Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis

Dynamic cellular processes such as differentiation are driven by changes in the abundances of transcription factors (TFs). However, despite years of studies, our knowledge about the protein copy number of TFs in the nucleus is limited. Here, by determining the absolute abundances of 103 TFs and co-factors during the course of human erythropoiesis, we provide a dynamic and quantitative scale for TFs in the nucleus. Furthermore, we establish the first gene regulatory network of cell fate commitment that integrates temporal protein stoichiometry data with mRNA measurements. The model revealed quantitative imbalances in TFs’ cross-antagonistic relationships that underlie lineage determination. Finally, we made the surprising discovery that, in the nucleus, co-repressors are dramatically more abundant than co-activators at the protein level, but not at the RNA level, with profound implications for understanding transcriptional regulation. These analyses provide a unique quantitative framework to understand transcriptional regulation of cell differentiation in a dynamic context. [Display omitted] •Absolute quantification of endogenous transcription factors in human erythropoiesis•Co-repressors are in large excess while co-activators are limiting in the nucleus•Quantitative model of erythropoiesis integrating changes in protein and mRNA amounts•A website for human erythropoiesis transcription factors proteins and transcripts Protein stoichiometry in the nucleus is mostly unknown. Gillespie et al. use targeted mass spectrometry to quantify over a hundred transcription factors during human erythropoiesis. The data reveal co-repressors are on average 100 times more abundant than co-activators. Furthermore, a quantitative model of erythropoiesis integrating mRNA and protein abundances is generated.