Genome‐wide binding‐site analysis of REVOLUTA reveals a link between leaf patterning and light‐mediated growth responses

Abstract

SUMMARYUnlike the situation in animals, the final morphology of the plant body is highly modulated by the environment. During Arabidopsis development, intrinsic factors provide the framework for basic patterning processes. CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) transcription factors are involved in embryo, shoot and root patterning. During vegetative growth HD-ZIPIII proteins control several polarity set-up processes such as in leaves and the vascular system. We have identified several direct target genes of the HD-ZIPIII transcription factor REVOLUTA (REV) using a chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) approach. This analysis revealed that REV acts upstream of auxin biosynthesis and affects directly the expression of several class II HD-ZIP transcription factors that have been shown to act in the shadeavoidance response pathway. We show that, as well as involvement in basic patterning, HD-ZIPIII transcription factors have a critical role in the control of the elongation growth that is induced when plants experience shade. Leaf polarity is established by the opposed actions of HD-ZIPIII and KANADI transcription factors. Finally, our study reveals that the module that consists of HD-ZIPIII/KANADI transcription factors controls shade growth antagonistically and that this antagonism is manifested in the opposed regulation of shared target genes.

Tryptophan-dependent auxin biosynthesis is required for HD-ZIP III-mediated xylem patterning

“…It has been shown that REV is able to stimulate auxin biosynthesis by regulating TAA1 and YUC5 in the shoot (Brandt et al, 2012). Therefore, it is likely that specific feedback mechanisms regulate auxin biosynthesis and HD-ZIP III expression in the root to control vascular patterning.…”

PIFs: Systems Integrators in Plant Development

“…Intriguingly, several transcription factors involved in the regulation of flowering (AP1, SVP, LFY, AG, and SEP3) have also been identified to bind PIFs (Kaufmann et al, 2009(Kaufmann et al, , 2010Moyroud et al, 2011;Tao et al, 2012;Gregis et al, 2013;ÓMaoiléidigh et al, 2013), suggesting a direct link to the reported flowering phenotype of pif mutants (Brock et al, 2010;Nozue et al, 2011;Kumar et al, 2012). Finally, binding by REV and AGL15 (Zheng et al, 2009;Brandt et al, 2012) suggests that some of the PIFs might be involved in leaf patterning or embryogenesis, a possibility that needs to be explored.…”

Regulation of MIR165/166 by class II and class III homeodomain leucine zipper proteins establishes leaf polarity

“…Because additional HD-ZIPIII genes such as PHABU-LOSA (PHB) and PHAVOLUTA (PHV) work redundantly with REV to promote adaxial cell fate (2, 7), we also tested whether HAT3 and ATHB4 interact with these two HD-ZIPIIIs to bind the cis-element by yeast one-hybrid assays. PHV-HAT3 and PHV-ATHB4 combinations also tested positive for DNA binding, although with weaker specificity in comparison with REV-HAT3 and REV-ATHB4 (14). Fold changes relative to ACT2 in response to DEX treatment (+DEX; green and red bars) and in control conditions (0.1% ethanol; −DEX; gray bars) are plotted.…”

“…Hence, loss-of-function mutations in genes promoting adaxial cell identity typically cause an abaxialized phenotype that correlates with the ectopic expression of abaxial genes, whereas loss-of-function mutations in abaxial genes produce an adaxialized phenotype that is accompanied by the expanded expression of adaxial genes. This antagonistic interaction between adaxial and abaxial factors may be mediated by mutually antagonistic regulation (12) or through opposing regulation of common targets (9,(13)(14)(15)(16).…”