Reading the genome: how do transcription factors achieve target specificity?

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Animal development and the normal physiological responses of the body rely upon the precise control of the activity of genes within the genome, a process controlled by regulatory proteins known as transcription factors. How transcription factors identify the genes they control by binding to specific DNA sequences in the nucleus remains a considerable challenge for biologists. We know that information dictating where and when a gene is switched on is encoded in the DNA sequence; however, we do not yet understand this regulatory code. One group of regulatory proteins known to control multiple aspects of development, the Hox family, includes a set of closely related factors found in all animals, from flies to humans. Our current understanding is that specific Hox proteins are responsible for controlling the structures that are produced along the body axis, such as where arms, legs or ribs develop. Mutations in Hox genes have dramatic consequences on the way animals look, for example the loss of the Ultrabithorax gene in the fly can result in the production of a four wing rather than a normal two wing fly and Hox mutations in humans can result in limb abnormalities such as the development of extra digits. While it is clear from genetics that individual Hox proteins have very different effects on development, paradoxically all Hox proteins are very similar and appear to recognise virtually identical DNA sequences that are believed to dictate the sets of genes they control. This general problem of specificity is common to most families of transcription factors. Some of the specificity may come from specific interactions with co-factor DNA binding proteins and we will explore this. To understand more about how the important class of Hox proteins are able to control specific sets of genes we use the fruit fly as a model system. The Hox proteins of the fly are closely related to those in humans but the fly genome is 20 times smaller, making analysis much easier. We can test Hox gene interactions with DNA, and the functional consequences of binding, by expressing Hox proteins under controlled conditions in a defined fly cell culture system. Understanding how Hox genes recognise specific genomic sequences and control genes is important for our basic understanding of how all animals develop and it is also important if we wish to gain insights into how evolution has produced the huge range of body plans we see around us. Our experiments will use a cell culture system to determine where all core Hox proteins bind in the genome and the effects they have on gene expression with and without their key DNA binding cofactors. We will then relate this binding to general features of the DNA in the nucleus, essentially how available a stretch of DNA sequence is for binding, to further understand the rules that determine where Hox proteins bind. This will help us to determine how these very similar proteins give rise to different regulatory outcomes. We will use these data to better understand the rules by which Hox proteins are able to recognise the DNA sequences that control genes, and discover differences for each of the Hox proteins. Since the Hox genes of mammals are organised and operate in the same way as those in flies, our work will help us understand how Hox genes control development of higher animals, including man. In addition, it has recently become clear that Hox genes are involved in several diseases, including cancers, thus a better understanding of how Hox genes work may, in the future, be useful when studying aspects of human disease. Since most families of gene regulators show similar properties to Hox proteins, our studies will also help address the more general issue of how genes are specifically controlled by sets of similar regulators. By studying the basis for this specificity, we will be able to make progress in understanding the regulatory code of the genome.