Enhancers: holding out for the right promoter

Abstract

Some transcriptional enhancers work best with one type of promoter, while ignoring others. How widespread is such specificity across the genome? A new study finds that, in a fair fight, most enhancers prefer to activate promoters resembling those of their parent genes.

Figure 1

Using the STARR-seq technique to measure enhancer-promoter specificity. (A) Summary of STARR-seq. Random genomic DNA fragments were cloned into vectors containing either a developmentally regulated core promoter (dCP, green), based on a developmentally regulated gene, or a housekeeping core promoter (hkCP, pink), taken from a constitutively expressed gene. When transfected into cultured cells, enhancers “self-transcribed” if they were compatible with the core promoter in the vector. Vector-specific cDNAs were sequenced and mapped onto the genome: a representative UCSC Genome Browser view of a region containing unique dCP and hkCP enhancer peaks is shown. (B) Summary of key differences between dCP- and hkCP-preferring enhancers and their target genes.