Shifts in Ribosome Engagement Impact Key Gene Sets in Neurodevelopment and Ubiquitination in Rett Syndrome

Regulation of translation during human development is poorly understood, and its dysregulation is associated with Rett syndrome (RTT). To discover shifts in mRNA ribosomal engagement (RE) during human neurodevelopment, we use parallel translating ribosome affinity purification sequencing (TRAP-seq) and RNA sequencing (RNA-seq) on control and RTT human induced pluripotent stem cells, neural progenitor cells, and cortical neurons. We find that 30% of transcribed genes are translationally regulated, including key gene sets (neurodevelopment, transcription and translation factors, and glycolysis). Approximately 35% of abundant intergenic long noncoding RNAs (lncRNAs) are ribosome engaged. Neurons translate mRNAs more efficiently and have longer 3ʹ UTRs, and RE correlates with elements for RNA-binding proteins. RTT neurons have reduced global translation and compromised mTOR signaling, and >2,100 genes are translationally dysregulated. NEDD4L E3-ubiquitin ligase is translationally impaired, ubiquitinated protein levels are reduced, and protein targets accumulate in RTT neurons. Overall, the dynamic translatome in neurodevelopment is disturbed in RTT and provides insight into altered ubiquitination that may have therapeutic implications. [Display omitted] •Parallel TRAP-seq and RNA-seq quantify developmental shifts in ribosome engagement•Thirty percent of neurodevelopmentally expressed genes are translationally regulated•Translation is globally repressed in cortical neurons from RTT patients•Translation dysregulation in RTT affects E3-Ub ligases and target protein levels Rodrigues et al. investigate ribosome engagement of RNA during human neurodevelopment. They discover translational regulation of key gene sets and identify ribosome-engaged lincRNAs. In Rett syndrome neurons, global translation and ribosome engagement of NEDD4-family ubiquitin ligases are decreased, leading to accumulation of target proteins that escape proteasome degradation.