Fig. 4: Chromosome rearrangement during metabolic differentiation.

a 3C-seq and RNA-seq performed after 24 h in MP5 growth medium (C1 condition). Same legend as Fig. 3 except that the bacteria were grown in MP5 medium. The replicate of this experiment is presented in Supplementary Fig. 6b. b Level of gene expression depending on gene location within boundaries or domains. The box-plot presents the sense-transcription (DESeq2 normalized number of reading per kb, normRPK) depending on gene location in exponential phase either in MP5 (C1) or in YEME10 (C6), or after 48 h of growth in MP5 medium (C4). The expression in the C1 condition of the genes at the boundaries of domains in common between C1 and C6 conditions (‘Common C1 & C6’) is also presented. The p-values of two-sided Wilcoxon rank-sum tests with continuity correction (boundaries versus domains) are indicated above each box. The number of analyzed genes (‘#’) per condition is indicated. c Level of gene persistence depending on gene location within boundaries or domains. The box-plot presents the persistence index depending on gene location in exponential phase (C1: MP5; C6: YEME10; in common between both conditions: ‘Common C1 & C6’) or after 48 h of growth in MP5 medium (C4). The p-values of two-sided Wilcoxon rank-sum tests with continuity correction (boundaries versus domains) are indicated above each box. The number of analyzed genes (‘#’) per condition is also indicated. Please note that the persistence was not calculated for functional RNA encoding genes. All boxplots of this figure represent the first quartile, median and third quartile. The upper whisker extends from the hinge to the largest value no further than 1.5*the inter-quartile range (IQR, i.e. distance between the first and third quartiles) from the hinge. The lower whisker extends from the hinge to the smallest value at most 1.5*IQR of the hinge. For clarity, outliers were excluded from these graphical representations (but were taken into account for the numerical exploitation of the data). d Dispersion index of the left, central and right compartments plotted as a function of genomic distance. Long-range DNA contacts within the terminal compartments (>100 kb) are more variable than within the central compartment in the exponential phase. e 3C-seq and RNA-seq were performed after 48 h in MP5 growth medium (C4 condition). Same legend as Fig. 3 except that the bacteria were grown in MP5 medium during 48 h. The arrow indicates the position of the congocidine BGC. The replicate of this experiment is presented in Supplementary Fig. 6c. f. Focus on the genomic region (50 kb) encompassing the congocidine BGC contact maps (squares) after 24 h (top) or 48 h (bottom) of growth in the MP5 medium. The focus was performed on the 3C-contact maps presented in the a and e panels. The detailed genetic organization of the congocidine BGC is presented.