Extended Data Fig. 3: Condensability measurements of human embryonic stem cell (H1-hESC) and mouse embryonic stem cell (E14 mESC).
From: Native nucleosomes intrinsically encode genome organization principles
a, Comparison between condensability (blue) and transcription level (red) along all chromosomes of H1-hESC. b, Snapshot of UCSC genome browser for the condensability profile of H1-hESC along with many other cis-regulatory elements. c, All genes were grouped into five quantiles according to the transcription level of H1-hESC (quantile 1 through 5 for increasing transcription). Condensability, methylated CpG density, and H3K36me3 along the transcription unit coordinate averaged for each quantile (left column). Views zoomed around TSS are shown for condensability, H3K4me3 and H3K9ac (right column). d, Native nucleosomes are prepared from mouse embryonic stem cells (E14 mESC) and condensed by spermine titration (the titration curve is the mean value of three replicates and error bar represents the standard deviation). NEB Low Molecular Weight DNA ladder was used for the first lane as marker. e, Genome segmentation into chromatin states based on histone PTM ChIP-seq data (right). All mono-nucleosomes of chromosome 1 were categorized using ChromHMM, and their condensability distribution for each chromatin state is shown (boxplot: the center is median and the lower/upper bound is the 1st/3rd quartile of data). Statistically significant differences between ChromHMM states are noted. The statistics were computed via two-sided Welch’s t-test over more than 400 nucleosomes of each state from two biological replicates. f. Promoter condensability (averaged over 10 kb window around TSS) for E14 mESC and mCD8 T cells. Each gene is colored according to their relative expression levels in the two cell types. Black symbols are for embryonic stem cell marker genes. g, All genes in chromosome 1 were grouped into five quantiles according to the transcription level (quantile 1 through 5 for increasing transcription) and condensability along the transcription unit coordinate averaged for each quantile is shown.
