Figure 3.

cDT-scanner analysis of vertebrate Delta-like 1 enhancers. Alignment of vertebrate neural and mesodermal specific cDTs with the Dll1 upstream CSBs identifies its neural and mesodermal enhancers. Dll1 CSBs of 6 bp or greater were curated using the EvoPrint-parser from the EvoPrint shown in Figure 2 and aligned with cDTs from the vertebrate neural and mesodermal cDT-libraries described in Table 2. Designations adjacent to the aligned cDTs indicate the number of perfect matches to CSBs within neural (n) or mesodermal (m) enhancers analyzed in this study. Transcription factor DNA-binding site searches of the Delta-like 1 CSBs and their aligning cDTs revealed that many contained putative binding sites and, in several cases, the shared sequence elements correspond exactly to, or had significant sequence overlap with, the characterized binding sites. For example, several cDTs that align to H-I enhancer CSBs correspond to known binding sites: these include a YY1 binding site (GCCATTT), an E-box (CAGATG; reviewed by [30]), a variant Oct1 site (ATGAAAAT) and a predicted core Lef-1 binding site (underlined) within a cDT (GCAAAGA). Within H-II conserved sequences, one common and one neural specific cDT aligned with the E-boxes (CAGGTG and CAGCTG), respectively.