Fig. 6

Histone modifications associated with potato genes. a H3K27me3 for active genes in RT tubers. b H3K27me3 for active genes in cold tubers. c The ratio of H3K27me3 signal intensity between cold vs. RT tubers. d H3K4me3 for active genes in RT tubers. e H3K4me3 for active genes in cold tubers. f The ratio of H3K4me3 signal intensity between cold vs. RT tubers. The same set of active genes (n = 19,482) and constitutively silenced genes (n = 12,532) were used in all analyses. Each active gene showed transcription (FPKM > 1) in both RT and cold tubers. Constitutively silenced genes did not show transcription in either RT or cold tubers (FPKM = 0). “Random intergenic regions” were randomly selected from regions that were at least 2 kb away from any annotated genes. The length and number of the random intergenic regions were the same as constitutively silenced genes. Genes were divided into 100 bins and aligned together from TSSs to TTSs. Genes flanking regions (± 1 kb) were analyzed in 100 bins. Histone modification signal was measured by quantifying the mid-point of pair-end ChIP-seq reads within each bin and normalizing by ChIP-seq read number per bp genome region per million mapped reads