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Background  The ubiquitin protein E3A ligase gene ( UBE3A ) gene is imprinted with maternal-specific expression in neurons and biallelically expressed in all other cell types. Both loss-of-function and gain-of-function mutations affecting the dosage of UBE3A are associated with several neurodevelopmental syndromes and psychological conditions, suggesting that UBE3A is dosage-sensitive in the brain. The observation that loss of imprinting increases the dosage of UBE3A in brain further suggests that inactivation of the paternal  UBE3A  allele evolved as a dosage-regulating mechanism. To test this hypothesis, we examined  UBE3A  transcript and protein levels among cells, tissues, and species with different imprinting states of  UBE3A .    Results  Overall, we found no correlation between the imprinting status and dosage of UBE3A. Importantly, we found that maternal Ube3a protein levels increase in step with decreasing paternal Ube3a protein levels during neurogenesis in mouse, fully compensating for loss of expression of the paternal  Ube3a  allele in neurons.    Conclusions  Based on our findings, we propose that imprinting of  UBE3A  does not function to reduce the dosage of  UBE3A  in neurons but rather to regulate some other, as yet unknown, aspect of gene expression or protein function.    Electronic supplementary material  The online version of this article (doi:10.1186/s13072-017-0134-4) contains supplementary material, which is available to authorized users.

Genomic imprinting does not reduce the dosage of UBE3A in neurons