UCSF

The eukaryotic nucleus houses deoxyribonucleic acid (DNA) along with scaffolding proteins which together form chromatin. Cells organize their chromatin as transcriptionally silent, compacted heterochromatin and active, relaxed euchromatin. Heterochromatin is enriched at the nuclear periphery in metazoans and peripheral position correlates with transcriptional repression. Here, we remove three nuclear lamins and lamin B receptor (LBR) in mouse embryonic stem cells (mESCs) and show that heterochromatin detaches from the nuclear periphery. Heterochromatic loci marked by histone H3 lysine 9 di-methylation (H3K9me2) are enriched at the nuclear periphery; however, the effect of spatial position on H3K9me2-modified genes has not been defined. Chapter 1 is a brief overview of genome organization and the major players studied in this dissertation. Chapter 2 focuses on the effect of heterochromatin spatial position on the transcription and chromatin state of H3K9me2-modified genes in naïve mESCs and differentiated Epiblast-like cells (EpiLCs). Chapter 3 shows preliminary work on the effects of heterochromatin spatial position on nuclear shape, on heterochromatin-associated factors such as H3K9me3, HP1α and HP1β, on a degron system to rapidly deplete LBR, and on structure-function rescue experiments to identify regions in LBR that are important for peripheral enrichment of H3K9me2. This work shows that the nuclear periphery controls the spatial position and repressive functions H3K9me2, as well as potentially other heterochromatin marks.