Periodic Reporting for period 3 - NucleolusChromatin (Analysis of the nucleolus in genome organization and function) Reporting period: 2021-09-01 to 2023-02-28 Summary of the context and overall objectives of the project 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. Increasing evidence indicated that large-scale folding of chromatin affects gene expression by locating genes to specific sub-nuclear compartments that are either stimulatory or inhibitory to transcription. Nuclear periphery (NP) and nucleolus are two important nuclear landmarks where repressive chromatin domains are often located. The interaction of chromosomes with NP and nucleolus is thought to contribute to a basal chromosome architecture and genome function. However, while the role of NP in genome organization has been well documented, the function of the nucleolus remains yet elusive.To fully understand how genome organization regulates chromatin and gene expression states, it is necessary to obtain a comprehensive functional map of genome compartmentalization. However, so far, only domains associating with NP (LADs) have been identified and characterized while nucleolar-associated domains (NADs) remained under-investigated. The aim of this project is to fill this gap by developing 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 historically been used by pathologists as a prognostic indicator of cancerous lesions, suggesting that changes in nucleolus structure can affect genome organization and have an impact in disease. Furthermore, nucleolus structure undergoes changes during the early developmental phases, a time where the genome undergoes drastic remodeling in order to establish totipotency and then pluripotency after the fusion of the parental genomes. Thus, the understanding of the link between nucleolus and the genome has the potential to provide information relevant to regenerative biomedicine. The overall objectives of this project are to establish robust and 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 in deciphering how genome structure and position in cells affects gene expression and cell fate. Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far To obtain a more comprehensive understanding of how the genome is organized within the cell it is necessary to establish methods able to map the genome at the different nuclear compartments. The nucleolus is the largest subnuclear compartment in the cells. Although evidence indicates a role of the nucleolus in genome organization, the genomic regions in contact with the nucleolus (i.e nucleolar-associated domains, NADs) have remained under-investigated, mainly due to the lack of methods able to catch genomic contact with this compartment. To date, the only method employed to identify NADs is based on the sonication of cells followed by purification of nucleoli. However, this method is biased toward heterochromatin, which is resistance to sonication-mediate DNA fragmentation, thereby affecting the complete identification of NADs. Furthermore, the purity of isolated nucleoli is subjected to great variations that depend on cell types. In this proposal, we aimed to establish a robust method for the identification of NADs, overcoming the technical limitation of previous methods. This will allow us 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 and providing novel insights into basic principles of genome organization and its role in gene expression and cell function that yet remain elusive.We have successfully established methods for the identification of NADs. Nucleolar-DamID is based on in vivo chemical modification of genomic regions in contact with the nucleolus. This modification can be then measured with next generation sequencing methods, allowing the identification of NADs. We applied this method to identify and functionally characterize NADs in mouse embryonic stem cells (ESCs) and derived neural precursor (NPCs). We have also established and implemented computational methods to identify genomic contacts with rRNA genes using HiC data (HiC-rDNA). The results revealed unprecedented layers of genome compartmentalization by showing distinct repressive transcriptional and chromatin states based on the interaction with the nucleolus, nuclear lamina, or both. Remarkably, contacts with the nucleolus demarcate repressed regions of the genome that are enriched in H3K9me2 and depleted in H3K27me3 relative to sequences only contacting the NL, highlighting a specific repressive chromatin landscape that depends on the interactions with the nucleolus. Furthermore, we showed that genes moving away from the nucleolus upon ESC differentiation into NPCs are implicated in neuron development, indicating that the detachment from the repressive nucleolar compartment marks a first step toward activation in later stages of differentiation. The results revealed the role of the nucleolus as repressive compartment that is implicated in the control of gene expression program during lineage commitment. The establishment of these method and generation of high-quality maps of NADs that can be finally used by the community and will feed the study of genome organization will finally make possible to include the contribution of the nucleolus in future studies investigating the relationship between nuclear space and genome function. Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far) We developed novel methods, of Nucleolar-DamID and HiC-rDNA, for the identification of genomic contacts with the nucleolus (nucleolar associated domains, NADs) in mouse embryonic stem cells (ESCs) and derived neural precursor (NPCs). These novel methodologies allowed us to finally distinguish distinct layers of chromatin organization that depend on the interaction with the nucleolus, nuclear lamina, or both. These methodologies can be applied to every cell type, and we predict they will be highly relevant for future works aimed to understand basic principles of genome organization and its role in gene expression and cell function. These initial results laid the basis not only to determine how NADs are tethered to nucleoli but also to establish methods for single cell/nucleoli detection of NADs that were prohibitive with the previous biochemical based-methods. Furthermore, we are also developing novel technologies to dissect nucleolar proteome and genome. Considering that structural changes in the nucleolus are often observed in diseases, such as cancer, the results of our work will also have a biomedical impact for the understanding how changes in nucleolus structure and activity might affect genome function in disease. Genome organization around the nucleolus
