Supplementary Figure 1: Developmentally stable and regulated genes in D. melanogaster.

(a) Time points selected for the analysis of chromatin marking in genes regulated during fly development. From the available modENCODE RNA-seq data, we selected the 12 points for which ChIP-seq experiments on histone modifications were also available. (b) Expression of one stable gene (NUCB1) and one regulated gene (Cy30401). The value of the coefficient of variation for NUCB1 is 0.15. Cy30401, in contrast, shows a peak of expression in one embryonic stage, and its coefficient of variation is consistently 2.49. (c) Distribution of the coefficients of variation on fly genes. We calculated the coefficients of variation of expression for the 12,867 genes for which modENCODE has expression data along Drosophila development. The coefficient of variation distribution uncovers a large class of genes with low coefficients of variation (constant expression during development) and two other minor classes containing genes whose expression is highly variable during development—often restricted to a limited set of stages. For most of the analysis, we arbitrarily considered the top 1,000 genes with the lowest coefficients of variation as stable and, the top 1,000 genes with the highest coefficients of variation as genes regulated throughout development (Supplementary Fig. 4). (d) Time point of maximum expression of regulated genes.