Fig. 1: SARS-CoV-2 restructures the host 3D genome.

a, The experimental design of this work. Created with BioRender.com. b, Hi-C 3.0 contact matrices of an example region (chr9: 100–130 Mb, hg19) in mock or infected conditions. Black arrowheads denote reduced short-distance interactions along the diagonal. Grey boxes show regions with altered compartmentalization. Bin size, 80 kb. c, Pearson correlation matrices of Hi-C 3.0 in the same region as in b. Arrowheads point to regions with virus-altered A–B (black) or A–A (cyan) compartmental interactions. Bin size, 80 kb. Colour scales indicate Pearson correlation coefficient (left and middle), and changes in the correlation matrices after infection (SARS-CoV-2/Mock, Pearson) are shown on the right. d, Zoom-in Hi-C snapshots of a 700 kb region in b and c (chr9: 95.7–96.4 Mb, hg19). Pink and cyan arrowheads show changed dot-shaped loops and domains, respectively. Bin size, 5 kb. e, Top: P(s) curve showing the relationship between the Hi-C contract frequency (P) of intra-chromosomal interactions ranked by genomic distance (s) in both mock (grey) and SARS-CoV-2 (red) conditions. Bottom: log₂FC of Hi-C contact frequency ranked by distances (infection/mock), with dotted lines marking the crossing points of the two curves. In b and d, colour scales indicate Hi-C contact frequencies (left and middle), and log₂FC of SARS-CoV-2/mock contact frequencies (right).