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Briefings in Functional Genomics and Proteomics Advance Access originally published online on February 23, 2006
Briefings in Functional Genomics and Proteomics 2006 5(1):24-31; doi:10.1093/bfgp/ell003
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© Oxford University Press, 2006, All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org

Special Issues Papers

The positive aspects of stress: strain initiates domain decondensation (SIDD)

Silke Winkelmann, Martin Klar, Craig Benham, AK Prashanth, Sandra Goetze, Angela Gluch and Juergen Bode

Corresponding author. Juergen Bode, GBF German Research Center for Biotechnology/Epigenetic Regulation Mascheroder Weg 1, D-38124 Braunschweig, Germany. Tel: +49 (531) 6181 251; Fax: +49 (531) 6181 262. E-mail: jbo{at}gbf.de

The conventional string-based bioinformatic methods of genomic sequence analysis are often insufficient to identify DNA regulatory elements, since many of these do not have a recognizable motif. Even in case a sequence pattern is known to be associated with an element it may only partially mediate its function. This suggests that properties not correlated with the details of base sequence contribute to regulation. One of these attributes is the DNA strand-separation potential, known as SIDD (stress-induced duplex destabilization) which facilitates the access of tracking proteins and the formation of local secondary structures. Using the type 1 interferon gene cluster as a paradigm, we demonstrate that the imprints in a SIDD profile coincide with chromatin domain borders and with DNAse I hypersensitive sites to which regulatory potential could be assigned. The approach permits the computer-guided identification of yet unknown, mostly remote sites and the design of artificial elements with predictable properties for multiple applications.

Keywords: chromatin domains, interferon gene cluster, remote control elements, non-viral episomes, SIDD, DNAse I hypersensitive sites


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