P124 Transcriptional regulation of the human type I IFN locus

• Published in: Cytokine (Philadelphia, Pa.) Pa.), 2012-09, Vol.59 (3), p.559-559
• Main Author: Horvath, C.
• Format: Article
• Language: English
• Subjects: Beta gene; Chromatin; chromosome 9; Convergence; DNA sequencing; DNA-directed RNA polymerase; Elongation; Enhancers; Gene mapping; Gene regulation; genomics; Immune response; Immunomodulation; Immunoprecipitation; Infection; Integration; Interferon; Mediator protein; Nuclease; Nucleosomes; Phosphorylation; Polymerase chain reaction; Promoters; Sendai virus; Transcription activation; Transcription factors; Transcription initiation
• ISSN: 1043-4666; 1096-0023
• DOI: 10.1016/j.cyto.2012.06.216

Transcriptional activation of type I interferon (IFN-1) genes (including IFN beta and multiple IFN alpha subtypes) is essential to the immediate cellular response to virus infection and is a key antiviral defense. The induction of IFN-1 causes immunomodulation and serves to prime and coordinate subsequent innate and adaptive immune responses. Virus induction of IFN beta gene expression is well known to involve rapid and dynamic changes in enhancer occupancy, nucleosome positioning, and RNA polymerase recruitment. To better understand the integration of these events and to extrapolate them to the broader type I IFN gene cluster on human chromosome 9 (9p21-22), nucleosome occupancy was examined throughout the locus. Nucleosome protected DNA, generated using micrococcal nuclease digestion, was significantly enriched by a direct genomic selection process and followed by deep sequencing to generate nucleosome maps of the entire locus throughout a time course of Sendai virus infection. In parallel, the early transcriptional initiation events leading to IFN gene activation have been studied by chromatin immunoprecipitation followed by quantitative PCR. Nucleosome protected DNA, generated using micrococcal nuclease digestion, was significantly enriched by a direct genomic selection process and followed by deep sequencing to generate nucleosome maps of the entire locus throughout a time course of Sendai virus infection. Results affirm the presence of a positioned nucleosome that obscures the transcriptional start site of the IFN beta gene, and this nucleosome is evicted by 4h post infection. All of the IFN-1 genes share the presence of a TSS-obscuring nucleosome in an analogous position, which is clearly distinct from the reported +1 nucleosome position of most human genes at steady state. CHIP Results indicate that no pre-existing paused, poised, or otherwise classified Pol II is present at the IFN beta promoter prior to virus infection. Instead de novo recruitment of virus-induced transcription factors, Mediator proteins, RNA Polymerase II (Pol II), and associated Pol II elongation factors to the promoter of the IFN beta gene were observed. Nonetheless, this newly recruited Pol II has features consistent with a paused polymerase, including its phosphorylation on serine-5 of the heptad repeat, its associations with negative elongation factor (NELF), and its sensitivity to a cyclin dependent kinase inhibitor. These findings suggest a common mechanism of virus-induc