University of California, Berkeley
401 Barker Hall #3204
Berkeley, CA 94720-3204
1985 Searle Scholar
My lab studies gene networks that control animal development and disease. Research focuses largely on how noncoding regions of the genome function to control the differential patterns of gene expression, both spatial and temporal, that define cell behavior. The developmental stage of multicellular organisms in particular requires very explicit control of gene expression in order to layout different cell tissue types. Using model developmental systems, including the early Drosophila embyro, the sea squirt, Ciona intestinalis, and the flour beetle, Tribolium castaneum, we are working to develop a deeper understanding of genetic regulatory codes.Current Projects
Whole genome CHiP-chip analysis of the RNA polymerase II DNA binding in the early Drosophila embryo revealed that many of the spatially patterned regulatory genes load polymerase to the promoter and initiate transcription independent of enhancer activity. Enhancer loading by the appropriate activating factors is required for transcription to proceed past promoter-proximal region, but not polymerase binding. We are investigating the molecular mechanisms involved in this form of regulation and its biological consequences for gene regulation.
Similar CHiP-chip experiments for the primary Dorsal-ventral patterning transcription factors, Dorsal, Twist and Snail revealed novel DV enhancer elements. From these experiments, we have been able to show that some genes have multiple enhancers--secondary “shadow enhancers” located in more distal regions which drive the same pattern as the originally discovered primary enhancers. We are investigating the evolutionary context of these multiple enhancers by probing how they change across different Drosophilid and other insect species. We are also investigating the possible functional roles of these duplicate elements in the control of developmental patterning.
One of the most amazing properties of developmental patterning systems is their reliability and robustness to perturbation. Despite the stochastic nature of the underlying reactions that control development, the whole process exhibits precise spatial regulation on the level of single cells separated by mere microns and surprising temporal coordination. We have developed quantitative population based assays to measure natural variability in the temporal and spatial expression patterns of individual genes, between cells in the same embryo and between different embryos of the same age. With this methods we have recently shown that genes which regulate the initiation step of transcription are activated in a much more stochastic fashion than the elongation regulated genes. We are adapting these methods to gain new insights into the reliability and robustness of Drosophila embryonic patterning.
As simple chordates, sea squirts are the invertebrates most closely related to vertebrates. The genome of the sea squirt Ciona intestinalis has been sequenced and assembled and represents a simplified version of vertebrate genomes. The Ciona tadpole is initially composed of just ~1,000 cells and there is complete lineage information. It is possible to introduce transgenic DNAs into thousands of developing embryos at once using simple electroporation methods. A provisional circuit diagram is now available for the specification of the major larval tissues during embryogenesis. This diagram provides a foundation for understanding the differentiation of key organs such as the notochord, central nervous system, and heart. We are now using a combination of confocal imaging, cell sorting, and microarray assays to identify the genes and gene interactions responsible for specification, morphogenesis, and differentiation in these tissues. For instance, using these techniques we found that the transcription factor FoxF directly activates a key rate-limiting effector of protrusive activity in migrating heart precursors.
We are also interested in investigating how vertebrates could have evolved from a protochordate ancestor like the sea squirt. We have recently shown that vertebrates and sea squirts are unique in that they both possess facial muscles that share a common lineage with the heart. In sea squirts, this cardiopharyngeal mesoderm gives rise to the beating heart as well as siphon muscles. In vertebrates, some of the precursors that split away from the heart to form lower jaw muscles actually contribute to the heart at a later stage- they form the so-called Second Heart Field (SHF). On the basis of these similarities and differences, we propose a pre-vertebrate origin for the jaw muscles and SHF of vertebrates. We believe the SHF arose from cooption of jaw muscle precursors back towards the heart. This increased contribution would have allowed for the elaboration of the vertebrate heart relative to its sea squirt counterpart. There are many other examples of vertebrate structures and cell types that likely owe their origin to a pre-existing structure in the protochordate ancestor, and we are in the process of uncovering these hidden connections and their underlying molecular mechanisms.
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