Extended Data Fig. 9: The regulatory models of Rpd3S complex.

a. A representative HDAC assay measuring the activity of Rpd3S complex in sufficient time, where only H3K9ac can be retained over time. b. A “seeding mark” model of “Rpd3S-NuA3/NuA4” enzymatic pairs in balancing chromatin acetylation levels during transcription. The complexes are shown in a cartoon model. The Rpd3S complex recognizes H3K36me3 and removes most N-terminal acetylation marks of H3 and H4, except for H3K9ac. The Rpd3S-resistent H3K9ac, along with H3K36me3, may serve as “seeding marks” that can recruit NuA3 and NuA4 for the reestablishment of hyperacetylated histones H3 and H4, respectively. c. The H3K56ac modification is not directly affected by the Rpd3S complex in vivo. Western blot shows H3 acetylation levels at different sites in Rpd3S wild-type and Rco1-deleted strains. The alterations observed in H3K9ac and H3K56ac are not significant in comparison to other H3 sites in Rco1-deleted strains. The black vertical lines in the figure indicate that the rearranged lanes are from non-adjacent lanes within the same gels. The catalytic models of Rpd3S with di-nucleosome (d–f). d. The two CHD domains of Eaf3-A and Eaf3-B with PHD1 of Rco1-A are involved in recognizing one nucleosome, and PHD1 of Rco1-B is involved in recognizing another nucleosome. e and f. Two Rpd3S can bind to two nucleosomes, respectively, at a suitable 40bp linker DNA length. The latter Rpd3S complexes may be assembled on two nucleosome discs respectively. One representative example of three (a,c) independent experiments is shown.