Tissue-specific evolutionarily conserved regulation of gene expression

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Virtually every cell in a multicellular organism contains the same DNA genome yet each celltype looks and functions differently to perform its required role in the organism. It is the differences in the way each gene in the genome is expressed in each cell type that accounts for these dramatic differences in cellular functions. Even though there is a wide variety in appearance between vertebrates separated by millions of years of evolution, they are fundamentally made up of similar cell-types and organs. Brain, liver and heart from different vertebrate species share more common gene expression within the same organ than between different organs within the same species. This commonality indicates that the mechanisms that regulate gene expression in each tissue are highly conserved through evolution. We lack, however, an understanding of these mechanisms and are not able to pinpoint most of the regions of the genome that are not in genes, but that are responsible for this remarkable conservation.****This proposal will investigate the mechanisms that specify tissue-specific gene expression through identifying active enhancers of gene expression that are functionally conserved through 450 million years of evolution. Identifying these enhancers is challenging as they are short and often located in regions of the genome without genes where sequence conservation is low. Although a small number of developmentally important enhancers have been predicted based on very similar DNA sequences found in vertebrates ranging from fish to humans, this small number does not account for the remarkable genome-wide conservation in gene expression across these species. The proposed research will allow for a better understanding not only of how to identify enhancers of expression in complex genomes but also which DNA-binding proteins regulate gene expression in different cellular contexts. ****The objectives of this proposal are; ***1) To determine how gene expression is modulated in different cell types by identifying active enhancers in embryonic stem cells, trophoblasts and fibroblasts using computational approaches and genome-wide experimental validation of enhancer activity. ***2) To determine how enhancer activity and gene expression is modulated through evolution by investigating gene expression levels and identifying enhancers active in fibroblasts from 10 vertebrate species. ***This will be the first investigation of enhancer activity across evolution and the first genome-wide identification of active enhancers in vertebrate genomes. This innovative approach will focus on well characterized cell types which can be maintained in cell culture to develop the research methods, but over the long term we will apply our expertise to more complex situations in living organisms to develop an understanding of how gene expression is controlled through development and how this has changed during evolution.*** **