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

Silke Winkelmann, Martin Klar, Craig Benham, A. K. Prashanth, Sandra Goetze, Angela Gluch, Juergen Bode

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


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.

Original languageEnglish
Pages (from-to)24-31
Number of pages8
JournalBriefings in Functional Genomics and Proteomics
Issue number1
StatePublished - Mar 2006
Externally publishedYes


  • Chromatin domains
  • DNAse I hypersensitive sites
  • Interferon gene cluster
  • Non-viral episomes
  • Remote control elements
  • SIDD


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