Extended Data Fig. 8: Cell-to-cell single-base variation is associated with variation in nucleosome positioning and variation in gene expression across different single cells.

a, CC, GG and GC frequency is higher in the nucleosome-occupied region than in the flanking region, whereas AA, TT, AT and TA frequency shows the opposite pattern. b, CC, GG and GC frequency in flanking regions increases as nucleosome variance within a cell (left) or across different single cells (right) increases. c, AA, TT, AT and TA frequency in flanking regions decreases as nucleosome variance within a cell (left) or across different single cells (right) increases. d, Nucleosome variances within a cell and across different single cells are reversely correlated with the percentage of AA, TT, AT and TA in flanking regions. e, Weblogos sequences logos for sequence preferences across MNase cleavage sites are shown for subgroups of nucleosomes with different positioning variance across cells. f, An example showing a CTCF motif with the reference base (green) in some cells and alternative base (red) in other cells. scMNase-seq data show that the reference base is associated with subnucleosome-sized particles, whereas the alternative base is associated with the nucleosome structure. Fragments from DNase-seq and CTCF ChIP-seq datasets within the window are also shown with the bases at single-nucleotide polymorphism location highlighted. Tracks for tag densities of CTCF ChIP-seq, DNase-seq, and nucleosomes and subnucleosome-sized particles from pooled single cells are shown in a zoomed-out window. g, The number of CTCF-motif matches containing alternative or reference bases at the single-nucleotide polymorphism locus occupied by nucleosomes, subnucleosome-sized particles, sequence reads obtained by DNase-seq and by CTCF ChIP-seq. P value was calculated using one-sided Fisher’s exact test. The ratio between alternative and reference bases is also shown (bottom). h, Single-nucleotide polymorphism frequency is correlated with nucleosome variation across different single cells. Variant frequencies at each position relative to nucleosome midpoint for four nucleosome subgroups with different levels of nucleosome variance across cells are shown. i, Single-nucleotide polymorphism frequency within transcription-factor motifs at DHSs for four DHS subgroups, sorted by nucleosome variance around DHS across different single cells (each subgroup has 22,139 DHSs that contains at least one transcription-factor motif match). j, Single-nucleotide polymorphism frequency within transcription-factor motifs at DHSs in promoters for gene subgroups, sorted by expression variation across different single cells (each subgroup has 2,136 genes). P value in i, j is defined as the probability of observing a larger difference than current result between two groups by random. P value calculation is described in Supplementary Methods. SNP, single-nucleotide polymorphism.