Fig. 3

Links between differentially modified enhancers and gene regulation events. a ChromHMM modeling of H3K27ac (top), H3K4me1 (middle), and co-marked regions (bottom) in GSCs and NSCs, and their co-localization with genomic features as labeled at the lower right. State numbers are assigned at the far left. Abbreviations are used to describe cell identities. G GSC, N NSC. Enrichment level increases as color migrates from white to dark red. b Line plot showing the number of co-marked peaks gained, lost, or shared by different numbers of GSCs. Embedded stacked bar graph shows both gained and lost peaks for each GSC (labeled at top of each bar) compared to NSC. Y-axis denotes the number of peaks. Blue: gain; red: loss. c Genomic distribution of H3K4me1 and H3K27ac co-marked regions commonly gained (top) and lost (bottom) in different numbers of GSCs (labeled to the left of each bar) relative to NSCs. Genome features are color-coded in the legend bar. Bars are arranged in order of their conservation. X-axis shows the accumulated percent genomic occupancy of each feature. d Ontology illustrating biological processes associated with genes within 50 kb of gained (top, pink bars) and lost (bottom, blue bars) co-marked regions in GSC. X-axis denotes log10-transformed binomial P value. e Tag-density plots showing the transcript abundance of five gene clusters in a 100-kb window centered on regions gaining (top) and losing (bottom) co-marked regions in GSCs. Gene clusters were generated automatically by deepTools2 based on the enrichment pattern. f Browser view of H3K27ac peaks (top five tracks) and RNA-seq reads (bottom five tracks) at the HOXC locus. Scale bar: 100 kb