Properties of differentially activated ORIs during vegetative development. (A) Distribution into chromatin states of ORIs stronger in 4-d-old seedlings (left) or in 10-d-old seedlings (right), as a function of the number of ORIs obtained by varying the threshold. To simplify the analysis, ORIs have been grouped into those associated with genes (states 2, 1, 3, 7, and 6), with Polycomb chromatin (states 4 and 5), and with heterochromatin (states 8 and 9). Dotted lines represent the average values for the entire genome. (B) Weighted average of several genomic and epigenomic properties for the set of all ORIs and the ORIs preferred at 4- or 10-d-old seedlings, as indicated. For the set of all ORIs, we have used as weight the NSS of the two developmental stages. For the sets of differentially expressed ORIs, we have only used the stronger weight. Measurements were transformed to Z-score with respect to the whole genome, which produces positive values when they are higher than a generic genomic region. (C) Weighted average of the scores NSSmax (upper) and NSSlen (lower) measured at 10 d (dark blue) and 4 d (light blue) for the set of all ORIs weighted with the NSS of the two developmental stages and the set of differentially expressed ORIs weighted with the stronger NSS. Note that although ORIs stronger at 10 d have weak NSS score both at 4 and 10 d, ORIs stronger at 4 d have a score weak at 10 d but strong at 4 d. (D) Distribution into chromatin states at the reference threshold t = 0.9 of ORIs preferentially used at two developmental stages defined as in A colocalizing with different chromatin states in 4-d-old (empty bars) and 10-d-old seedlings (solid bars).
