Fig. 4

H3K4me3 marks at bidirectional genes mirror transcriptional status of gene pair. Cumulative enrichment of H3K4me3 at all bidirectional gene pairs separated by 1 nucleosome distance is shown. The gene pairs are classified into symmetrically or asymmetrically expressed gene pairs based on transcript abundances of each gene in the pair relative to its partner as described in ‘Methods’. Cumulative expression is calculated by summation of fold enrichment signal at every location in a 4 Kb window for each category and dividing by the highest value of signal in the respective category as described in ‘Methods’. ChIP-seq data from two different cell lines was analyzed, namely CD4⁺ T cells (a, n = 117; b, n = 319) and H1 human embryonic stem cells (c, n = 189; d, n = 264). Unidirectional genes are used as a control where the number of unidirectional genes is equal to the number of bidirectional gene pairs plotted. The expression range of uni-directional genes chosen is identical to the bidirectional dataset. (e, n = 500) Cumulative enrichment of H3K4me3 on unidirectional genes in CD4⁺ T cells. (f, n = 500) Cumulative enrichment of H3K4me3 on unidirectional genes in H1 ES cells. The genes transcribed on the plus and minus strands are denoted by the blue and brown colored lines respectively for the asymmetrically expressed genes. For the symmetrically expressed genes, genes that are silent are represented as the black line whereas the genes expressed from both strands are depicted with the red line. For unidirectional genes, the black and red lines represent the genes transcribed from the plus and minus strand respectively