3D organization of the mammalian genome

The human genome project has given us the entire DNA sequence of building blocks of the human genome, but we still know little about how the genome is controlled to express the correct subsets of genes in the different cell types of the body. This proposal will assess for the first time the 3 dimensional arrangement of the entire genome in a particular cell type. Recent scientific evidence suggests that the genome is highly organized within the space of the cell nucleus in such a way as to maximize efficient expression of the desired or required subset of genes while keeping all of the other genes silent. This radically changes the way that scientist think about the genome and gene regulation in general. Genes are not functioning in isolation but preferentially grouping together with other similarly regulated genes to cooperate in their control and efficient expression. The results will have fundamental implications for modern genomic medicines such as gene therapy and stem cell therapies as well as give important clues to health and genetic diseases such as cancer. This knowledge is vitally important to ensure that future genomic and cell therapies are safe, reliable and designed from a position of knowledge and insight rather than trial and error.

Surprisingly little information is available to describe how the genome is organized within the three-dimensional space of the nucleus. It has been known for some time that individual chromosomes take up preferred positions relative to one another in the nucleus and that these arrangements are tissue-specific, suggesting a role in gene expression. Recent technological advances are beginning to uncover spatial relationships and interactions between genes and regulatory elements in the nucleus and are revealing an unexpectedly extensive network of communication within and between chromosomes. A crucial question is the extent to which this organization affects gene function. Our preliminary studies shows that similarly regulated genes in cis and trans preferentially cluster at a limited number of transcription sites in the nucleus, suggesting that individual transcription factories are specialized to transcribe specific networks of genes. These data indicate that specific ?active? genes are more likely to be transcribed if they associate with specialized factories containing other genes that utilize the same trans-acting factors for expression, suggesting that genes cooperate for efficient transcription. In this proposal we will use a novel unbiased technology to assess genome-wide, interactions between all transcriptionally active genes at transcription factories. The data will permit the elucidation of all transcription networks and produce the first, functional, 3D maps of the genome, providing unprecedented insights into the relationships between genome conformation and function. We will test the molecular mechanisms that may be responsible for genome organization using genetically modified mice in which mutant forms of a transcription factor have been knocked in to the endogenous locus. These experiments are essential to understand fundamental mechanisms of genome function and regulation in health and diseases such as cancer. In addition, this knowledge will form part of an essential foundation that must underpin modern genomic medicines such as gene therapy and stem cell therapies.