Molecular cell

Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells.

PMID 28416141


The study of enhancers has been hampered by the scarcity of methods to systematically quantify their endogenous activity. We develop Mosaic-seq to systematically perturb enhancers and measure theirxa0endogenous activities at single-cell resolution. Mosaic-seq uses a CRISPR barcoding system to jointly measure a cell's transcriptome and its sgRNA modulators, thus quantifying the effects of dCas9-KRAB-mediated enhancer repression in single cells. Applying Mosaic-seq to 71 constituent enhancers from 15 super-enhancers, our analysis of 51,448 sgRNA-induced transcriptomes finds that only a small number of constituents are major effectors ofxa0target gene expression. Binding of p300 and RNAPII are key features of these constituents. We determine two key parameters of enhancer activity in single cells: their penetrance in a population andxa0their contribution to expression in these cells.xa0Through combinatorial interrogation, we find that simultaneous repression of multiple weak constituents can alter super-enhancer activity in a mannerxa0greatly exceeding repression of individual constituents.