title: The positive aspects of stress: strain initiates domain decondensation (SIDD).
abstract: 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.
authors.affiliation: GBF German Research Center for Biotechnology/Epigenetic Regulation, Mascheroder Weg 1, D-38124 Braunschweig, Germany.
authors.forename: Silke
authors.initials: S
authors.lastname: Winkelmann
authors.forename: Martin
authors.initials: M
authors.lastname: Klar
authors.forename: Craig
authors.initials: C
authors.lastname: Benham
authors.forename: Ak
authors.initials: A
authors.lastname: Prashanth
authors.forename: Sandra
authors.initials: S
authors.lastname: Goetze
authors.forename: Angela
authors.initials: A
authors.lastname: Gluch
authors.forename: Juergen
authors.initials: J
authors.lastname: Bode
mesh_terms: D002843:Chromatin / Q000235:genetics; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D004278:DNA, Superhelical / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D007370:Interferon Type I / Q000235:genetics; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation
chemical_list: D002843:Chromatin; D004278:DNA, Superhelical; D007370:Interferon Type I; D004247:DNA