Preserving nuclear proteostasis through branched ubiquitin – mediated protein degradation

Branched ubiquitin chains are emerging as a more efficient signal for protein degradation and have been observed upon stress, such as at sites of DNA damage. However, their formation, recognition and function in the nucleus remain poorly understood, due to limited tools for studying these complex ubiquitin modifications. This proposal aims to reveal how branched ubiquitin regulates nuclear stress response pathways by driving nuclear protein degradation. I hypothesise that defining the nuclear proteins modified with branched ubiquitin upon stress and identifying the readers that decode these signals will be key to defining the molecular circuit of branched ubiquitin-dependent degradation. To address this, I will combine structural, biochemical and cell-based approaches employing unique tools such as nanobodies used as cellular sensors to identify nuclear proteins targeted for branched-dependent degradation. Using branched ubiquitin chains of defined architectures, I will discover their nuclear readers and elucidate the molecular mechanism of recognition. In parallel, I will perform CRISPR screening to identify the molecular players that control timely degradation of key substrates during stress. Together, this research will reveal how cells activate and resolve nuclear stress by selectively eliminating branched ubiquitin-modified nuclear proteins and provide mechanistic insights into how branched ubiquitin signalling safeguards nuclear integrity.