CINDy: Chromosome interaction network dynamics in adipose stem cells

We are 3-dimensional (3D), our cells are 3D and our chromosomes are 3D. We have studied changes in the organization of our genes (the genome) during differentiation of fat tissue stem cells into fat cells (adipocytes). For this, we have first developed a new computational software, Chrom3D, which allows us to visualize and analyze our genes in the 3D genome. The program is freely available and is now being used by many research groups in the world. Our work shows that during fat cell differentiation, regions of chromosomes (which are called TADs) come together to form aggregates of compact and silent chromatin domains, which segregate from more active regions. We call these domains ?TAD cliques?. TAD cliques are pulled towards the periphery of the cell nucleus when they form, providing a means of turning genes off as a group. Our Chrom3D software has also allowed us to analyze, for the first time, the effect of mutations in proteins of the nuclear envelope (called lamins) which cause disease. We show that some of these mutations greatly affect the 3D organization of chromosomes, and disrupts gene expression programs. We have also found that in fat stem cells, a common lamin mutation that cause lipodystrophy increases the expression of a particular gene which codes for a small RNA molecule that blocks fat differentiation. We have discovered the molecular mechanisms by which this occurs, providing new views on how these mutations can cause disease.

Understanding the molecular details of adipogenesis is critical as dysregulated function of adipose tissue is often linked to obesity, diabetes and cardiovascular diseases. Much is known on the regulation of genes controlling adipogenic differentiation of adipocyte progenitors. These mechanisms have been disclosed considering a 2-dimensional (linear) genome. However, chromatin integrates genetic and epigenetic information and converts this information into gene expression outcomes as a 3-dimensional (3D) hub. Spatial organization of chromatin within boundaries of the cell nucleus is modulated by 3D genome folding, intra- and inter-chromosomal interactions, and interactions of genomic loci or domains with the nuclear envelope, in particular the nuclear lam ina. We hypothesize that developmentally regulated nuclear lamin A, a component of the lamina, impacts the 3D genome organization, gene expression outcomes and stem cell differentiation capacity. This project investigates the impact of lamin A as a determ inant of stem cell 3D genome folding and gene expression programs in adipose stem cells (ASCs). Our approach combines stem cell and chromatin biology, genomics, 3D imaging and computational biology. OBJECTIVE 1 aims to determine how adipogenic differentia tion remodels genome-wide lamin A-genome interactions in ASCs. OBJECTIVE 2 identifies transitions in 3D genome conformation genome-wide and at lamin A target loci during adipogenic differentiation. OBJECTIVE 3 assesses the impact of lamin A on 3D genome f olding in ASCs. The results will bring our appreciation of somatic stem cell differentiation potential to a whole new 3D level. Impact of the work extends beyond the fundamentals of gene regulation, and aims to build a conceptually new platform for opport unities to approach tissue repair. Two postdocs with experience in genomics will be hired carry out this project with in-house assistance and that of collaborators.