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Nucleic Acids Research Advance Access originally published online on March 27, 2007
Nucleic Acids Research 2007 35(8):e56; doi:10.1093/nar/gkm108
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Nucleic Acids Research, 2007, Vol. 35, No. 8 e56
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique

George A. Follows1,*, Mary E. Janes1, Ludovic Vallier2, Anthony R. Green1 and Berthold Gottgens1

1Department of Haematology and 2Department of Surgery, Cambridge Institute for Medical Research, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 2XY, UK

*To whom correspondence should be addressed. Email: gf246{at}cam.ac.uk

Received December 22, 2006. Revised February 5, 2007. Accepted February 6, 2007.

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.


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