Quantification of Proteins and Histone Marks in Drosophila Embryos Reveals Stoichiometric Relationships Impacting Chromatin Regulation

• Published in: Developmental cell 2019-12, Vol.51 (5), p.632-644.e6
• Main Authors: Bonnet, Jacques, Lindeboom, Rik G.H., Pokrovsky, Daniil, Stricker, Georg, Çelik, Muhammed Hasan, Rupp, Ralph A.W., Gagneur, Julien, Vermeulen, Michiel, Imhof, Axel, Müller, Jürg
• Format: Article
• Language: English
• Subjects: absolute proteome quantification; Drosophila; H3K27 methylation; histone modification quantification; PRC2
• ISSN: 1534-5807; 1878-1551
• DOI: 10.1016/j.devcel.2019.09.011

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 and methyl marks on selected lysine residues in histone H3 during two stages of Drosophila embryogenesis. 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. For some histone modifications, the levels in Drosophila embryos are substantially different from those previously reported in tissue culture cells. Genome-wide profiling of H3K27 methylation during developmental progression and in animals with reduced PRC2 levels illustrates how mass spectrometry can be used for quantitatively describing and comparing chromatin states. Together, these data provide a foundation toward a quantitative understanding of gene regulation in Drosophila. •Accurate quantification of 4,000 proteins in embryo nuclei by mass spectrometry•Data reveal stoichiometric relationships between chromatin regulators and histones•Repressive histone PTM abundance in embryos differ from those in cultured cells•Copy number information enables quantitative analysis of chromatin state changes Understanding stoichiometric relationships among relevant components can provide insight into biological systems. Bonnet et al. determine the absolute copy numbers of proteins and histone modifications in Drosophila embryonic nuclei. These data enable a quantitative understanding of how a chromatin state is established and maintained during embryogenesis.