Genome-Wide Identification of KANADI1 Target Genes

Abstract

Plant organ development and polarity establishment is mediated by the action of several transcription factors. Among these, the KANADI (KAN) subclade of the GARP protein family plays important roles in polarity-associated processes during embryo, shoot and root patterning. In this study, we have identified a set of potential direct target genes of KAN1 through a combination of chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) and genome-wide transcriptional profiling using tiling arrays. Target genes are over-represented for genes involved in the regulation of organ development as well as in the response to auxin. KAN1 affects directly the expression of several genes previously shown to be important in the establishment of polarity during lateral organ and vascular tissue development. We also show that KAN1 controls through its target genes auxin effects on organ development at different levels: transport and its regulation, and signaling. In addition, KAN1 regulates genes involved in the response to abscisic acid, jasmonic acid, brassinosteroids, ethylene, cytokinins and gibberellins. The role of KAN1 in organ polarity is antagonized by HD-ZIPIII transcription factors, including REVOLUTA (REV). A comparison of their target genes reveals that the REV/KAN1 module acts in organ patterning through opposite regulation of shared targets. Evidence of mutual repression between closely related family members is also shown.

SWP73 Subunits of Arabidopsis SWI/SNF Chromatin Remodeling Complexes Play Distinct Roles in Leaf and Flower Development

“…As KAN1 is a transcription repressor of AS2 and vice versa (Wu et al, 2008), this observation indicated that both abaxial and adaxial repressor activities were probably compromised in the swp73b mutant. Elevated KAN1 levels are known to result in feedback inhibition of KAN2, KAN3, and YAB5, which are involved in abaxial cell fate specification (Merelo et al, 2013;Huang et al, 2014). Accordingly, we found that transcript levels of KAN3, YAB2, YAB3, and YAB5 genes showed 2-to 10-fold reduction in swp73b rosette leaves correlating with their highly adaxialized downward curling phenotype ( Figure 4B).…”

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

“…For ChIP-qPCR, transgenic pML1::GR-LhG4_p6xOp::VENUS-HAT3 and pML1::GR-LhG4_p6xOp::REVr-2xVENUS plants were treated with DEX or 0.1% ethanol (vol/vol) for 4 h as previously described (15). Additional analysis details are described in SI Appendix.…”

“…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).…”

The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity

“…Furthermore, KAN proteins are excluded from the P0, which is defined by high levels of the KAN1-repressed target PIN1, and instead accumulate in a ring below initiating organs (Merelo et al, 2013;Yadav et al, 2014).…”

“…One possibility is that miR166 originates in the KAN-expressing region below the incipient leaf, an idea first posited in maize (Zea mays; Juarez et al, 2004). Indeed, MIR166A is a direct target of KAN1 and is not downregulated by this repressor protein (Merelo et al, 2013). Mobility of mature miR166 from a primordiumindependent source could provide the positional information required to pattern HD-ZIPIII activity until the mechanisms within the primordium itself resolve to maintain adaxial-abaxial polarity.…”