Extended Data Fig. 8: ChIP–seq analyses of APC/C- and WDR5-occupied gene targets.

a, Overall histone levels do not change upon release from mitosis. H1 cells were synchronized in mitosis by STLC and released into fresh medium. Indicated proteins were monitored by western blotting. This experiment was performed two independent times with similar results. b, Comparison between ChIP–seq and MNase ChIP–seq against anti-K11 from mitotic H1 human ES cells reveals that sonication shears polymeric ubiquitin linkages. c, Venn diagram of anti-K11 and anti-WDR5 ChIP peaks that colocalize with TSSs from MNase ChIP–seq experiments. MNase ChIP–seq experiments were performed from mitotic H1 human ES cells. d, Heat map of MNase ChIP–seq data from mitotic H1 human ES cells. Cluster 1 includes sites that are co-occupied by K11 and WDR5 near TSSs (within 100 bp); cluster 2 includes sites that are co-occupied by K11 and WDR5 outside of TSSs; and cluster 3 includes sites occupied only by K11, regardless of colocalization with TSSs. e, ChIP–qPCR analysis of candidate targets using K11- or K11/K48-linkage specific ubiquitin antibodies from mitotic H1 human ES cells. Mean of independent replicates ± s.d. n = 3 for K11/K48; n = 5 for IGG and K11 (except n = 4 for PUM1). f, ChIP–qPCR analysis of mitotic H1 human ES cells shows that K11 linkages synthesized at candidate sites are dependent on UBE2S and WDR5. This experiment was performed once. g, WDR5 inhibition prevents K11-ubiquitin chain formation at APC/C–WDR5-bound TSSs. H1 human ES cells were treated with or without 50 μM MM102 during mitotic synchronization with STLC before anti-K11 MNase ChIP–seq. Heat map of all APC/C–WDR5-bound TSSs are shown. h, Heat map of ChIP–seq peaks of individual genes co-occupied by Flag–CDC20 and Flag–WDR5. ChIP–seq against anti-Flag was performed on mitotic HEK293T cells that overexpress Flag–CDC20 or Flag–WDR5. i, Spatial profile of PUM1 of factor occupancy by ChIP–qPCR. This experiment was performed once. j, Spatial profile of E2F3 of factor occupancy by ChIP–qPCR. This experiment was performed once. k, Heat map of MNase ChIP–seq data of transcription-factor binding. Previously published MNase ChIP–seq data were obtained⁴⁷, and APC/C-bound sites were analysed as described in d.