Investigate the mechanism lamins regulate genome organization and gene expression during development

Abstract Lamins are type V intermediate filament nuclear proteins. Lamins assemble into a filamentous network and is the major structural element of the proteinaceous meshwork called the nuclear lamina located underneath the inner nuclear envelope. The chromatin regions interacting with this meshwork is called the nuclear Lamina Associated Domains (LADs). Studies using tissue culture cells in vitro show that the lamins maintain genome and nuclear integrity. Since mutations in the lamin genes cause a large number of human diseases, it is important to understand the basic functions of lamins in vivo. This proposal aims to determine the mechanism by which lamins regulate 3D genome organization and gene expression during development. The experimental plan builds upon a number of advances made in the last several years. By studying mouse embryonic stem cells (mESCs), a chromatin model, referred to as Histone Lamina Landscapes (HiLands), was developed to classify different types of chromatin based on histone binding, epigenetic modification, and LADs. Aided by this classification, it becomes clear that lamins differentially regulate two distinct LADs defined as HiLands-B and -P in mESCs. Further coupling of the LADs studies with Hi-C analyses, it is possible to discover that the HiLands-B LADs are detached from the nuclear lamina, while HiLands-P LADs are decondensed at the nuclear periphery. These LADs defects result in changes in global 3D chromatin interactions and gene expression in the lamin null mESCs. To enable the study of how lamins regulate development, several methods are developed to allow high quality mapping of LADs, Hi-C, and epigenome in a small number of cells isolated from embryonic tissues. Additionally, careful characterization of lamin deletions during mouse development points to two embryonic cell types, the embryonic cardiomyocytes and extraembryonic endoderm cells (EXE cells), as great models to investigate the mechanism by which lamins regulate genome organization. Importantly, these two cell types have classical (cardiomyocytes) or inverted (EXE cells) genome organization. Thus the proposed study will enable the investigate into whether and how lamins use similar or different means to regulate two distinct genome configurations during development.