Upf1 is a key member of several mRNA degradation pathways including Nonsense Mediated mRNA Decay (NMD). It is a key regulator of post-transcriptional gene expression, essential for development, and implicated as a genetic cause of neurodevelopmental disorders in humans. Little is known about how Upf1 and NMD regulates neuronal cell development.
Depletion of Upf1 from cortical neurons in-vitro caused altered neuronal cell connectivity associated with reduced network activity assessed by multi-electrode array. To interrogate the mechanism, we performed RNA-seq. We observed >1800 genes with differential expression, but surprisingly, the majority (62%) were downregulated. Gene set enrichment analysis identified that down regulated genes were associated with synaptic formation, and up-regulated genes were associated with chromatin modification. We postulated that NMD of mRNAs encoding chromatin regulators underpins neuronal synapse formation, connectivity and activity.
We performed transcriptome wide identification of genes in Upf1 depleted neurons that were up-regulated, post-transcriptionally stabilized (using intron-exon split analysis), and which also contained cis ‘NMD-inducing features’ to identify high-confidence NMD-targeted chromatin modifiers. Among these were genes encoding for neuronal cell activity-dependent DNA chromatin modifiers such as the Gadd45 family of DNA demethylases. We subsequently show that Upf1 expression is physiologically suppressed by neuronal cell activity, leading to upregulation of Gadd45b and demethylation of Gadd45b targeted loci such as the Bdnf promoter. Assessment of chromatin-immunoprecipitation (ChIP) data of other NMD-targeted chromatin modifiers from the mouse developing brain identified an enrichment at genes downregulated by Upf1 depletion, which were collectively associated with neuronal cell development.
These data support a model in which neuronal cell activity suppresses NMD leading to stabilization of mRNAs encoding epigenetic modifiers, which culminates in a global impact on gene expression programs essential for development of functional neuronal cell networks. These findings have relevance to both physiological brain development, and neurodevelopmental disorders underpinned by compromised NMD.