RNA-Seq analysis of wild-type and Hdac3-null E16.5 neurospheres and P0 cerebral cortex

Histone deacetylase 3 (HDAC3) is a unique epigenetic regulator forming stoichiometric complexes with several other proteins. Patients with mutations in genes encoding these proteins display intellectual disability, implying an important role of HDAC3 in this prevalent disease. Here we report that cerebrum-specific inactivation of the mouse gene causes striking developmental defects in the neocortex, hippocampus and corpus callosum; post-weaning lethality; and abnormal behaviors, including hyperactivity and anxiety. The developmental defects are due to rapid loss of neural stem and progenitor cells (NSPCs), starting at E14.5. Premature neurogenesis and abnormal neuronal migration in the mutant brain alter NSPC homeostasis. Mutant cerebral cortices display augmented DNA damage, apoptosis, and histone hyperacetylation. In agreement with these results, mutant NSPCs are impaired in forming neurospheres in vitro, and treatment of wild-type NSPCs with the HDAC3-specific inhibitor RGFP966 abolishes neurosphere formation. Transcriptomic analyses of neonatal cerebral cortices and cultured neurospheres support that HDAC3 regulates various transcriptional programs through interaction with multiple transcription factors, including NFIB. These findings establish HDAC3 as a major deacetylase critical for perinatal development of the mouse cerebrum and NSPCs, thereby suggesting a direct link of this enzymatic epigenetic regulator to human cerebral and intellectual development. To study the impact of cerebrum specific (Emx1-Cre) deletion of Hdac3 on embryonic neurospheres (cultured in vitro from E16.5 cerebrum) and neocortex from newborn pups (P0). Overall design: For neurospheres, cerebrums were dissected out from E16.5 embryonic brains (2 wild-type and 2 Hdac3 cKO), and cultured in neural stem cell culture media till day 4. The neurospheres were colleted for RNA isolation. For cerebral cortex, the dorsal part of the cerabral cortices from P0 brains (2 wild-type and 2 Hdac3 cKO) were collected for RNA isolation. The RNA samples were sequenced using the Illumina TruSeq stranded mRNA kit on HiSeq2500.