Effect of promoter compatibility and sequence positioning on high-throughput identification of cell type-specific enhancers using STARR-CRAAVT in HepG2 and HaCaT cells

Here, we present STARR-CRAAVT, a STARR-Seq-based platform to screen for enhancers in the AAV context. Employing two in-vitro models, HepG2 and HaCaT cells, we aimed to implement STARR-CRAAVT for the identification of cell type-specific enhancers.

We integrated epigenetic datasets into an in-silico library of putative HepG2 enhancers and captured corresponding fragments from sheared genomic DNA. The fragments were processed into AAV libraries and applied to HepG2 and HaCaT cells. Comparative STARR-CRAAVT analysis revealed a selective activity of the libraries confirming our HepG2-directed in-silico design and the specificity of single enhancer/promoter combinations could be validated using luciferase reporter assays.