Extended Data Fig. 7: Different HP1 isoforms can functionally substitute each other.

a, Scatterplots comparing mRNA expression changes after deletion of Adnp versus single, double or triple deletions of Cbx genes measured by RNA-seq. Green trend lines indicate a loess (locally weighted scatterplot smoothing) regression. n = 3 biological replicates (that is, three independent Adnp^−/−, Cbx1^−/−, Cbx3^−/−, Cbx5^−/−, Cbx1^−/−Cbx3^−/− double knockout, or Cbx1^−/−Cbx3^−/−Cbx5^−/− triple knockout mouse ES cell lines). b, MA plot displaying fold changes in gene expression for individual Cbx knockout cell lines versus wild type. x axis denotes the mean mRNA abundance, log₂(counts per million); y axis denotes the log₂(fold change) between knockout and wild type. Dashed red lines indicate fourfold up- or downregulation. c, UCSC genome browser shots of three lineage-specifying genes. RNA-seq profiles normalized by library size of representative wild-type and mutant ES cell lines are shown. Experiments were performed three times. d, Gene Ontology enrichment analysis of the genes that are upregulated in Cbx1^−/−Cbx3^−/−Cbx5^−/− triple-knockout (TKO) and Adnp^−/− knockout (KO) cells (orange group of genes in a), and of the genes that are upregulated in Cbx1^−/−Cbx3^−/−Cbx5^−/− triple-knockout but not Adnp^−/− knockout cells (grey group of genes in a). See also Supplementary Table 5. n = 3 independent cell lines. e, RNA-seq library statistics showing fraction of uniquely, multi- and non-mapping reads. Note the increase in multi-mappers in the HP1 triple-knockout cells. f, Quantification of reads mapping to the major repeat classes in counts per million mappable reads. g, Quantification of reads mapping to the different LINE and LTR elements in counts per million mappable reads. All mutant cell lines were derived from the same parental mouse ES cell line through direct genome editing and are therefore isogenic.