GSE172053
IFN? induces a dynamic and complex transcriptional, chromatin and enhancer landscape
Aims and methods: To analyze how IFN? induces coding and non-coding nascent transcriptional changes, SNU-seq is used to measure genome-wide changes in nascent transcription in untreated, 0.5hr, 2hr and 24hr IFN? treated Hep3B cells. SNU-seq identifies the last transcribed nucleotide at near single-nucleotide resolution. 3'-end RNA-seq is used to examine RNA levels. ChIPmentation and ATAC-seq are used to assess the differential chromatin landscape upon IFN? treatments, measuring H3K27ac, H3K4me3 and CTCF genome-wide changes as well as DNA accessibility in untreated, 0.5hr, 2hr and 24hr IFN? treated Hep3B cells. Higher-order chromatin structure is investigated upon IFN? treatments using Capture-C to measure promoter interactions of three gene promoters; IRF1, STAT1, and CD274. Results:  3'-end RNA-seq reveals IFN? stimulated genes. SNU-seq identifies dynamic transcription at genes and non-coding intergenic regions and is used to demonstrate differential APA upon IFN? treatments. By measuring transcription at nucleosome depleted regions, differential enhancer activity was demonstrated. IFN? induces hundreds of methylation changes and thousands of acetylation changes over 24hrs. Unlike H3K4me3 which is deposited at late timepoints, H3K27ac is dynamically deposited. This acetylation is sometimes sustained throughout 24hrs but is often transiently deposited. CTCF shows very few binding changes throughout the timecourse. IFN? induces significant changes in promoter:enhancer interactions at IRF1 and STAT1. The CD274 promoter loops to the nearest gene promoter; PLGRKT. Overall design: SNU-seq, 3'-end RNA-seq and ATAC-seq were performed in triplicate in untreated, 0.5hr, 2hr and 24hr treated Hep3B cells. ChIPmentation was performed in duplicate in untreated, 0.5hr, 2hr and 24hr treated Hep3B cells. Capture-C was performed in duplicate in untreated, 0.5hr, 2hr and 24hr treated Hep3B cells, capturing the IRF1, STAT1 and CD274 promoter.