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

Abstract

<jats:title>Abstract</jats:title> <jats:p>Ubiquitin E3 ligase 3A (UBE3A) encodes an E3 ubiquitin ligase whose loss from the maternal allele causes the neurodevelopmental disorder Angelman syndrome (AS). Previous studies of UBE3A function have not examined full Ube3a deletion in mouse, the complexity of imprinted gene networks in brain nor the molecular basis of systems-level cognitive dysfunctions in AS. We therefore utilized a systems biology approach to 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 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, compared to wild-type littermates. The dependency of genome-wide effects on parent-of-origin, Ube3a genotype and time (P2 and P9) was investigated through transcriptome (RNA sequencing 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 enriched in postnatal developmental processes including Wnt signaling, synaptic regulation, neuronal and glial functions, epigenetic regulation, ubiquitin, circadian entrainment and splicing. Furthermore, we showed that loss of the paternal Ube3a antisense transcript resulted in both unique and overlapping dysregulated gene pathways with maternal loss, predominantly at the level of differential methylation. Together, these results provide a holistic examination 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.</jats:p>

New genes involved in Angelman syndrome-like: Expanding the genetic spectrum

“…UBE3A interacts with most of the components of the proteasome [29] regulating the activity of signal transduction pathways such as Wnt signaling that regulates central nervous system development [30][31][32] and synaptic plasticity in both excitatory and inhibitory GABAergic axon terminals [33][34][35][36]. At the nucleus, UBE3A has been shown to regulate chromatin structure, DNA methylation and transcriptional regulation [37][38][39][40]. Interestingly, 8 out of the 10 genes found mutated in this study are mainly involved in synapsis (VAMP2, SYNGAP1, SLC6A1 and KCNQ3) [41][42][43][44] and chromatin remodeling or transcription regulation (TBL1XR1, SATB2, SMARCE1 and ASXL3) [45][46][47][48].…”

“…UBE3A has been shown to be present in euchromatin-rich nuclear domains indicating that it may influence neuronal physiology by regulating chromatin and gene transcription [59]. RNA-seq studies of UBE3A loss in rat cortex, mice hippocampus and SH-SY5Y cells have shown differential gene expression of KCNQ3 [60], SMARCE1, HSF2 [38], SPTAN1 and SATB2 [39] suggesting that these genes may be transcriptionally regulated by UBE3A. Moreover, UBE3A gain and loss in human SH-SY5Y cells has been shown to have significant effects on DNA methylation and chromatin modification in genes involved in transcriptional regulation and brain development including SATB2, ASXL3, SMARCE1 and TBL1XR1 [38].…”

Wnt/β-Catenin-Dependent Transcription in Autism Spectrum Disorders

“…Similarly, mutations in the E3 ubiquitin ligase UBE3A gene are responsible for the Angelman Syndrome ( Khatri and Man, 2019 ) and de novo ASD linked missense variant T485A was shown to enhance Wnt/β-catenin signaling activation through stabilization of β-catenin in HEK293T cells ( Yi et al, 2017 ). More recently, RNA-seq of cortex and hypothalamus from Ube3a deficient mice showed dysregulation of Wnt target genes ( Lopez et al, 2019 ).…”

An Integrative Synthetic Biology Approach to Interrogating Cellular Ubiquitin and Ufm Signaling

“…Deletion or loss-of-function mutations in human UBE3A gene are associated with Angelman syndrome (AS), while duplication of the chromosomal region (15q11-13) containing UBE3A has been discovered in 1.0-3.0% familial ASD (Autism Spectrum Disorders) worldwide [31]. UBE3A/E6AP was involved in many biological processes, such as Wnt signaling, circadian rhythms, imprinted gene networks, immunity responses, synapse plasticity and early brain development [32,33]. As UBE3A related neurodevelopmental diseases with incompletely understood mechanisms, suggesting yet undiscovered roles of UBE3A-mediated ubiquitination signal in diverse pathophysiological contexts [34,35].…”