Nonlinear control of transcription through promoter-enhancer interactions [RNA-seq]

Chromosome structure in mammals is thought to regulate transcription by modulating spatial proximity between enhancers and promoters. However, the mechanisms by which this occurs remain elusive, and reports suggested moderate to no correlation between physical proximity and transcription. Whether and how chromosome structure is actually translated into transcriptional outputs thus remains unclear. Here we use a novel assay to position an enhancer at hundreds of different chromosomal sites relative to a fixed promoter and quantitatively measure promoter output. Overall design: We identify active promoters in mouse embryonic stem cell by performing total RNA-seq in triplicates