Trash Day in the Cell: Analysis of Ubiquitinated Chromatin Proteins
Proteins are an essential component of life on Earth and provide the basis for many important functions across all organisms. Proteins can be edited by post-translational modifications (PTMs), which in turn can affect gene expression. Ubiquitination is one such PTM that is a central player in protein and gene expression. One place where proteins are especially important to gene expression is in their interactions with chromatin. In this study, we employ cellular fractionation to isolate the chromatin fraction of cells and apply the novel one-step isotopically balanced quantification of ubiquitination (IBAQ-Ub) workflow to identify and quantify ubiquitinated chromatin-bound proteins. These analyses show the breadth and diversity of ubiquitinated proteins that interact with chromatin and highlight specifically important chromatin-bound proteins involved in gene expression. Through these analyses, we show the effectiveness of one-step IBAQ-Ub and its potential to answer important biological questions related to ubiquitination.