The different domains were identified in 293 T-REx cells at all time points with hiddenDomains v3.0 (52), with the command “hiddenDomains -g $chromInfo_file -b $bin_size -t $expBam -c $inputbam -o $outputFilePrefix.” A window size of 50 or 100 kb was used (Figs. 2 and 3 and fig. S3 for example). To more precisely identify overlap between ChIPs within these domains, peaks were detected within the domain as noted in the main text and figure legends. Briefly, peaks were detected using SeqMonk v1.41 (www.bioinformatics.babraham.ac.uk/projects/seqmonk/), merging biological replicates using a 1 × 10−5 cutoff, filtered to identify only peaks contained within the domains, and transformed to the heatmap representation noted below (Figs. 2 and 3).

To retrieve the common K27me3 peaks by overlap in DIPG cells (Fig. 5), MACS2 v2.1.0 was used (macs2 callpeak -t $bam_file_vector -c $input_file_vector -n $experiment_name --outdir $output_folder_nomodel_broad -f $format -g $genome_size -s $tag_size --nomodel --extsize $elongation_size --keep-dup $artefact_threshold --broad --broad-cutoff 1 × 10−5).

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