Figure 1: Adjacent insertions of a sensor gene showed different activities, highlighting the regulatory architecture of the corresponding locus (see Ruf et al., 2011).
Figure 2: Abnormal skull development in mice with a deletion of distal enhancers engineered by in vivo recombination (see Marinic, et al. 2013).
The Spitz group aims to understand how the intricate distribution of regulatory elements along the genome is transformed into specific gene expression profiles.
Previous and current research
The patterning of the embryo and the specification of its different cell types are driven by the implementation of cell-specific gene expression programs. In vertebrates, the cis-acting elements that regulate transcription can be located hundreds of kilobases away from the genes they control, particularly for genes with important functions during development. Because of this, the genome appears to be composed of intermingled arrays of unrelated genes and cis-regulatory elements. Therefore, the mechanisms that regulate enhancer-promoter interactions are essential to transform this apparent genomic and regulatory conundrum into gene- and tissue-specific expression programmes. Recent data reveal that genomic loci adopt specific chromatin structures and conformations in the nuclei of different cell types, correlating with differential gene activity. Yet, the cis-acting genomic elements that determine how a genomic locus folds into specific structural and regulatory architectures, and the precise roles of the chromatin, protein-complexes and non-coding RNAs suggested to contribute to this process, are still unclear.
Our lab has developed several experimental approaches to explore the regulatory architecture of the mouse genome and characterise functionally the mechanisms that organise it. Towards this aim, we have established an efficient in vivo system that, through the combined used of transposases and recombinases, allows the reengineering, in a systematic manner, of the mouse genome. With this approach, we generated a unique resource comprising hundreds of mouse strains carrying regulatory sensors throughout the genome, and series of specific chromosomal rearrangements in selected loci. This genomic resource enables us to dissect functionally the genomic information and the mechanisms that organise a linear genome into structurally distinct domains and chromatin loops, so as to implement long-range specific regulatory interactions.
Future projects and goals
Structural conformation and regulatory organisation of the genome
By combining advanced genomic engineering with chromatin profiling (ChIP-Seq) and conformation analyses (4C-chromatin conformation capture, super-high resolution FISH), we aim to learn how the genomic organisation of a locus determines the specific chromatin structures and conformations that it adopts in the nucleus, and determines their functional significance in the context of a developing embryo.
Regulatory architecture, disease and evolution
Our mouse models provide insights into the consequences of structural variations or chromosomal aneuploidies found in humans, both at the phenotypic and molecular level. Comparison of the regulatory architecture of developmental gene loci between different species can reveal how large-scale changes in chromosomal organisation may have contributed to evolution of body forms.