Probing the Function of Metazoan Histones with a Systematic Library of H3 and H4 Mutants

Replication-dependent histone genes often reside in tandemly arrayed gene clusters, hindering systematic loss-of-function analyses. Here, we used CRISPR/Cas9 and the attP/attB double-integration system to alter numbers and sequences of histone genes in their original genomic context in Drosophila melanogaster. As few as 8 copies of the histone gene unit supported embryo development and adult viability, whereas flies with 20 copies were indistinguishable from wild-types. By hierarchical assembly, 40 alanine-substitution mutations (covering all known modified residues in histones H3 and H4) were introduced and characterized. Mutations at multiple residues compromised viability, fertility, and DNA-damage responses. In particular, H4K16 was necessary for expression of male X-linked genes, male viability, and maintenance of ovarian germline stem cells, whereas H3K27 was essential for late embryogenesis. Simplified mosaic analysis showed that H3R26 is required for H3K27 trimethylation. We have developed a powerful strategy and valuable reagents to systematically probe histone functions in D. melanogaster. •Generation of histone-deletion lines in Drosophila by CRISPR/Cas9•Histone gene dosage affects oogenesis and spermatogenesis in Drosophila•Hierarchically assembled 40 histone mutants provide a platform for PTM studies•A mosaic system allows functional studies of essential histone mutations Histone PTMs modulate chromatin structure and gene expression. Zhang et al. generate a resource of Drosophila lines with histone H3 and H4 gene copy number alterations and single residue mutations covering modifiable histone residues to systematically investigate histone gene dosage effects during oogenesis and spermatogenesis and dissect histone function.