*2.1. Sets of Retrograde Controlled Genes Used in This Study*

Primary expression data sets for genes being controlled by retrograde signals identified under influence of NF and LIN treatments were taken from previously published studies [26,27]. Data sets for retrograde controlled genes in the *pap7-1* mutant as well as for light-controlled genes in wild-type plants were taken from our own data sets [25]. The study on LIN effects was performed as a kinetic experiment with samples taken 0.5, 1, 4 and 24 h after a light intensity shift. In pre-selection comparisons we observed that the number of overlapping genes between the *pap7-1* and LIN data sets increased with time. The 24 h LIN data set, therefore, was used as base for further meta-analysis. Only genes that exhibited a significant relative expression change (repression or induction) in response to plastid dysfunction of at least log2 ≥ 1 and a *p*-value ≤ 0.05 in all data sets were included in our comparisons.
