Extended Data Figure 1. Overview of 3D chromatin architectures and quality control of SARS-CoV-2 infection in our study.

a. A diagram showing the typical contact maps in Hi-C (and Hi-C 3.0 or other modified Hi-C approaches) that define A/B compartments, Topologically Associating Domains (TADs), chromatin loops or intra-TAD interactions (which perhaps include most enhancer-promoter contacts). This is an overall summary of these structures, but the exact definition of some structures may be subject to variable interpretation, and the terminology may not always be used consistently^2,3,9,19.

Often, A/B compartmentalization is illustrated by a checkerboard pattern of Hi-C contact matrices over large genomic sizes, indicating preferential interactions between genomic regions belonging to the same type of compartments (A: euchromatin and transcriptionally active; B: heterochromatin, transcriptionally inactive). TADs or chromatin domains are often characterized as a square or triangle-like structure on contact maps, reflecting a higher contact frequency between any regions inside the same TAD than with regions outside of the TAD. Intra-TAD enhancer-promoter contacts are considered to be facilitated by TADs, while TAD boundaries prevent aberrant interaction with regions outside of TADs.

In Hi-C maps, the dot-shaped structures on the tip of domains suggests local enrichment of spatial interaction between a pair of two loci over nearby regions, and is regarded as a chromatin loop in this work. But loops may be subjected to other definitions in other studies. For example, enhancer-promoter contacts often do not appear as dot-shaped structures in Hi-C, but may be defined as loops by other work or other methods. For additional discussion, see^2,9.

b. Cartoon diagrams describe A-A and B-B association preference within regions of similar epigenetic features, which compartmentalizes chromosomes into A and B (the left part of the diagram). The diagram in the middle depicts a current model of cohesin loop extrusion inside TADs that generates such structures. The right side shows a zoom-in view of a part of a TAD that harbors enhancer-promoter contact that may play roles in gene transcriptional regulation.

c. A barplot showing the percentage of RNA-Seq reads mapped to SARS-CoV-2 genome in Mock, 6-hr post infection (6 hpi, 0.1 MOI), and 24 hpi (0.1 MOI) conditions (n = 2). Mean and standard deviation were calculated based on two biological replicates of RNA-Seq. This data is consistent with previous observations⁴⁰. Shorter term infection for 6-hr resulted in ~20% RNA-Seq reads attributed to the virus genome, suggesting insufficient viral infection/replication in cell populations.

d. Confocal images showing immunofluorescence staining of DAPI (DNA, blue) and the Spike protein of SARS-CoV-2 (red) in Mock and 24hpi (0.1 MOI) infected A549-ACE2 cells. Scale bars are shown.

e. Quantification of infection rates in panel d. SARS-CoV-2 Spike protein was used as a marker for SARS-CoV-2 infection. From left to right, n= 3 and 4 quantifications.