Chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq) detection of histone H3 lysine 14 acetylation (H3K14ac) and KAT7 (HBO1) in E14.5 mouse neural stem and progenitor cells (NSPCs)

Tissue specific deletion of the gene encoding the histone acetyltransferase KAT7 (HBO1) in the developing mouse central nervous system using cre-recombinase expression driven by regulatory sequences of the nestin locus (NesCre transgene) resulted in defective cerebral cortex development, a complete failure of neural stem cells to give rise to neurons and oligodendrocytes during in vitro differentiation and a failure to express the neuronal differentiation program. KAT7 genome occupancy and histone H3 lysine 14 acetylation (H3K14ac) levels were assessed by ChIP-seq in proliferating Kat7 deleted vs. Kat7 intact neural stem and progenitor cells (NSPCs). KAT7 and H3K14ac were completely absent in the Kat7 deleted cells. IN KAT7 intact cells, KAT7 occupancy levels and H3K14ac levels within the body of genes correlated strongly and positively. Both were higher in genes that were expressed strongly than in genes with lower or no expression. However, KAT7 and H3K14ac were present in all genes including silent genes and in all other regions of the genome, including intergenic regions and regions decorated with histone H3 lysine 9 trimethylation (H3K9me3), an indicator of constitutive heterochromatin. Overall design: KAT7 genome occupancy and H3K14ac levels assessed by ChIP-seq at passage 5 day 3 of proliferating Kat7lox/loxNesCreT/+ and Kat7+/+NesCreT/+ neural stem and progenitor cells (NSPCs) originally isolated at E14.5 cultured as floating colonies (neurospheres). NSPC isolates from 4 Kat7 intact and 3 Kat7 deleted animals per genotype were assessed for H3K14ac and NSPC isolates from 3 Kat7 intact and 1 Kat7 deleted animal per genotype were assessed for KAT7 occupancy. IgG controls were also assessed.