Scanning the appb genomic region of zebrafish by enhancer trapping using BACs represented schematically (summary of results from reference). The two BACs C and D used in this study overlap one another and contain different lengths of sequences upstream of appb gene. They are shown schematically as the top two lines. The inverted triangle represents enhancer-trap in Tn10 transposon, which is comprised of 0.35 kb of DNA immediately upstream of appb (UE), followed by EGFP gene with basal promoter, and ~1 kb intron 1 enhancer (IE). The entire enhancer-trap cassette is named BP-EGFP. The appb gene region in the BACs, with the thick blue arrow to represent the total length of exons and introns of the gene, is drawn to scale and shown below it. Insertion of the enhancer-trap into the appb BAC DNA and subsequent Cre recombination between the transposed loxP and the BAC-end loxP deletes the BAC DNA from that end and simultaneously inserts the enhancer-trap (shown as BP-EGFP). The enhancer-trap is in front of loxP in the transposon and is retained in the BAC after Cre-mediated loxP-loxP deletion. This end-truncation is represented by the bent line to illustrate the location of that transposon-end retained in the BAC after the loxP-Cre deletion. The earlier study  found that appb BACs that had the enhancer-trap located close to the appb transcription start site expressed EGFP fluorescence in neurons (e.g. BACs Δ74D, Δ70D, Δ94C, Δ92C Δ84C, Δ80C, Δ75C), while appb BACs that had the enhancer-trap inserted further upstream beyond -31 kb of the appb gene expressed EGFP fluorescence in the notochord (e.g. BACs Δ72C, Δ52C, Δ38C, Δ29C). The vertical blue dotted lines, separated by ~31 kb, mark these locations on the appb BACs. The names of BACs are indicated adjacent to the pictures of EGFP expression in zebrafish neurons or the notochord.
Shakes et al. BMC Genomics 2012 13:451 doi:10.1186/1471-2164-13-451