(259f) Analyzing Natural Variation in Drosophila Gene Expression to Elucidate Novel Regulatory Paths

The proper control of gene regulation is important to ensure proper development as well as maintaining healthy adult tissues. Errors in these processes can lead to disease states, such as cancer.  Therefore a complex system of gene regulatory circuits exists to buffer this system against noise, minimizing mistakes in gene expression and preventing patterning defects or disease states.  One way to better understand this regulation is to analyze the control mechanisms involved in different stages of development in model organisms.  The fruit fly, Drosophila melanogaster, is a commonly used and well-studied model organism.  The anterior-posterior axis of the developing Drosophila embryo is patterned by a complex gene regulatory network that includes a cascade of gene expression.  The precise expression of these genes is important for proper development, and a number of different interactions between these genes ensures accuracy in the patterning process.  Much work has been done to find the binding sites and enhancer regions that properly position gene expression domains.  This work has generally been performed using brute force methods; however we propose a new method to discover these enhancers and important gene regulatory regions.  Our method explores differences in natural expression patterns due to subtle genomic differences.  We used a selection of wild-caught lines and quantified gene expression differences of two genes responsible for early tissues patterning, namely Krüppel and even-skipped.  These differences were then correlated to genomic differences to find novel regulatory regions.  We were then able to test and validate these enhancer regions using enhancer traps.  Variations due to levels of gene expression instead of position were also analyzed using RNA-seq and qPCR.  Together this work was able to elucidate novel regulatory pathways in the early developing Drosophila embryo.