In eukaryotic cells, the higher-order organization of genomes is functionally important to ensure correct execution of gene expression programs. For instance, as cells differentiate into specialized cell types, chromosomes undergo diverse structural and organizational changes that affect gene expression and other cellular functions. However, how this process is achieved is still poorly understood. The elucidation of the mechanisms that control the spatial architecture of the genome and its contribution to gene regulation is a key open issue in molecular biology, relevant for physiological and pathological processes.
One important aspect of this regulation is the spatial positioning of genes in the nuclear space. This is exemplified by the location of repressive chromatin domains at the nuclear periphery (i.e. lamina associated domains, LADs) or around nucleoli (nucleolar associated domains, NADs). While LADs have been extensively studied, including at the single cell level, the field has eagerly awaited a deeper understanding of NADs, which have remained underinvestigated mainly due to technical limitations in identifying DNA sequences associated with a membraneless compartment like the nucleolus. However, to fully understand how genome organization regulates chromatin and gene expression states, it is necessary to obtain a comprehensive functional map of genome compartmentalization.
In this project we aimed to develop methods to identify and characterize NADs and analyse the role of the nucleolus in genome organization, moving toward the obtainment of a comprehensive functional map of genome compartmentalization for each cell state. This will also provide novel insights into basic principles of genome organization and its role in gene expression and cell function that yet remain elusive.
Understanding how genome organization affects gene expression and cell state is of high medical relevance and, consequently, has an impact on health and society. This is particularly evident by the fact that alterations in nucleolus size and number have documented in several diseases such as cancer, neurogenerative disorders, and accelerated ageing. Thus, the establishment of technologies to understand the link between nucleolus and the genome has a potential impact to unravel novel pathways linked to disease with nucleolar alterations that might reveal to be useful for diagnosis and therapy.
The overall objectives of this project are to establish precise methods to identify and functionally characterize genomic regions located close to the nucleolus and determine how the nucleolus affects genome organization, chromatin state, and cell fate. This effort will contribute to deciphering how genome structure and position in cells affects gene expression and cell fate.
