Expression of the regulator sensor is correlated with surrounding enhancers up to large distances. (A) Enrichment of insertions showing LacZ activity in a given tissue relative to limb EP300 binding sites. Enrichment for insertions with expression in the limb (green) compared with random insertions is calculated at increasing distances from the nearest EP300 site (x-axis). Error bars represent one standard deviation from the mean. Enrichments of insertions with activity in other tissues but not in the limb (heart: purple; forebrain: blue; midbrain: red) or with no LacZ activity (gray) are also displayed. Results for EP300 sites from other tissues are shown in Supplemental Figure 1. (B) Comparison of enhancer and sensor activity. Different groups were considered, according to the relative distance between the insertions and the enhancers (number of insertion–enhancer pairs indicated above each bar). The two random data sets are described in the Methods section. The proportions of concordant enhancer–insertion pairs in different groups were compared using Fisher's exact test. (C–E) Examples of concordant enhancer–insertion pairs. The different loci are schematized (enhancer: blue oval with VISTA reference; sensor: drawing of transposon; endogenous genes: arrows or gray bars with black exons), with putative target genes of enhancers indicated by labeling the gene the same color as the enhancer. Photos of representative embryos of the in vivo enhancer assays are from the Vista Enhancer Browser (Visel et al. 2007). (C) The sensor reported the activity of an intronic diencephalon/midbrain enhancer, which likely contributes to the regulation of the distant Lhx2 gene (Gray et al. 2004). (D) Heart-specific expression of the sensor when inserted adjacent to a heart-specific enhancer, possibly regulating the adjacent Myocd gene (Wang et al. 2001). The eye expression shown on the representative transgenic embryo (*) is ectopic. (E) The sensor, inserted next to Znf503 (McGlinn et al. 2008), showed expression in the posterior forelimb, which overlapped with the activity of a distant enhancer (fl, blue/white arrow). The enhancer was also active in the neural tube, but the sensor was not expressed in that region.
