Structure meets function at the mouse X chromosome inactivation center
Seminar Room 1, Newton Institute
Characterizing the folding principles of mammalian chromosomes is of capital importance to understand the complexity of gene expression regulation, particularly during the major transcriptional changes occurring in development. This may help elucidating the mechanisms by which regulatory elements contact gene promoters (i.e. by looping out intervening DNA), understand what is the cell-to-cell variability of these interactions and how it does reflect transcriptional variability. We analyzed a 4.5 Mb region of the X chromosome that includes the X-inactivation center by Chromatin Conformation Capture Carbon-Copy (5C), in order to gain insights into how chromatin structure is organized during early mouse embryonic stem cell (ESC) differentiation. We uncovered that chromatin is organized into Topologically Associating Domains (TADs), within which genomic elements preferentially interact. To fully reconstruct the statistical repertoire of chromatin conformations that give rise to these domains, we have used a combination of Monte Carlo simulations of a polymer model, high-resolution DNA FISH and quantitative RNA FISH. We show that in the TAD that contains the Tsix ncRNA (a master regulator of X-chromosome inactivation), enhancer-promoter contacts take place in a subset of cells where the whole domain is compacted, rather than resulting from stable DNA loops. In these cells, the probability of transcribing a gene is higher than in cells where the domain is in an elongated conformation. We thus show a correlation between the spatial proximity of a promoter and an enhancer and their transcriptional activity at the single cell level.