Fig. 1: Infection model system reveals changes in chromatin architecture, accessibility, and gene expression over time.

a Schematic representation of the experimental design where Modified Vaccinia virus Ankara (MVA) was used to infect Vero cells with an MOI of 0.40. Figure cartoon created with Biorender. Vero cells cultivated in the same flask were divided for Hi-C, ATAC-seq, and RNA-seq experiments to provide paired data sets for direct comparison. Cells from mock-infected (control) and MVA-infected cultures were collected at 12, 18, and 24 hours post infection (hpi) with two biological replicates each. A total of 12 Hi-C libraries, 12 ATAC-seq libraries, and 12 RNA-seq libraries were prepared. b Infection efficiency was verified by immunofluorescence using an anti-vaccinia virus monoclonal antibody (green). Cell density and morphology can be seen in the bright-field images. c Principal component analysis of genome-wide chromatin accessibility from ATAC-seq data, d Chromatin contacts from Hi-C sequencing data, e Gene expression levels from RNA-seq data demonstrate clear separation between mock-infected control and MVA-infected cultures.