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. Author manuscript; available in PMC: 2022 Nov 8.
Published in final edited form as: Dev Cell. 2021 Nov 8;56(21):2995–3005.e4. doi: 10.1016/j.devcel.2021.10.010

Figure 4. Polycomb-based repression is critical to maintain the imprinted X chromosome.

Figure 4

(A) Pie chart showing the proportion of regulator dependent or independent genes for imprinted XCI. A gene was called “regulator dependent” if the allelic ratio changes between WT and KO by ≥ 20% for any regulator. UpSet plot shows the intersection between the four disrupted regulator members: ΔDnmt1, ΔG9a-GLP, ΔRnf2, and ΔEed. The inset Venn diagram highlights the high overlap between ΔEed and ΔRnf2 dependent X-linked genes. Genes that escape imprinted XCI were excluded from this analysis.

(B) Regulator-independent X-linked genes are organized into distinct spatial clusters. Allelic ratios of maternally expressed X-linked genes and the corresponding changes between wildtype (BDF1xCAST) and regulator disrupted ExE lineages are shown (X-linked gene matrix ranked by the genomic position). Regulator-independent X-linked genes are indicated. A gene was called “regulator independent” if the allelic ratio changes between WT and KO is < 20% for every regulator.

(C) Regulator independent regions occur in domains with high Xist enrichment and repressive chromatin. 1Mb windows summarizing (average) paternal X expression changes between WT and PRC, for Xist enrichment over input (RAP) (Engreitz et al., 2013) and for H3K27me3 and H2AK119ub enrichment on the inactive X (Żylicz et al., 2019) across the entire X-chromosome.