**2.1 Rationale for using BACs to understand gene regulation**

BACs offer a large span of DNA that can house most, if not all, the sequences recognized by DNA-binding regulatory proteins that act in concert to regulate expression of the gene. But more importantly, the binding sites of regulatory proteins in the BAC DNA exist in their chromosomal contexts, with sequences flanking *cis*-acting sites that have evolved for millions of years, preserved. This cannot be said of small plasmid constructs used for expressing genes where multiple, easily-recognizable distal *cis*-acting sequences are excised from their surrounding DNA in the chromosome and cobbled together to create artificial junctions.
