Fig. 1: Condense-seq measures genome-wide single-nucleosome condensability.
From: Native nucleosomes intrinsically encode genome organization principles
a, Schematic of the condense-seq workflow. b, The total amount of NCP or nucleosomal DNA remaining in the supernatant was measured by ultraviolet–visible (UV–VIS) spectrometry. Left; graph of three biological replicates, error bars denote standard deviation, and the statistical significance of the difference between DNA and NCP is shown as a P value, obtained by two-sided Welch’s t-test, marked with an asterisk: 0.0034, 0.06, 0.007 and 0.013, respectively. Right, their integrity was checked by 2% agarose gels; lane 1 is a low-molecular-weight DNA ladder, and other lanes are supernatant nucleosomes or nucleosomal DNA after condensation with various spermine concentrations. c, Genome segmentation into chromatin states based on histone PTM ChIP-seq data (right). All mononucleosomes of chromosome 1 were categorized and their condensability distribution for each chromatin state is shown (boxplot in which the centre is the median and the lower and upper bounds are the first and third quartiles, respectively). The P values were computed using two-sided Welch’s t-test comparing the condensabilities between chromatin states. Cohen’s d metric denotes the effect-size comparison over more than 7,000 nucleosomes for each state from two biological replicates (also shown in Extended Data Fig. 2i). d, RNA-seq data (red) and condensability (blue) over the entire chromosome 1 (Spearman correlation is −0.8 in 100-kb bins); positions are given in Mb. e, All genes were grouped into five quantiles according to the transcription level (quantiles 1–5 (Q1–Q5), in order of increasing transcription). Top, condensability, AT content and H3K27ac level along the transcription unit coordinate averaged for each quantile. Bottom, heat maps show the same quantities for each gene, rank ordered by increasing gene expression. f, Promoter condensability (averaged over a 5-kb window around the TSS) for H1-hESC and GM12878. Each gene is coloured according to its relative expression level in the two cell types. Black symbols indicate embryonic stem cell marker genes. FPKM, fragments per kilobase of transcript per million mapped reads; a.u., arbitrary units. Illustration in a created in BioRender (Park, S. (2025) https://BioRender.com/q73ofz1).
