Extended Data Fig. 9: Variations of genomic DNA supercoiling between cell states and types, and the role of DNA supercoiling in the regulation of gene expression.

(A) Percentage of dead cells in normal and quiescent cell population analyzed by flow cytometry, after cell staining with Live/Dead fixable near-IR dead cell stain kit. (B) Distribution of the DNA supercoiling level within each genomic 100-kb bin in GM12878 cells and HCT116 cells. (C) Distribution of DNA supercoiling level and the transcription activity (GRO-seq) in two example regions in GM12878 and HCT116 cells, at 500-bp resolution. Dotted lines mark the TSS of DEGs to show the corresponding supercoiling difference. Pink areas highlight the DNA supercoiling difference in genomic regions without transcription or DEGs. (D) DNA supercoiling in an example genomic region in GM12878 and HCT116 cells, at 100-kb and 10-kb resolutions. Pink areas highlight the difference. (E) Pearson correlation coefficients of the genome-wide DNA supercoiling between technical duplicates, between ATMP-seq normalized by naked gDNA and nucleosome-bound chromatin, if any nucleosome effect, and between GM12878 and HCT116 cells, at 100-kb, 10-kb, and 1-kb resolutions. (F-G) Biological duplicate dataset of nascent transcription activity of protein-encoding genes in negative SDs (negative, n = 2,487) or positive SDs (positive, n = 271), upon the AID depletion of TOP1 (F) or TOP2A (G) P values were calculated using nonparametric Wilcoxon two-sided tests. Auxinole (AUX) for the control, IAA for AID depletion. Boxplots show the median, first and third quartiles as a box, and the whiskers indicate the most extreme data point within 1.5 lengths of the box.