Histone modifications play a key role in regulating gene expression and cell fate during development and disease. Current methods for cell-type specific genome-wide profiling of histone modifications require dissociation and isolation of cells and are not compatible with all tissue types. Here we adapt Targeted DamID to recognise specific histone marks, by fusing chromatin binding proteins or single-chain antibodies to Dam, an E. coli DNA adenine methylase. When combined with Targeted DamID (TaDa), this enables cell-type specific chromatin profiling in intact tissues or organisms. We first profiled H3K4me3, H3K9ac, H3K27me3 and H4K20me1 in vivo in neural stem cells of the developing Drosophila brain. Next, we mapped cell-type specific H3K4me3, H3K9ac and H4K20me1 distributions in the developing mouse brain. Finally, we injected RNA encoding DamID constructs into 1-cell stage Xenopus embryos to profile H3K4me3 distribution during gastrulation and neurulation. These results illustrate the versatility of Targeted DamID to profile cell-type specific histone marks throughout the genome in diverse model systems.
Overall design: Targeted DamID recognising binding profiles of histone modifications was performed in Drosophila melanogaster 3rd instar larval neural stem cells, expressing Dam fusions with the GAL4 system; in mouse embryonic forebrain targeting radial glial cells (using Hes5 promoter), neurons (using Tα1 promoter) and intermediate progenitors (using ND1 promoter) with the use of inter-uterine electroporation to express Dam fusions; and in stage 11 and stage 21 (dorsal and ventral) Xenopus laevis embryos using mRNA injection to express Dam fusions. The histone marks tested were as follows: in Drosophila NSCs, H3K4me3 (with TAF3-phd domain), H4K20me1 (with H4K20me1-specific nanobody 15f11), H3K9ac (with H4K20me1-specific nanobody 19e5) and H3K27me3 (with Cbx7); in mouse RGCs H3K4me3, H4K20me1 and H3K9ac was tested with the same Dam-fusions. In Xenopus and mouse IPCs and neurons, only H3K4me3 was tested.
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