Fig. 5

Coordination between H3.3 and H2A.Z in regulating H3K27me3 deposition in mES cells. a Western blot to analyze the dynamic changes of H2A.Z and H3K27me3 protein level upon knockdown of H3.3 in mES cells. No change was observed on the global levels of H2A.Z or H3K27me3 after H3.3 knocking down in mES cells. b Heat map for the dynamic changes of H3K27me3 and H2A.Z levels upon H3.3 knocking down in mES cells. Cluster analysis was performed for the dynamic changes of both H3K27me3 and H2A.Z levels upon H3.3 knocking down in mES cells. Two different subgroups were highlighted by a red box (type I, top part) and blue box (type II, bottom part). The y-axis coordinates with 4,445 H3K27me3 peaks in mES cells. The zero point of x-axis corresponds with the center of each H3K27me3 peak and expands from 5 kb upstream to 5 kb downstream to form H3K27me3 peak regions. c–d Scatterplots for average reads densities of H3K27me3 at type I (panel c) and type II (panel d) H3K27me3 peak regions (as shown in b) in wild-type mES cells (Ctr. KD) and H3.3 knockdown mES cells (H3.3 KD). e–f Scatterplots for average reads densities of H2A.Z at type I (panel e) and type II (panel f) H3K27me3 peak regions (as shown in b) in wild-type mES cells (Ctr. KD) and H3.3 knockdown mES cells (H3.3 KD). g Schematic procedure of all-trans retinoic acid (tRA) cessation experiment, the transcription of CYP26a1 was agitated by adding tRA and then was gradually ceased after tRA removal. h RT-qPCR analysis of the cessation of CYP26a1 expression during tRA withdrawal. i Schematic view of the CYP26a1 promoter region (+ 1) and gene body region (+ 2 kb). The positions for primers are indicated by arrows. j Dynamics of H2A.Z (upper left), H3.3 (upper right, represented by HA), chromatin structure/compaction (bottom left), and H3K27me3 (bottom right) at the promoter region of CYP26a1 during tRA cessation