UBE3A-mediated regulation of imprinted genes and epigenome-wide marks in human neurons

Abstract

The dysregulation of genes in neurodevelopmental disorders that lead to social and cognitive phenotypes is a complex, multilayered process involving both genetics and epigenetics. Parent-of-origin effects of deletion and duplication of the 15q11-q13 locus leading to Angelman, Prader-Willi, and Dup15q syndromes are due to imprinted genes, including UBE3A, which is maternally expressed exclusively in neurons. UBE3A encodes a ubiquitin E3 ligase protein with multiple downstream targets, including RING1B, which in turn monoubiquitinates histone variant H2A.Z. To understand the impact of neuronal UBE3A levels on epigenome-wide marks of DNA methylation, histone variant H2A.Z positioning, active H3K4me3 promoter marks, and gene expression, we took a multi-layered genomics approach. We performed an siRNA knockdown of UBE3A in two human neuroblastoma cell lines, including parental SH-SY5Y and the SH(15M) model of Dup15q. Genes differentially methylated across cells with differing UBE3A levels were enriched for functions in gene regulation, DNA binding, and brain morphology. Importantly, we found that altering UBE3A levels had a profound epigenetic effect on the methylation levels of up to half of known imprinted genes. Genes with differential H2A.Z peaks in SH(15M) compared to SH-SY5Y were enriched for ubiquitin and protease functions and associated with autism, hypoactivity, and energy expenditure. Together, these results support a genome-wide epigenetic consequence of altered UBE3A levels in neurons and suggest that UBE3A regulates an imprinted gene network involving DNA methylation patterning and H2A.Z deposition.

Emerging Gene and Small Molecule Therapies for the Neurodevelopmental Disorder Angelman Syndrome

“…UBE3A even acts as its own substrate [44]. Moreover, UBE3A expression is correlated with the regulation of various genes involved in protein catabolism, cell cycle, brain morphology, and transcriptional regulation [45,46]. Contributing to its complexity UBE3A is localized in pre-and post-synaptic neurons and localized to either cytoplasm or nucleus by isoform permitting for the widespread functional nature of the protein [47].…”

Epigenetics in Prader-Willi Syndrome

“…Furthermore, the largest conserved cluster of microRNA (miRNA) in the mammalian genome is found within the KOS14 imprinted locus and is responsible for regulating neuronal maturation and mTOR growth pathways ( Winter, 2015 ). Experimental evidence is emerging for regulatory cross-talk between different imprinted gene loci ( Stelzer et al, 2014 ; Jung and Nolta, 2016 ; Martinet et al, 2016 ; Vincent et al, 2016 ; Lopez et al, 2017 ), but this emerging “imprinted gene network” hypothesis ( Fauque et al, 2010 ; Haga and Phinney, 2012 ; Monnier et al, 2013 ; Ribarska et al, 2014 ) has been understudied in the context of the developing nervous system.…”

UBE3A: An E3 Ubiquitin Ligase With Genome-Wide Impact in Neurodevelopmental Disease

“…UBE3A degrades RING1B, a known UBE3A target that monoubiquitinates histones H2A and H2A.Z, thereby regulating H2A.Z monoubiquitination. Additionally, we took a multi-layered genomics approach to identify the global effects of different UBE3A expression levels in human neuronal cell culture models revealing significant effects on DNA methylation leading to differentially methylated regions (DMRs) in genes involved in transcriptional regulation and brain development (Lopez et al, 2017). This revealed a significant effect of reduced UBE3A levels on the methylation of up to half of known imprinted genes, suggesting a role for UBE3A in a neuronal imprinted gene network.…”