Fig. 3

Knockdown of bptf leads to loss of chromatin accessibility at gene promoters in planarian stem cells. A) Schematic of the experimental setup used to assay the chromatin state of planarian stem cells isolated from control(RNAi) and bptf(RNAi) animals. B) A representative locus at which there are multiple ATAC-seq peaks, including one that shows significant loss of accessibility after bptf(RNAi). Gene nkx2.2 = h1SMcG0021724. C) Pie chart summarizing the locations of ATAC-seq peaks across the planarian genome (relative to their nearest gene models) in control(RNAi) stem cells. D) Pie chart summarizing the locations of differentially accessible (DA) peaks in bptf(RNAi) stem cells (compared to control(RNAi) stem cells). E) Histogram summarizing the log2FC of all differentially accessible (DA) ATAC-seq peaks in bptf(RNAi) stem cells (binwidth = 0.1 log2FC). 4652 peaks have decreased accessibility (blue bars), 1411 have increased accessibility (orange bars). F) Profile plot comparing ATAC-seq signal in control(RNAi) and bptf(RNAi) stem cells averaged across all gene models and centered at transcription start site (TSS). Signal is represented as Reads Per Kilobase per Million mapped reads (RPKM). The shaded area represents the standard error. G) Profile plot comparing ATAC-seq signal at distal intergenic peaks (identified in C). The shaded area represents the standard error