The three-dimensional structure of the genome is associated with regulation of gene expression.

A: Each point represents data from all genes within a single TAD; the estimated log2 fold difference in expression between in planta and in culture conditions for these genes within that TAD are plotted (i.e., points above zero represent TADs for which genes are generally more highly expressed in planta). Vertical lines represent uncorrected 95% confidence intervals of this estimate; TADs are coloured by chromosome. TADs with statistically significant effects after applying a false discovery rate of 0.01 are labelled by chromosome and TAD number. Genes contained in these TADs are listed in S5 Table. B: The proportional excess ([observed - expected]/observed) of contacts between members of the 5% of genes with the highest expression in culture. Along the x-axis, these interactions are broken down by the genomic distance between interacting gene pairs. 95% confidence intervals for expected number of contacts (grey shaded area) for each observation were obtained by counting the number of contacts from 1,000 random gene sets. Points falling outside the shaded space represent genomic distances at which highly-expressed genes contact each other more than would be expected by chance. C: As with B, but for the 5% of genes with the lowest expression in culture.