Fig. 4: Stable nucleosome formation in E. coli in long-term growth experiment.
From: Creating a bacterium that forms eukaryotic nucleosome core particles
a A schematic for long-term passage and assay of the nucleosome-forming strain, Ec-r-pXen, grown at 37 °C, treated with 1 µM IPTG. b Histone gene expression (dot-line plot; Log2TPM) and nucleosome peak number (bar plot; mean ± SEM) detected in the nucleosome-forming E. coli (clones 1–4) through the passages. p2, p6, p10, and p14 denote passages 2, 6, 10, and 14. TPM, transcript per million. Histone gene expression data: n = 4 biological replicates for p2, p6, and p10; n = 3 for p14. Nucleosome peak count data: n = 4 for p2, p6, and p14; n = 3 for p10. c Heatmaps and averaged profile (top panel) of dyad nucleosome occupancy for the nucleosome-forming E. coli from passages 2, 6, 10, and 14. The dyads from each passage are plotted in the same order based on their occupancy ranking in passage 14. The right panel shows the smoothed curve of the GC content for dyad sequences. For panels (c–f), data were generated from the E. coli clones 1–4 as those in panel (b). d Correlation of nucleosome occupancy between corresponding dyads for paired passages of the nucleosome-forming E. coli. r, Pearson’s correlation coefficient. e Averaged nucleosome distribution in genic regions of the nucleosome-forming E. coli from passages 2, 6, 10, and 14. Darker lines (smoothed) and associated lighter bands represent the mean and SEM of averaged dyad frequency, respectively. The distribution for each passage was derived from the data of 2448 transcripts. NFR, nucleosome-free region. f Nucleosome occupancy for genes cynR, arnB, cdaR, and pstS, from passages 2, 6, 10, and 14. For panels (b–f), for the long-term growth experiment, Ec-r-pET29a strains treated with 1 μM IPTG were used as control. Since no mono-nucleosome-protected DNA was recovered from them, no data for Ec-r-pET29a were included. g Heatmaps of the transcriptome (organized in hierarchical clustering) for the nucleosome-forming E. coli from passages 2, 6, 10, and 14 of clone 1, which is a representative result of four different clones. The color scheme represents log2-transformed TPM. The Pearson correlations are greater than 0.97 for clone 1 among different passages (n = 4). Source data are provided as a Source Data file.
