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. Author manuscript; available in PMC: 2022 Nov 30.
Published in final edited form as: Nat Cell Biol. 2022 Feb 24;24(3):384–399. doi: 10.1038/s41556-022-00850-x

Extended Data Fig. 1|. In MLL-rearranged (MLL-r) acute leukemia, EZH2 exhibits the noncanonical ‘solo’-binding pattern at sites enriched for the gene-activation-related histone marks and co-binding of RNA polymerase II (POL2), (co)activators and cMyc, in addition to its canonical EZH2:PRC2 sites showing H3K27me3 co-binding.

Extended Data Fig. 1|

(a-b) Heatmaps showing the K-means clustered EZH2 and H3K27me3 ChIP-seq signal intensities ± 3 kb around peak centers in MV4;11 (a) and EOL-1 (b) cells. EZH2-’solo’ and EZH2-’ensemble’ refer to noncanonical EZH2+/H3K27me3- peaks (cluster 9 in MV4;11 and cluster 8 in EOL-1 cells) and canonical EZH2+/H3K27me3+ ones (clusters 1–8 in MV4;11 and clusters 1–7 in EOL-1 cells), respectively.

(c) Averaged EZH2 and H3K27me3 ChIP-seq signals around ± 3 kb from the centers of the EZH2-’solo’-binding peaks in MV4;11 (top) and EOL-1 (bottom) cells.

(d) Venn diagram showing the overlap between the called EZH2 and H3K27me3 peaks in MV4;11 (top) and EOL-1 (bottom) cells.

(e) Motif search analysis of the EZH2-’solo’-binding peaks in MV4;11 cells by using the SeqPos tool in Cistrome.

(f) Co-immunoprecipitation (co-IP) using anti-HA antibodies for assaying interaction between Flag-EZH2 and HA-p300 in 293T cells.

(g) Co-IP for endogenous EZH2 and MAX using anti-cMyc antibody in EOL-1 or MOLM-13 cells after the treatment of benzonase and ethidium bromide.

(h) Co-IP for interaction between endogenous cMyc and EZH2 in 293T cells by using either anti-cMyc (upper) or anti-EZH2 (bottom) antibodies.

(i) Co-IP using anti-HA antibodies for interaction between endogenous EZH2 and the transiently expressed HA-cMyc in 293T cells.

(j) Co-IP using anti-cMyc antibodies for interaction between the transiently expressed Flag-EZH2 and endogenous cMyc in 293T cells.

(k) Pearson correlation analysis of cMyc ChIP-seq profiles generated by using two independent anti-cMyc antibodies in MV4;11 and EOL-1 cells.

(l) Pie-chart plot showing the genomic distribution of peaks with both EZH2-’solo’-binding and cMyc-binding in MV4;11 (top) or EOL-1 (bottom) cells.

(m) Heatmaps of EZH2, SUZ12, H3K27me3 and cMyc ChIP-seq signal intensities ± 5 kb from the centers of the called EZH2 peaks in the GM12878 lymphoblast cells (left), human umbilical vein endothelial cells (HUVEC; middle) and K562 chronic myeloid leukemia (CML) cells (right).