Correlation of transcriptional kinetics with histone modifications in mouse ES cells. (A)-(C) Box plots that compare burst size (A), burst frequency (B), and the average fraction of time that a gene spends in the inactive state (C) in the four groups. Given the annotated chromatin state of the two histone modifications by , we classified all expressed genes with a normalized read count greater than 50 in at least one cell that have chromatin state annotations into four groups: H3K4me3 only (n = 6,291), H3K27me3 only (n = 10), H3K4me3 + H3K27me3 (n = 630) and none (n = 492). The H3K4me3 group is significantly different from the others except the H3K27me3 group: P < 10-16 for si/kon,i, P < 10-16 for kon,i, P < 10-16 for koff,i/(koff,i + kon,i), by the Mann-Whitney U-test. Due to the small number of samples of the H3K27me3 group, the H3K4me3 group is less significantly different from the H3K27me3 group: P = 0.0486 for si/kon,i, P = 2.73 × 10-5 for kon,i, P = 8.12 × 10-5 for koff,i/(koff,i + kon,i). In each box plot, the central red line indicates the median value, the top and bottom edges of the box are the 75th (q3) and 25th (q1) percentiles, and the ends of the whiskers denote q3 + 1.5(q3 - q1) and q1 - 1.5(q3 q1). (D)-(L) The profiles of H3K4me3, H3K27me3, and H3K36me3 ChIP-seq reads mapped near TSSs (Transcription Start Sites) are shown for genes with values of the three kinetic quantities in the top 10% (red), middle 10% (green), and bottom 10% (blue) of the relevant distribution. The y-axis is the total number of reads mapped to each position.
Kim and Marioni Genome Biology 2013 14:R7 doi:10.1186/gb-2013-14-1-r7