Figure 4

Changes in genes involved in retrograde signaling under extended darkness. (a) DNase-seq and RNA-seq tracks indicate a gene model for GLK1 in the UCSC genome browser. The gene models are shown in purple, with the direction marked by an arrow. The brown and yellow colors represent DHS signals under extended darkness and control condition, respectively. The dark red and light red colors represent that expression signals under extended darkness and control condition, respectively. (b) Expression changes in GLK1-induced genes under extended darkness. (c) DHS changes in GLK1-induced genes under extended darkness. (d) Venn diagram showing down-regulated genes by RS and 519 down-regulated and DHS-diminished genes under extended darkness. The P-value for the overlap in these 519 genes (hypergeometric distribution) is shown at the top. (e) Subcellular location of 519 DHS-diminished and down-regulated genes. The P-value for chloroplast in these 519 genes (hypergeometric distribution) is shown to the left. (f) Venn diagram showing down-regulated genes by RS and up- or down-regulated under extended darkness. (g) A model for darkness-influenced retrograde signaling. Darkness can repress some genes in chloroplasts in term of expression or diminished DHS, which regulate GLK1 binding to conserved motifs in the promoters of PhANGs to promote gene expression by retrograde signaling.