Unexpected Compensatory Increase in Transcripts in Knock-Out Mice Having Partial Deletions of Exons.

Genetic variants of the SH3 and multiple ankyrin repeat domains 3 () gene, which encodes excitatory postsynaptic core scaffolds cause numerous brain disorders. Several lines of knock-out (KO) mice with deletions of different exons have previously been generated and characterized. The different KO mouse lines have both common and line-specific phenotypes. Shank3 isoform diversity is considered a mechanism underlying phenotypic heterogeneity, and compensatory changes through regulation of expression may contribute to this heterogeneity. However, whether such compensatory changes occur in KO mouse lines has not been investigated in detail. Using previously reported RNA-sequencing analyses, we identified an unexpected increase in transcripts in two different mutant mouse lines ( and ) having partial deletions of exons. We validated an increase in transcripts in the hippocampus, cortex, and striatum, but not in the cerebellum, of heterozygous (HET) and KO mice, using qRT-PCR analyses. In particular, expression of the N-terminal exons 1-12, but not the more C-terminal exons 19-22, was observed to increase in mice with deletion of exons 13-16. This suggests a selective compensatory activation of upstream promoters. Furthermore, using domain-specific Shank3 antibodies, we confirmed that the increased transcripts in KO mice produced a small Shank3 isoform that was not detected in wild-type mice. Taken together, our results illustrate another layer of complexity in the regulation of expression in the brain, which may also contribute to the phenotypic heterogeneity of different KO mouse lines.