Fig. 3: In vivo nucleosome assembly with varying histone expression levels in E. coli.

a A schematic of experimental design for titration of in vivo nucleosome assembly in E. coli by varying Xenopus histones expression levels through inducing with different IPTG concentrations for ~ 1 h. b SDS-PAGE analysis for expression of Xenopus histones, induced by IPTG at different concentrations for ~ 1 h. c ecMNase assay for titration of nucleosome formation at different IPTG concentrations, for which prolonged MNase digestion conditions were used. M, DNA standards. d Quantification of histones expression levels represented by tag-H2A (b) and mono-nucleosome DNA fragments (c) in E. coli at different IPTG concentrations. Data are normalized with the maximum value as 100%, and represent mean ± SEM of three independent experiments (n = 3) for H2A protein, and four independent experiments (n = 4) for mono-nucleosomal DNA. e Genome-wide coverage of nucleosome-protected fragments along the E. coli genome in IPTG-titration experiments. Peak height represents the coverage depth of nucleosome-protected fragments. Values in brackets represent the range of the Y-axis. The identity of each sample is listed to the right. f (left) Violin plots with boxplots showing the peak density variation in Ec-r-pXen cells at different IPTG concentrations, and (right) correlation matrix of peak density distribution between paired IPTG concentrations. Peaks were called for each IPTG concentration using reads randomly drawn from two biological replicates (n = 2) (Methods). The violin plots show the summary statistics (the median, first and third quartiles, 1.5× interquartile range) and kernel distribution of peak density (n = 912). g Density plot for nucleosome peaks relative to those of 1 μM IPTG treated cells. Nucleosome peaks from Ec-r-pXen cells treated with 10, 25, 50, 75, 100, 200, and 400 μM of IPTG are aligned to the center of closest peaks from cells treated with 1 μM of IPTG. For panels (e–g), because no sufficient mono-nucleosome protected DNA from 0 μM IPTG treatment was recovered for MNase-sequencing under the same conditions, no 0 μM IPTG treatment data from Ec-r-pXen were presented. Source data are provided as a Source Data file.