Fig. 4: CC-DCA for assessing genome-wide epistasis.
From: Mycobacterium abscessus pathogenesis identified by phenogenomic analyses
CC-DCA was used to identify co-evolving variants among ~1012 potential variant combinations of 2,366 clinical M. abscessus isolates. a, Circos plot of the M. abscessus chromosome showing the 100,000 top variant-to-variant couplings with a distance of >100 bp (black lines), coupling density (green; range 0–56,307 couplings per 5 kb) and SNP density (red; range 14–1,961 SNPs per 5 kb). b, Significant variant–variant couplings identified through DCA were pooled to gene–gene couplings. Whereas variant–variant couplings indicate the total number of co-evolutionary signals within a single gene, gene–gene couplings reflect the number of putative gene interactions. NR, non-ribosomal. c, Networks of co-evolving (and therefore probably epistatic) genes based on the 1,000 strongest DCA-derived gene–gene couplings ranked by coupling number, colour coded by functional class. The strength and number of couplings are shown by edge colour and thickness respectively. d, Example of a highly coupled gene network (highlighted by a circle in c) involving components of the mycobactin biosynthesis pathway e, CRISPR-induced transcriptional repression of several genes within this cluster demonstrates impaired mycobacterial survival within macrophages. Experiments were done in triplicate (with three guides per gene) on at least three separate occasions, are presented as mean ± s.e.m., and compared with the empty vector control using a two-sided unpaired t-test, **P < 0.001, ***P < 0.0001 (MbtD knockdown d2: P = 0.0002; MbtE kd d1: P = 0.0006, d2: P = 4.3 × 10−5; MbtF kd d1: P = 0.0001, d2: P = 1.3 × 10−5; MAB_4071 kd d1: P = 0.008; MAB_4072 kd d1: P = 0.0002).
