Fig. 8

Enrichment of promoter-interacting fragments for regions capable of driving transgene expression in mESCs. TRIP (Thousands of Reporters Integrated in Parallel) assesses the influence of local chromatin context on gene expression. This is achieved by integrating a barcoded transgene reporter into thousands of genomic locations in parallel and monitoring the transcriptional activity at each location [24]. Normalised RNA read counts from reporter insertions are separated according to (i) their overlap with HindIII fragments engaging or not in interactions; (ii) their promoter-other end distance. For non-interacting HindIII fragments, distance is measured from the nearest promoter in the linear sequence. Blue and green box plots indicate read count summary statistics for promoter-interacting and non-interacting HindIII fragments, respectively. Each dashed line shows the regression of median log-normalised read counts against promoter-other end distance bin, considering promoter-interacting (blue) and non-interacting (green) HindIII fragments separately