Protein-Deoxyribonucleic Acid Interactions Linked to Gene Expression: DNase I Digestion

Mapping DNase I hypersensitive sites can often localize the control regions in a eukaryotic gene. It is generally believed that chromosomal regions with loose or more open conformation are sensitive to DNase I cleavage. By comparing the patterns of hypersensitive sites obtained by digestion of silent genes with those obtained when the genes are actively transcribed, regions that participate in gene regulation (either induction or suppression) can be identified. A major strength of this method is that it is an “unbiased” approach to characterize the location of control sequences for the regulation of a gene. A good example of the power of DNase I hypersensitivity mapping is the rat Osteocalcin gene. Osteocalcin gene expression is detected only in bone tissues and in fully mature osteoblasts. DNase I cleavage is not observed in the OC gene in nonbone tissues or in immature osteoblasts (where OC is not transcribed). However, two DNase I hypersensitive sites are detected in the OC gene in bone tissues and in mature osteoblasts where the gene is actively transcribed. The first DNase I region encompasses the basal promoter regions that contain regulatory sequences for the RUNX, C/EBP, activator protein-1, and TFIID transcription factors. The second DNase I hypersensitive domain is mapped to a region 0.5 kilobases upstream of the transcription initiation site. This region contains a vitamin D enhancer element and regulatory sequences for RUNX factors. The sequences at these hypersensitive sites are both sufficient and necessary for basal and bone-tissue specific expression of the Osteocalcin gene.