ABSTRACT Several studies have shown a role for Stag proteins in cell identity. Our understanding of how Stag proteins contribute to cell identity have largely been focused on its roles in chromosome topology as part of the cohesin complex and the impact on protein-coding gene expression. Furthermore, several Stag paralogs exist in mammalian cells with non-reciprocal chromosome structure and cohesion functions. Why cells have so many Stag proteins and what specific functions each Stag protein performs to support a given cell state are poorly understood. Here we reveal that Stag1 is the dominant paralog in mouse embryonic stem cells (mESC) and is required for pluripotency. Through the discovery of diverse, naturally occurring Stag1 isoforms in mESCs, we shed new light not only on the unique ends of Stag1 but also the critical role that their levels play in stem cell identity. Furthermore, we revel a new role for Stag1, and specifically its unique N-terminal end, in regulating nucleolar integrity and safeguarding mESCs from totipotency. Stag1 is localised to repressive perinucleolar regions, bound at repeats and interacts with Nucleolin and TRIM28. Loss of the Stag1 N-terminus, leads to decreased LINE-1 and rRNA expression and disruption of nucleolar structure and function which consequently leads to activation of the two-cell-like (2C-LC)-specific transcription factor DUX and conversion of pluripotent mESCs to totipotent 2C-LCs. Our results move beyond protein-coding gene regulation via chromatin loops into a new role for Stag1 in repeat regulation and nucleolar structure, and offer fresh perspectives on how Stag proteins contribute to cell identity and disease.

The N-terminus of Stag1 is required to repress the 2C program by maintaining rRNA expression and nucleolar integrity