BACKGROUND: Mapping DNaseI hypersensitive sites is commonly used to identify 
regulatory regions in the genome. However, currently available methods are 
either time consuming and laborious, expensive or require large numbers of 
cells. We aimed to develop a quick and straightforward method for the analysis 
of DNaseI hypersensitive sites that overcomes these problems.
RESULTS: We have developed a modified Multiplex Ligation-dependent Probe 
Amplification (MLPA) approach for the identification and analysis of genomic 
regulatory regions. The utility of this approach was demonstrated by 
simultaneously analysing 20 loci from the ENCODE project for DNaseI 
hypersensitivity in a range of different cell lines. We were able to obtain 
reproducible results with as little as 5 x 10(4) cells per DNaseI treatment. Our 
results broadly matched those previously reported by the ENCODE project, and 
both technical and biological replicates showed high correlations, indicating 
the sensitivity and reproducibility of this method.
CONCLUSION: This new method will considerably facilitate the identification and 
analysis of DNaseI hypersensitive sites. Due to the multiplexing potential of 
MLPA (up to 50 loci can be examined) it is possible to analyse dozens of DNaseI 
hypersensitive sites in a single reaction. Furthermore, the high sensitivity of 
MLPA means that fewer than 10(5) cells per DNaseI treatment can be used, 
allowing the discovery and analysis of tissue specific regulatory regions 
without the need for pooling. This method is quick and easy and results can be 
obtained within 48 hours after harvesting of cells or tissues. As no special 
equipment is required, this method can be applied by any laboratory interested 
in the analysis of DNaseI hypersensitive regions.