Figure 1

The location of HSE-αB within the proximal promoter (−162/+44) of the cryab gene. (A) Human and rat sequences in the proximal promoter of the cryab gene are highly conserved. The numbering shown above is for the rat sequence [20], TSS, transcription start site (thick blue arrow). The promoter element HSE-αB (black line), a 30-nucleotide promoter sequence, was used for earlier gel-shift studies [24, 25]. The TATA box (thin line) and the GPS (determined in this investigation) are boxed (thick line). The positions of two Pax6 sites [22] (pink) are shown. (B) A graphic representation of the composition of HSE-αB (−64/−35). This plot was generated from the results of the BLASTN homology search of the human genomic database using HSE-αB (x-axis), as the query sequence. Various parts of this sequence pick up homologous DNA sequences starting with various start positions. We calculated the frequency of each start position. The y-axis shows the frequency of start positions with homology in the 30-bp query sequence. Note that about 90% of the homology searches start from position 11 of this sequence. Position 11 is the first base of the 5'-NGAAN-3′ pentamer, the first of the three inverted sequence motifs (arrows) that make the HSE. There were no significant searches that start after position 18. The inset contains a plot of relative information content per base (bits) at each of the 30 positions in the HSE-αB, derived from top 100 BLASTN hits using http://weblogo.berkeley.edu. Based on this analysis, we designate the first 10 bp as gene-specific promoter sequence (GPS), while sequences from positions 11 to 25 constitute the canonical HSE (15 bp) with high-frequency representation in the genome. This analysis is based on 3,336 Blast hits using a maximum number of sequences = 20,000 in the NCBI BLASTN program.