STARR-seq for high-throughput identification of plant enhancers.

Abstract

Self-transcribing active regulatory region sequencing (STARR-seq) is a convenient method for genome-wide identification of plant enhancers. The basic principle is that an enhancer is able to activate the reporter gene expression (e.g., GFP) in a well-designed transient expression vector. The constructed vectors, which harbor the enhancer candidates, are transiently transformed into tobacco leaves or various protoplasts. The resulting reporter transcripts are enriched for sequencing. In the original design, the locations and activities of the enhancers are predicted by mapping to the reference genome and enrichment analysis. Recent research in plants showed the robustness of adding barcode sequences to link transcripts to the candidates placed upstream. The enhancer activities can, thus, be evaluated as the relative reporter expression level driven by the candidate versus the negative control.