1. Volume 8, Issue 8, Pages 1237-1252 (August 2015)
Identification of Early Nuclear Target Genes of Plastidial Redox Signals that Trigger the Long-Term Response of Arabidopsis to Light Quality Shifts 
Lars Dietzel, Christine Gläßer, Monique Liebers, Stefan Hiekel, Florence Courtois, Olaf Czarnecki, Hagen Schlicke, Yan Zubo, Thomas Börner, Klaus Mayer, Bernhard Grimm, Thomas Pfannschmidt 
Molecular Plant 
Volume 8, Issue 8, Pages (August 2015)
DOI: /j.molp
Copyright © 2015 The Author Terms and Conditions

2. Figure 1
Long-Term Response of Photosynthetic Acclimation in Mutants with Defects in ROS-Mediated and Plastidial Signaling Pathways.
For LTR measurements plants were grown under different light quality regimes as described (Wagner et al., 2008) and photosynthetic acclimation was monitored by determination of the Chl fluorescence parameter Fs/Fm (A) and Chl a/b ratios (B). All data represent means of at least three independent measurements with 12–15 individuals each (n ≥ 3) ± SD. All values of plants grown under permanent light conditions (PSI, PSII) were found to be significantly different from the corresponding light-shift variants (PSI-II, PSII-I) (t-test for independent samples, P ≤ 0.05). The Fs/Fm values between the different experiments were normalized by setting the value of the WT control grown under permanent PSI light to WL, white light.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

3. Figure 2 Strategy for Identification of Early Redox-Regulated Genes.
(A) Plants acclimated to PSI light (oxidized PQ) were shifted for 30 or 60 min, respectively, from PSI light to PSII light, which results in an immediate reduction (signal) of PQ inducing the LTR. The stn7 mutant does not respond to the PQ redox signal and the LTR is blocked. LHCII phosphorylation kinetics as a measure of STN7 kinase activity in WT was determined at the start of the experiment (0 min) and at 30 min, 60 min, and 48 h after setting the PQ reduction signal (top panel).
(B) Overview of gene expression changes on full-genome scale. Numbers given in the yellow circles are significantly regulated genes with a minimum of log2-fold change = 0.5. Numbers in red circles indicate genes that did not change significantly. The red number in the middle gives the real redox-regulated genes. Here, genes that responded in the same direction in the stn7 mutant were subtracted.
(C) Hierarchical clustering visualizes the relatedness of expression profiles between WT and stn7 mutant after shift to PSII light (cladogram left). The intersection of all significantly regulated genes between WT and stn7 mutant is shown. The color code gives the relative change in gene expression with respect to PSI light as the fold change on a log2 scale (red, up-regulation; blue, down-regulation).
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

4. Figure 3
Classification of Redox-Responsive Genes into Functional Groups.
(A) Categorization of early responsive genes. Genes were classified into functional groups using the MapMan annotation. Only genes that were significantly regulated 30 min after the PSI-light to PSII-light shift by at least a fold change of log2 = 0.5 in WT are shown. ∗ Genes influenced by the redox signal.
(B) Comparison of the early response in specific metabolic pathways between WT and the stn7 mutant. Genes that were significantly regulated in WT 30 min after the PSI-light to PSII-light shift are displayed in the functional groups of mitochondrial electron transport, tetrapyrrole metabolism, photosynthesis, and lipid metabolism (left panel). The response of the same set of genes is shown for the stn7 mutant (right panel). Note that in the stn7 mutant, some genes do not respond to the reduction signal, hence they appear as not significantly regulated (white boxes). Up-regulated genes are depicted in blue boxes, down-regulated genes in red boxes using a color code on a fold change scale in log2 as indicated. DGDG, Digalactosyldiacylglycerol synthesis.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

5. Figure 4 Mitochondrial Gene Expression.
(A) The mean expression changes in the array of all annotated chondrome-encoded genes were calculated. Blue, fold change in a log2 scale in WT; red, fold change in a log2 scale in the stn7 mutant.
(B) Regulation of the mitochondrial transcription rate after reduction of the photosynthetic electron transporter plastoquinone by the site-specific inhibitor DBMIB. The transcriptional rate of 29 representative mitochondrion-encoded genes was determined by organellar run-on transcription experiments. The diagram represents the means of the mitochondrial transcription rate of DBMIB treatment versus mock control on log2 scale ± SD from two independent biological replicates.
(C) Same experiment as in (B) with DCMU, which induces a PQ oxidation signal.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

6. Figure 5
Comparison of Early Responses in Groups of Transcription Factors between WT and stn7 Mutant.
(A) Log2 expression changes with respect to the 0 min time point are depicted in the heatmap with blue for up-regulation and red for down-regulation. Every box in the left panel represents a significant expression change of a single gene in WT.
(B) Promoters of significantly regulated genes 30 min after the reduction signal were investigated using a discrete FIRE analysis. The unique gene element CATG, over-represented in 30 min after setting a reduction signal, is displayed. For all gene clusters containing the element, see Supplemental File 8. The fold over-representation with respect to random values is given in yellow, the fold under-representation is given in blue.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

7. Figure 6
Expression Changes of Factors Involved in Chromatin Activity and Chromosome Location of Co-regulated Neighboring Genes (Regulatory Chromosomal Hot Spots).
(A) Early responding factors related to chromatin remodeling that were significantly regulated in WT are displayed at log2-fold change (left panel). The respective expression values in the stn7 mutant are given in the right panel. Blue, up-regulation; red, down-regulation.
(B) Comparison of regulatory chromosomal hot spots between WT and the stn7 mutant 30 min after induction of the reduction signal. Neighboring genes that were significantly regulated were considered as regulatory hot spots and mapped to their corresponding chromosomal location. In WT, hot spots are depicted as blue lines on light gray chromosomes; in the stn7 mutant, hot spots are depicted as cyan-blue lines on dark gray chromosomes.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions