ChroMet - Coupling metabolic state to spatial chromatin organization in adipose progenitor cells

Sugars and amino acids are processed in stem cells so they can divide and differentiate into various cell types. Recent work points to a link between cell metabolism and gene expression control. In this project, we study how the metabolic state of cells influences gene organization and expression, in human fat stem cells and liver cells, and in mouse liver. In this project, we have shown that mimicking the induction of a ?fatty liver syndrome? in human liver cells causes changes in gene expression and in the association of chromosomes with the periphery of the nucleus. This correlates with a repositioning of genes in the nucleus, which can be predicted from computational modeling. We have also reset the 24h internal clock of mice by starving them and refeeding them to trigger strong metabolic changes. We found in the liver of these mice oscillating patterns of expression of metabolic genes (every 6, 12, 18 or 24h). Specific chromosome regions also bind to, and detach from, the nuclear periphery in a rhythmic manner. These results altogether suggest that not only gene expression, but also 3D genome conformation, is under metabolic and rhythmic influence. Future work will be necessary to understand the mechanisms regulating cell metabolic status and the spatial reorganization of the genome.

-Establishment of genomic resource datasets available for the scientific community, though data deposition at NCBI GEO accession number GSE (nuclear lamin ChIP-seq data, RNA-seq data) -Awareness on the potential negative impact of cytotoxic drugs on the market (e.g. the immunosuppressant cyclosporin A) on genome organization (and gene expression) in liver cells. -Openings to new follow up research projects in this area.

Determination of stem cell fate has been long ascribed to signaling pathways affecting gene regulation, and as a result shifting cell identity to self-renewal or differentiation. Recently, cellular metabolism has emerged as a key determinant of stem cell function, adding a new layer of complexity to understanding stem cell fate. Given recent evidence linking nutrient availability and chromatin modifications, we will examine the nature of a dynamic relationship between metabolic state and chromatin organization in adipose stem cells (ASCs). Our preliminary data show, during adipogenic differentiation of human ASCs, a dynamic interaction of nuclear lamins (in particular lamin A; LMNA) with chromatin regions enriched in in O-linked beta-N-acetylglucosamine modification of histone H2B (H2B-S112GlcNAc). As H2BGlcNAc is seen as a nutrient sensor, we aim to test the main hypothesis that cellular metabolic status modulates spatial genome organization through H2B GlcNAcylation and developmentally regulated association with nuclear lamins. We will test two hypotheses. The first is that domains of H2BGlcNAc predict LMNA-genome interactions during adipogenesis. This will be tested by replacing H2B by a non-S112-GlcNAcylabe H2BS112A mutant and assessing impact on LMNA-chromatin interactions during adipogenic differentiation. The second is that H2BGlcNAc-LMNA interactions mediate the impact of metabolic insults on genome organization. After evaluating global effects of altering glucose metabolism on protein GlcNAcylation, we will assess the remodeling of genomic distribution of H2BGlcNAc and LMNA as a result of these metabolic changes, and the function of H2BGlcNAc and LMNA redistribution on adipogenic differentiation. The project combines adipose stem cell biology, metabolic studies, chromatin biology and high-throughput genomics, and is designed for a PhD student.