Epigenetic effects (H3K9ac, H3K14ac, H3K23ac and Pol II) of Kat6b loss in mouse neural stem cells (CUT&Tag)

Heterozygous mutations in the histone acetyltransferase gene KAT6B (MYST4/MORF/QKF) cause cognitive disorders. Congruently, KAT6B is required for brain development, neural stem cell self-renewal and neuronal differentiation in mice. Despite the clear requirement for KAT6B in brain development, its molecular roles remain unexplored. Here we use CUT&Tag sequencing to determine the effects of loss or gain of KAT6B on H3K9ac and H3K23ac histone marks and on RNA Pol II. Overall design: Kat6b knock-out mice were constructed on the C57BL/6 background. Transgenic Tg(Kat6b) mice that overexpress Kat6b were also constructed and maintained on a FVBxBALB/c hybrid genetic background. The mixed genetic background was chosen because Tg(Kat6b) mice are not viable on the C57BL/6 background. Neural stem and progenitor cells were isolated from the dorsal telencephalon of E12.5 mouse embryos. Samples were taken from Kat6b–/– knockout embryos and wild-type embryos on the C57BL/6 background, and from Tg(Kat6b) transgenic embryos and wild-type embryos on the FVB x BALB/c genetic background. All samples were also spiked with a fixed amount of DNA from Drosophila S2 cells to aid with normalization. CUT&Tag profiles were constructed for H3K9ac, H3K14ac, H3K23ac and RNA Pol II. Four biological replicates were undertaken for each genotype and CUT&Tag antibody.