Imprinting effects of UBE3A loss on synaptic gene networks and Wnt signaling pathways

The genomically imprinted UBE3A gene encodes a E3 ubiquitin ligase whose loss from the maternal allele leads to the neurodevelopmental disorder Angelman syndrome. However, the mechanisms by which loss of maternal UBE3A contribute to severe neurodevelopmental phenotypes are poorly understood. Previous studies of UBE3A function have focused on mouse models or single targets, but these approaches do not accurately reflect the complexity of imprinted gene networks in the brain nor the systems-level cognitive dysfunctions in Angelman syndrome. We therefore utilized a systems biology approach to better elucidate how UBE3A loss impacts the early postnatal brain in a novel CRISPR/Cas9 engineered rat Angelman model of a complete Ube3a deletion. Strand-specific transcriptome analysis of offspring derived from maternally or paternally inherited Ube3a deletions revealed the expected parental expression patterns of Ube3a sense and antisense transcripts by postnatal day 2 (P2) in hypothalamus and day 9 (P9) in cortex, when compared to wild-type sex-matched littermates. The dependency of genome-wide effects on parent-of-origin, Ube3a genotype, and time (P2, P9) was investigated through transcriptome (RNA-seq of cortex and hypothalamus) and methylome (whole genome bisulfite sequencing of hypothalamus). Weighted gene co-expression and co-methylation network analyses identified co-regulated networks in maternally inherited Ube3a deletion offspring correlated with postnatal age that were enriched in developmental processes including Wnt signaling, synaptic regulation, neuronal and glial functions, epigenetic regulation, ubiquitin, circadian entrainment, and splicing. Furthermore, using this novel rat model, we showed that loss of the paternally expressed Ube3a antisense transcript resulted inboth unique and overlapping dysregulated gene pathways, predominantly at the level of differential methylation, when compared to loss of maternal Ube3a. Together, these results provide the most holistic examination to date of the molecular impacts of UBE3A loss in brain, supporting the existence of interactive epigenetic networks between maternal and paternal transcripts at the Ube3a locus. Author Summary The neurodevelopmental disorder Angelman syndrome is caused by loss of UBE3A from the maternal chromosome. UBE3A is a genomically imprinted gene, which results in parent-of-origin specific expression of a protein from the mother and a noncoding RNA from the father. While mouse models have been useful in investigating diverse roles for UBE3A, their partial mutations are of limited utility for investigating parental imprinting effects or identifying a complete list of downstream differences in gene pathways relevant to developing therapies for Angelman syndrome. To address this limitation, we utilized a novel rat model with a CRISPR/Cas9 engineered full UBE3A deletion and systems biology approaches to better understand how UBE3A loss affects early postnatal brain development. We discovered that UBE3A loss has widespread effects on many important neuronal and cellular pathways and uncovered interesting interactions between maternal and paternal genes that were not previously considered. Taken together, our findings provide the most comprehensive view of UBE3A’s influences in the brain, which are relevant to the understanding and development of treatments for Angelman syndrome and related neurodevelopmental disorders.