Mapping sites within the genome that are hypersensitive to digestion with DNaseI 
is an important method for identifying DNA elements that regulate transcription. 
The standard approach to locating these DNaseI-hypersensitive sites (DHSs) has 
been to use Southern blotting techniques, although we, and others, have recently 
published alternative methods using a range of technologies including 
high-throughput sequencing and genomic array tiling paths. In this article, we 
describe a novel protocol to use real-time PCR to map DHS. Advantages of the 
technique reported here include the small cell numbers required for each 
analysis, rapid, relatively low-cost experiments with minimal need for 
specialist equipment. Presented examples include comparative DHS mapping of 
known TAL1/SCL regulatory elements between human embryonic stem cells and K562 
cells.