Identification and promoter activity of DNase I hypersensitive sites in the region of the Hox-1.3 gene.

The Hox genes encode transcriptional regulatory proteins that play a critical role in rostrocaudal specification in the developing embryo. The genes lie in four clusters in the mouse and human genome and are arranged such that a colinear relation exists between a gene's position in the cluster and the time of activation of the gene's expression. We have analyzed the Hox-1.3 region within the Hox-1 gene cluster for DNase I hypersensitive sites to identify putative regulatory sequences. Fragments identified in this way were then analyzed for transcriptional activity using gene transfer experiments in embryonal carcinoma (EC) cells. Three DNase I hypersensitive sites were identified, one of which includes the Hox-1.3 promoter and another, located 550 bp upstream, which enhances the Hox-1.3 promoter activity. The third occurs in the intron and may represent a Hox binding site. Significantly, the DNase I hypersensitive site pattern of this region of the Hox-1 cluster is not altered when F9 stem cells are differentiated with retinoic acid, suggesting that sequential activation of Hox genes by retinoic acid is not due to a sequential opening of the chromatin structure in the Hox gene region.