STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [single_cell_RNA-Seq]

Enhancers are distal regulators of gene expression that shape cell identity and regulate cell fate transitions. Mouse embryonic stem cells (mESCs) are a typical example of cells whose pluripotent identity is maintained by a complex enhancer landscape, that is drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for enhancer location, strength and dynamics. Here, we applied STARR-seq, a genome-wide plasmid-based assay, to measure the enhancer potential of genomic loci in a plasmid context in “ground-state” (2i+LIF; 2iL-ESCs) and “metastable” (serum+LIF; SL-ESCs) embryonic stem cells. Single cell RNA-seq (Celseq2) of one 2i+LIF WT, one serum+LIF WT and two independent Zic3 knockout cell line were cultured in 2i+LIF or serum+LIF (biological replicates). 6 plates were sequenced in total.