Figure 1
Dynamics of nucleosome organization during somatic cell reprogramming.
(A) Genome-wide comparison of nucleosome occupancy for pre-iPSCs vs. MEFs. Colours indicate the change in nucleosome occupancy in each 10 kb region between two samples. Red indicates a ≥ 1.5-fold nucleosome occupancy increase in pre-iPSCs, green indicates a ≥1.5-fold nucleosome occupancy decrease in pre-iPSCs, grey indicates no nucleosomes detected and yellow indicates regions with a <1.5-fold change in nucleosome occupancy. (B) Genome-wide comparison of nucleosome occupancy between iPSCs vs. pre-iPSCs as in (A). Red indicates a ≥1.5-fold nucleosome occupancy increase in pre-iPSCs, green indicates a ≥1.5-fold nucleosome occupancy decrease in pre-iPSCs, grey indicates no nucleosomes detected and yellow indicates regions with a <1.5-fold change in nucleosome occupancy. (C) Boxplot showing nucleosome coverage rates for both genic and intergenic regions among MEF, pre-iPSCs and iPSCs (***p < 2.2 × 10−16). (D) Violin-plot showing pair-wise comparison of nucleosome fuzziness among MEF, pre-iPSCs and iPSCs. At left: nucleosome fuzziness distribution for common nucleosomes in pre-iPSCs and MEFs. At right: distribution of common nucleosomes in pre-iPSCs and iPSCs. Nucleosome fuzziness was calculated as the standard deviation of tag locations around the nucleosome dyad. Common nucleosomes between pre-iPSCs/MEFs or iPSCs/pre-iPSCs are defined as those when the distance between two nucleosome dyad locations is less than 73 bp (approximately half the size of nucleosome). Two-tailed and paired t-test was used to evaluate whether the observed difference between two samples was significant.
