Transcriptome analysis of gene expression divergence in BBX11 mutation in red light

phytochrome B (phyB) acts as the red light photoreceptor and negatively regulates the growth-promoting factor PHYTOCHROME INTERACTING 4 (PIF4) through a direct physical interaction, which in turn changes the expression of a large number of genes. phyB-PIF4 module regulates a variety of biological and developmental processes in plants. In this study, we demonstrate that B-BOX PROTEIN 11 (BBX11) physically interacts with both phyB and PIF4. BBX11 negatively regulates PIF4 accumulation as well as its biochemical activity, consequently leading to the repression of PIF4-controlled genes' expression and promotion of photomorphogenesis in the prolonged red light. This study reveals a regulatory mechanism that mediates red light signal transduction and sheds a light on phyB-PIF4 module in promoting red light-dependent photomorphognenesis. Overall design: Col-0, bbx11-1 and pif4-2 mutant seedlings were grown in constant red (94 µmol/m2/s) light for 4 d. The samples were harvested and used to isolate total RNA with an RNeasy Plant Mini Kit (Qiagen).