Recruitment to the nuclear periphery enhances repression of H3K9me2-marked genes and transposons to shape cell fate [CUT&Run II]

Heterochromatic loci marked by histone H3 lysine 9 dimethylation (H3K9me2) are enriched at the nuclear periphery in metazoans, but the effect of spatial position on heterochromatin function has not been defined. 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. Mutant mESCs sustain naïve pluripotency and maintain H3K9me2 across the genome but cannot repress H3K9me2-marked genes or transposons. Further, mutant cells fail to differentiate into epiblast-like cells (EpiLCs), a transition that requires the expansion of H3K9me2 across the genome. Mutant EpiLCs can silence naïve pluripotency genes and activate epiblast-stage genes. However, H3K9me2 cannot repress markers of alternative fates, including primitive endoderm. We conclude that the nuclear periphery controls the spatial position, dynamic remodeling, and repressive capacity of H3K9me2-marked heterochromatin to shape cell fate decisions. Overall design: Cleavage Under Target and Release Under Nuclease (CUT & RUN) for Lamin B1 (LMNB1) and Lamina-associated polypeptide 2 beta isoform (LAP2B) in naive mouse embryonic stem cells (mESCs) and epiblast-like cells (EpiLC), and the histone modification tri-methylated lysine 9 on histone H3 (H3K9me3) in naive mESCs.