A sequence conserved in both the chicken and mouse alpha 2(I) collagen promoter contains sites sensitive to S1 nuclease

We have examined the S1 nuclease sensitivity in the promoter of both the chicken and mouse alpha 2(I) collagen genes. When these DNAs are introduced into supercoiled plasmids and digested with S1 nuclease, a discrete region containing one or more cleavages is found in each promoter. These S1 cleavage sites were mapped by the distance of the S1 site from known restriction enzyme cleavage sites. In the chicken gene, the S1-sensitive segment is located 180 to 200 base pairs preceding the start site of transcription, whereas in the mouse promoter it is between -145 to -165 base pairs. This site in the chicken promoter maps to the segment that has previously been shown to be S1 and DNase I hypersensitive in chromatin. Although these S1 sites are found at different distances from the start site of transcription in the two promoters, the sequences at these sites are strongly conserved between the two species. Each sequence consists of an identical tandem repeat containing a short palindrome within each repeat. Since the DNA sequence does not exhibit the features that would favor either a left-handed Z-DNA configuration or a cruciform structure, an alternative model is discussed that could account for the S1 sensitivity of these sequences. The conservation of these sequences and their S1 sensitivity suggests they play a role in the activation or regulation of the alpha 2(I) collagen gene promoters.