Fig. 2: Profiling of the chromatin regulatory landscape in Schmidtea mediterranea using ATAC-seq and ChIP-seq.

a Schematic illustration of the ATAC-seq library generation workflow. b Representative fragment size distribution, with peaks at 100 and 200 bp reflecting nucleosome-free and mononucleosome-bound fragments. c Representative TSS enrichment analysis, revealing the expected enrichment of nucleosome-free region fragments (NFR, black) at the transcription start sites (TSS), flanked by enrichments of mononucleosomal fragments (mono, red). d Genome-wide peak size distribution of the 55,585 ATAC-seq peaks used in the subsequent analysis. e Schematic illustration of the ChIP-seq library generation workflow. f Genome-wide average TSS-centered coverage profiles and heatmaps of H3K27ac and H3K4me3 ChIP-seq read distributions, stratified by gene expression level quartiles. g Genome-wide peak size distribution of the 18,361 H3K4me3 and 38,923 H3K27ac ChIP-seq peaks. h Bar graph representation of the total number of H3K27ac, H3K4me3, and ATAC-seq peaks. i ATAC-seq peak categorization into putative promoters, putative enhancers, and uncharacterized peaks on basis of intersection with the two histone marks. j Averaged profiles of the H3K4me3 and H3K27ac ChIP-seq signal centered on the three predominant peak categories defined in h. k Stacked bar plots showing the distribution of the putative promoters, enhancers, and uncharacterized ATAC-seq peaks in relation to the high-confidence gene annotations. l Genome browser snapshot of the sp5 gene locus, showing the exon/intron representation of sp5 (blue, bottom right), a H3K4me3^+/ H3K27ac⁺ promoter overlapping with the TSS and a H3K4me3^-/ H3K27ac⁺ putative enhancer (red bar, asterisk) further upstream. m Close-up of the putative enhancer in l. Boxplots in b and d show the interquartile range (IQR), with whiskers extending to 1.5 times the IQR. Source data are provided as a Source Data file.