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Interferon induction of gene transcription analyzed by in vivo footprinting

: Mirkovitch, J.; Darnell, J.E.; Decker, T.

Molecular and Cellular Biology 12 (1992), No.1, pp.1-9
ISSN: 0270-7306
Journal Article
Fraunhofer ITA ( ITEM) ()
cell line; G-protein; gene expression regulation; genetic transcription; interferon; interferon alpha

The promoters of two interferon-induced genes (the ISG54 and guanylate-binding protein (GBP) genes) have been analyzed in whole cells and in isolated nuclei by using a new genomic sequencing technique. The ISG54 gene contains an interferon-simulating response element (ISRE), earlier shown to be necessary and sufficient for alpha interferon (IFN-alpha) induction, that appeared complexed with proteins in both transcribing and nontranscribing cells. However, the extent of protection and hypersensitivity to DNase 1 or dimethyl sulfate within the ISRE region was changed upon transcriptional induction, suggesting the binding of different factors in different transcriptional states. In addition to the ISRE, the GBP gene needs a newly recognized DNA element, called the GAS, that partly overlaps the ISRE for full induction by either IFN-alpha or IFN-gamma. This GAS element was transiently protected against DNase 1 in the nuclei of interferon-treated cells but was not protected at later times wh en transcription reached maximal levels. Thus, the GAS-binding activity may be necessary only transiently for the initial assembly of a transcription initiation complex on the GBP promoter. Dimethyl sulfate methylation of genomic DNA performed on intact cells showed a characteristic sensitivity over the GAS that correlated with transcription levels and that persisted longer than did DNase 1 protection over the GAS. These results demonstrate the involvement of the GAS in IFN-alpha and -gamma induction of GBP and suggest the presence of an altered DNA conformation or a small protein in the major groove of the GAS associated with ongoing GBP transcription.