Figure 4
Dynamics of H3K4 and H3K27 histone trimethylation at HCG and LCG promoters during reprogramming.
(A) Average nucleosome occupancy pattern around HCG and LCG promoters in MEFs, pre-iPSCs and iPSCs. (B) Most HCG promoters are marked by H3K4me3 (blue), while most LCG promoters exhibit neither mark (grey) in all three cell types. (C) H3K4me3 and H3K27me3 status at HCG promoters in pre-iPSCs and iPSCs are dependent on their status in MEFs (indicated at the bottom). The detailed proportion for each state in pre-iPSCs and iPSCs is indicated for the “K4K27” and “K27” states in MEFs. The transition from MEFs to pre-iPSCs and to iPSCs is shaded. HCG promoters marked by H3K4me3 only in MEFs tend to retain this mark, while promoters marked by neither mark tend to retain their original state. Promoters marked by H3K4me3 and H3K27me3 tend to lose one or both marks, while promoters marked by only H3K27me3 tend to convert to one of the other three states. (D) Expression levels of HCG genes marked by both H3K4me3 and H3K27me3 (left) or by H3K27me3 alone (right) change with the chromatin state during reprogramming. from MEFs to pre-iPSCs. Statistical significance, two-tailed t-test. From K4K27 to other states (left panel), *p = 0.011 (to K27), ***p < 2.2 × 10−16 (to K4), *p = 0.014 (to None). From K27 to other states (right panel), ***p < 2.2 × 10−16 (to K4), *p = 0.0098 (to None).
