In eukaryotes, thousands of genes have to be organized and expressed in the cell nucleus. Conformational and kinetic instability of nuclear structure and components appear to enable cells to use the encoded information selectively. The ubiquitin-proteasome system is active in distinct nuclear domains and plays a major role controlling the initial steps of gene expression, DNA repair and nuclear quality-control mechanisms. Recent work indicates that a tuned balance of ubiquitylation and proteasome-dependent protein degradation of nuclear proteins is instrumental in nuclear function and, when deregulated, leads to the development of diseases such as polyQ disorders and other neurodegenerative conditions.