recovery of essential genes using a visible marker to flag lethality in a genetic screen.

SELECTED PUBLICATIONS

1. Welsh, I.C. and T.P. O'Brien (2000). Loss of late primitive streak mesoderm and interruption of left-right morphogenesis in the Ednrb^s-1Acrg mutant mouse. Developmental Biology 225, 151-168.
2. Roix, J.J., Hagge-Greenberg, A.E., Bissonnette, D.M., Rodick, S.F., Russell, L.B. and T.P. O'Brien (2001). Molecular and functional mapping of the piebald deletion complex on mouse chromosome 14. Genetics 157, 803-815.
3. Peterson, K.A., King, B.L., Hagge-Greenberg, A.E., Roix, J.J., Bult, C.J. and T.P. O'Brien (2002). Functional and comparative genomic analysis of the piebald deletion region of mouse chromosome 14. Genomics 80, 172-184.
4. O'Brien T.P., Bult, C.J., Cremer, C., Grunze, M., Knowles, B.B., Langowski, J., McNally, J., Pederson, T., Politz, J., Pombo, A., Schmahl, G., Spatz, J.P. and R. van Driel. (2003). Genome Function and Nuclear Architecture: From Gene Expression to Nanoscience. Genome Research 13, 1029-1041.
5. Frank, A.C., Meyers, K.A., Welsh, I.C. and T.P. O'Brien. (2003). Development of an EGFP-based dual-color reporter to facilitate genetic screens for the recovery of mutations in mice. PNAS 100, 14103-14108.
6. O'Brien, T.P. and W.N. Frankel. (2004). Moving forward with chemical mutagenesis in the mouse. J. Physiology 554, 13-21.
7. Burgess, R.W., Peterson, K.A., Johnson, M. J., Roix, J.J., Welsh, I.C. and T.P. O'Brien. (2004). Evidence for a conserved function in synapse formation reveals Phr1 as a candidate gene for respiratory failure in newborn mice. Mol. Cell. Biol. 24, 1096-1105.
8. Shopland, L.S., Lynch, C.R., Peterson, K.A., Thornton, K., Kepper, N., von Hase J., Stein, S., Vincent, S., Molloy, K.R., Kreth, G., Cremer, C., Bult C.J. and T.P. O'Brien. (2006). Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence. J. Cell Biol. 174, 27-38.
9. Han, L., M. Dias Figueiredo, K. A. Berghorn, T. N. Iwata, P. A. Clark-Campbell, I. C. Welsh, W. Wang, P. O'Brien T, D. M. Lin and M. S. Roberson (2007). Analysis of the gene regulatory program induced by the homeobox transcription factor distal-less 3 in mouse placenta. Endocrinology 148, 1246-1254.