Summary: X-linked intellectual disability (XLID) is a heterogeneous syndrome affecting mainly males. Human genetics has identified >100 XLID genes, although the molecular and developmental mechanisms underpinning this disorder remain unclear. Here, we employ an embryonic stem cell model to explore developmental functions of a recently identified XLID gene, the RNF12/RLIM E3 ubiquitin ligase. We show that RNF12 catalytic activity is required for proper stem cell maintenance and neural differentiation, and this is disrupted by patient-associated XLID mutation. We further demonstrate that RNF12 XLID mutations specifically impair ubiquitylation of developmentally relevant substrates. XLID mutants disrupt distinct RNF12 functional modules by either inactivating the catalytic RING domain or interfering with a distal regulatory region required for efficient ubiquitin transfer. Our data thereby uncover a key function for RNF12 E3 ubiquitin ligase activity in stem cell and neural development and identify mechanisms by which this is disrupted in intellectual disability. : Bustos et al. show that the RNF12 E3 ubiquitin ligase regulates stem cell maintenance and neuronal differentiation. They demonstrate that RNF12/RLIM mutations identified in X-linked intellectual disability patients disrupt regions required for catalytic activity, which leads to compromised stem cell maintenance and abnormal neural differentiation. Keywords: ubiquitin, protein ubiquitylation, E3 ubiquitin ligase, proteasomal degradation, RNF12/RLIM, intellectual disability, X-linked intellectual disability, embryonic stem cells, neural differentiation
