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Nucleic Acids Research Advance Access published online on February 27, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp037
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© 2009 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

A library-based method to rapidly analyse chromatin accessibility at multiple genomic regions

Asjad Basheer, Harald Berger, Yazmid Reyes-Dominguez, Markus Gorfer and Joseph Strauss*

Austrian Research Centers, Fungal Genomics Unit and Department of Applied Genetics and Cell Biology, BOKU University Vienna, Muthgasse 18, A-1190 Vienna, Austria

*To whom correspondence should be addressed. Tel: +43 1 36006 6720; Fax: +43 1 36006 6392; Email: joseph.strauss{at}boku.ac.at

Received July 25, 2008. Revised January 8, 2009. Accepted January 9, 2009.

Traditional chromatin analysis methods only test one locus at the time or use different templates for each locus, making a standardized analysis of large genomic regions or many co-regulated genes at different loci a difficult task. On the other hand, genome-wide high-resolution mapping of chromatin accessibility employing massive parallel sequencing platforms generates an extensive data set laborious to analyse and is a cost-intensive method, only applicable to the analysis of a limited set of biological samples. To close this gap between the traditional and the high-throughput procedures we have developed a method in which a condition-specific, genome-wide chromatin fragment library is produced and then used for locus-specific DNA fragment analysis. To validate the method, we used, as a test locus, the well-studied promoter of the divergently transcribed niiA and niaD genes coding for nitrate assimilation enzymes in Aspergillus. Additionally, we have used the condition-specific libraries to study nucleosomal positioning at two different loci, the promoters of the general nitrogen regulator areA and the regulator of secondary metabolism, aflR.


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