Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET)

Abstract

While technologies for measuring transcriptomes in single cells have matured, methods for measuring proteins and their post-translational modification (PTM) states in single cells are still being actively developed. Unlike nucleic acids, proteins cannot be amplified, making detection of minute quantities from single cells difficult. Here, we develop a strategy to detect targeted protein and its PTM isoforms in single cells. We barcode the proteins from single cells by tagging them with oligonucleotides, pool barcoded cells together, run bulk gel electrophoresis to separate protein and its PTM isoform and quantify their abundances by sequencing the oligonucleotides associated with each protein species. We used this strategy, iDentification and qUantification sEparaTion (DUET), to measure histone protein H2B and its monoubiquitination isoform, H2Bub, in single yeast cells. Our results revealed the heterogeneities of H2B ubiquitination levels in single cells from different cell-cycle stages, which is obscured in ensemble measurements. Yandong Zhang, et al. develop iDentification and qUantification sEparaTion (DUET) to quantify target protein and its post-translational modification isoforms in single cells. Using their method, they report heterogeneities in the ubiquitination levels of histone H2B in single yeast cells and reveal the cell-cycle dynamics of H2B monoubiquitination.