Absolute quantification of proteins and histone modifications in Drosophila embryos reveals stoichiometric relationships in chromatin regulation

Gene transcription in eukaryotes is regulated through dynamic interactions of a variety of different proteins with DNA in the context of chromatin. Here, we used mass spectrometry for absolute quantification of the nuclear proteome during two stages of Drosophila embryogenesis. Before proteomics analysis, we counted the absolute amount of genomic copies and used a standard range of proteins (UPS2 standard) for absolute quantification of protein copy numbers per 1C genome. These analyses provide comprehensive information about the absolute copy number of several thousand proteins and reveal unexpected relationships between the abundance of histone-modifying and -binding proteins and the chromatin landscape that they generate and interact with. These data provide a foundation towards a quantitative understanding of gene regulation in Drosophila.