Fig. 4.

Comprehensive genome organization of Neurospora crassa derived from the DpnII and MseI double digest contact matrices. a) Heatmap displaying the raw (above diagonal) and Knight-Ruiz (KR) corrected read counts (below diagonal) of genomic interactions 10 kb bin resolution of the DpnII and MseI double digest in situ Hi-C dataset, which contained 76.5M valid reads. CenH3, H3K9me3, and H3K27me2/3 ChIP-seq enrichment tracks, as well as a gene track, presented above and to the left of the heatmap. b) Heatmap of the calculated observed vs expected signal of KR-corrected read count (above diagonal) and the KR-corrected read counts of the DpnII and MseI double digest in situ Hi-C dataset (below diagonal) at 10 kb resolution. Centromeric region highlighted in C is marked by a diagonal line. c) Heatmap of the calculated observed vs expected signal of the KR-corrected read counts across the centromere at 5 kb resolution. d) Triangle heatmaps of KR-corrected read count (top) and the plot of the calculated observed vs expected signal of KR-corrected read count at 5 kb bin resolution of the right arm of LG II, as in Fig. 3c, e, f) Heatmaps displaying the log₂ ratio of in situ Hi-C contacts at 10 kb resolution comparing the 76.5M valid reads of the double digest to a merged fastq file that combines fastq files containing 64.5M valid DpnII reads with 12.0M valid MseI reads (76.5M valid reads overall), processed as a single matrix. The change in raw read counts (above diagonal) or KR-corrected counts (below diagonal), across (e) LG II or (f), the centromere of LG II is displayed. CenH3, H3K9me3, and H3K27me2/3 ChIP-seq enrichment, as well as gene tracks presented with each heatmap.