DNA-Life

The tri-dimensional organization of the genome is clearly linked to its function as it varies during the cell cycle and upon differentiation in metazoan. However, the causal relationship between nuclear organization and function remains often elusive. Budding yeast has proven to be an excellent model system for testing the functional role of higher-order chromatin organization. Extensive studies over the last two decades have revealed a dynamic yet well-defined organization of the yeast genome, which impacts on gene expression and genome stability through mechanisms that are still poorly understood. However, most of these studies have been conducted in nutrient-replete conditions with cells undergoing exponential growth although in the wild, yeast cells like many organisms spend most of their time without dividing in a quiescent state. Despite the ubiquity and importance of quiescence, we have little understanding of the nature of this state that may vary depending on the cell’s history 2. Interestingly, budding yeast can reach different quiescent states depending on the conditions that induce the cell cycle exit, leading to different outcome in terms of chronological life span 3. Thus, deciphering the key features of the different quiescent states is essential to understand mechanisms that extend lifespan. Our recent data unveiled that chromosomes adopt distinct organizations according to the metabolic status of the cell. In particular, following carbon source exhaustion, the telomeres of quiescent cells group into a unique focus or “hypercluster”, localized in the center of the nucleus, thus constraining the global organization of the genome. Importantly, hypercluster formation occurs specifically in quiescent cells able to sustain long-term viability and contribute to lifespan extension by a yet unknown mechanism (Guidi et al, under review). Here, we aim at deciphering the mechanisms regulating the dynamics of nuclear architecture in relation to changes in genome activity and addressing how nuclear architecture impacts on chronological lifespan. Combining cell biology, genetics and omics approaches, we will investigate the interplay between the 3D folding of the genome, RNA expression (coding and non-coding) and the maintenance of genome stability upon major metabolic transitions and during prolonged quiescence. We will address two complementary questions: 1. What are the mechanisms underlying the dynamics of nuclear architecture in response to changes in environmental conditions? On the one hand we will study the physical parameters underlying telomere clustering in different metabolic state by investigating the dynamics and structure of chromatin and telomeric factors using advanced super-resolution microscopy based on single molecule approaches. On the other hand, we will conduct systematic genetic and proteomic screens to decipher the molecular factors regulating the formation of telomere clustering upon metabolic transition. 2. How change in nuclear architecture impacts on chronological lifespan ? We will explore three possible scenarii : i) telomere clustering impact on gene expression during quiescence or upon return to growth ; ii) telomere hyperclustering favor genome stability at telomere and/or at other loci ; iii) telomere hyperclustering allows the sequestering of specific factors that can have deleterious effects elsewhere in the cell during prolonged quiescence. As the analysis of yeast chronological lifespan has been often predictive of processes influencing lifespan in different species, we anticipate that basic principles will emerge from our studies with broad implications relevant in other organisms.