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. 2021 Sep 1;12:5222. doi: 10.1038/s41467-021-25461-2

Fig. 3. Influence of SMC and HupS on chromosome organisation.

Fig. 3

A Top panels: the normalised Hi-C contact maps obtained for the wild-type and smc, hupS and smc hupS double mutants (ftsZ-ypet derivatives, MD100, TM005, TM004, TM006, respectively) growing for 22 h or for 25 h (only in the case of the double hupS smc mutant) (in 5 ml cultures). Bottom panels: the corresponding differential contact maps in the logarithmic scale (log2) comparing the contact enrichment in the wild-type strain (red) versus the mutant strains (blue) are shown below each Hi-C contact map. B The number of FLAG-SMC binding sites along the chromosome of the wild-type (blue) (TM017) or parB mutant background (red) (KP4F4) determined by ChIP-Seq analysis at the time of sporogenic cell division (14 h of 50 ml culture growth). The number of FLAG-SMC binding sites (250 bp) was determined by normr analysis averaged over 0.5 Mbp sliding window every 1000 bp with a loess model fit. Points below the plot show positions of individual sites coloured according to their FDR (false discovery rate) values (yellow less significant, dark purple more significant). C The number of HupS-FLAG binding sites along the chromosome in the wild-type background (hupS deletion complemented with hupS-FLAG delivered in trans, TM015) determined by ChIP-Seq analysis at the time of sporogenic cell division (14 h of 50 ml culture growth). The number of HupS-FLAG binding sites was determined by differential analysis of the HupS-FLAG and wild-type strains using edgeR and averaged over 0.5 Mbp sliding window every 1000 bp. Smooth line shows loess model fit. The points below the plot show positions of individual sites coloured according to their FDR values (yellow less significant, dark purple more significant). D Heatmaps showing the number of reads for all 307 regions bound by HupS-FLAG in the wild-type background (TM015), smc mutant background (TM016) and negative control (the wild-type strain). The reads were normalised by the glmQL model from the edgeR package. For each region, position 0 is the position with the maximum number of reads. Regions are sorted according to their logFC values. E Comparison of HupS-FLAG binding in the wild-type (blue) and smc deletion background (red). The lines show mean values of reads (for 69 bp long regions) with 95% confidence intervals for all 307 sites differentially bound by HupS-FLAG protein. For all sites, 1000 bp long fragments were extracted from the chromosome centred around the best position as determined by edgeR analysis.