Fig. 1

Accessible chromatin is present in gene promoters and absent from heterochromatin. (A) A genome browser image showing ATAC-seq (blue), H3K27me3 (green) and H3K9me3 (red) localization across Linkage Group VII for the wild-type strain. (B) The metaplot shows enrichment of ATAC-seq experiments averaged across all Neurospora genes. (C) The heatmaps show the enrichment of ATAC reads in a 3000 bp window centered on the transcriptional start site for all genes (left) or genes with unambiguous promoters (right). Genes were grouped using k-means clustering (left; k = 3; right; k = 6) to illustrate the distinct patterns of chromatin accessibility found in Neurospora promoters. (D) Box plots depict the log2-transformed expression levels for genes with unambiguous promoters in the 6 clusters of from panel C (log₂ [TPM + 1]). The expression levels of individual genes in each cluster are plotted as points. (E) A genome browser shot of the cre-1 (carbon catabolite repression) gene illustrates an example gene with a large regulatory domain of accessible chromatin (2520 bp). (F) GO analysis shows enrichment for DNA binding and transcription factor activity of genes with large intergenic hyperaccessible domains