Computational and in vitro analysis of destabilized DNA regions in the interferon gene cluster: potential of predicting functional gene domains

Biochemistry. 2003 Jan 14;42(1):154-66. doi: 10.1021/bi026496+.


Recent evidence adds support to a traditional concept according to which the eukaryotic nucleus is organized into functional domains by scaffold or matrix attachment regions (S/MARs). These regions have previously been predicted to have a high potential for stress-induced duplex destabilization (SIDD). Here we report the parallel results of binding (reassociation) and computational SIDD analyses for regions within the human interferon gene cluster on the short arm of chromosome 9 (9p22). To verify and further refine the biomathematical methods, we focus on a 10 kb region in the cluster with the pseudogene IFNWP18 and the interferon alpha genes IFNA10 and IFNA7. In a series of S/MAR binding assays, we investigate the promoter and termination regions and additional attachment sequences that were detected in the SIDD profile. The promoters of the IFNA10 and the IFNA7 genes have a moderate approximately 20% binding affinity to the nuclear matrix; the termination sequences show stronger association (70-80%) under our standardized conditions. No comparable destabilized elements were detected flanking the IFNWP18 pseudogene, suggesting that selective pressure acts on the physicochemical properties detected here. In extended, noncoding regions a striking periodicity is found of rather restricted SIDD minima with scaffold binding potential. By various criteria, the underlying sequences represent a new class of S/MARs, thought to be involved in a higher level organization of the genome. Together, these data emphasize the relevance of SIDD calculations as a valid approach for the localization of structural, regulatory, and coding regions in the eukaryotic genome.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Animals
  • Base Pair Mismatch
  • Binding Sites / genetics
  • Cell Line
  • Chemical Phenomena
  • Chemistry, Physical
  • Chromosomes, Human, Pair 9 / chemistry
  • Chromosomes, Human, Pair 9 / genetics
  • Codon / analysis
  • Codon / chemistry
  • Computational Biology / methods*
  • DNA / analysis*
  • DNA / chemistry
  • DNA Fragmentation
  • Forecasting
  • Genes
  • Genes, Overlapping
  • Humans
  • Interferon Type I / analysis
  • Interferon Type I / chemistry
  • Interferon Type I / genetics*
  • Interferon-beta / chemistry
  • Interferon-beta / genetics
  • Interferon-beta / standards
  • Mice
  • Multigene Family*
  • Nuclear Matrix-Associated Proteins / chemistry
  • Nuclear Matrix-Associated Proteins / genetics
  • Nuclear Matrix-Associated Proteins / standards
  • Nucleic Acid Heteroduplexes / analysis*
  • Nucleic Acid Heteroduplexes / chemistry
  • Protein Structure, Tertiary / genetics
  • Repetitive Sequences, Nucleic Acid


  • Codon
  • Interferon Type I
  • Nuclear Matrix-Associated Proteins
  • Nucleic Acid Heteroduplexes
  • Interferon-beta
  • DNA