An integrated analysis of cell-type specific gene expression reveals genes regulated by REVOLUTA and KANADI1 in the Arabidopsis shoot apical meristem

Abstract

In the Arabidopsis thaliana shoot apical meristem (SAM) the expression domains of Class III Homeodomain Leucine Zipper (HD-ZIPIII) and KANADI (KAN) genes are separated by a narrow boundary region from which new organs are initiated. Disruption of this boundary through either loss of function or ectopic expression of HD-ZIPIII and KAN causes ectopic or suppression of organ formation respectively, raising the question of how these transcription factors regulate organogenesis at a molecular level. In this study we develop a multi-channel FACS/RNA-seq approach to characterize global patterns of gene expression across the HD-ZIPIII-KAN1 SAM boundary. We then combine FACS, RNA-seq and perturbations of HD-ZIPIII and KAN expression to identify genes that are both responsive to REV and KAN1 and normally expressed in patterns that correlate with REV and KAN1. Our data reveal that a significant number of genes responsive to REV are regulated in opposite ways depending on time after induction, with genes associated with auxin response and synthesis upregulated initially, but later repressed. We also characterize the cell type specific expression patterns of auxin responsive genes and identify a set of genes involved in organogenesis repressed by both REV and KAN1.

Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf

“…We also found that we have potentially obtained epidermal cells from each side of the leaf. Because expression of such polarity genes is highest in leaf primordia (Ram et al, 2020), we lose the ability to more confidently assign location in maturing leaf cells. Nonetheless, we found a substantial number of guard cells expressing adaxial or abaxial signatures (Table S6), which may provide insight into physiological processes prioritized by stomata originating from these different surfaces of the leaf (Mott, 2007).…”

Integration of Core Mechanisms Underlying Plant Aerial Architecture

“…Similar to the situation in leaves, in the shoot WOX4 and PRS are expressed roughly, where REV and KAN1 expression is low ( Caggiano et al, 2017 ; Yu et al, 2017 ; Eeda and Werr, 2020 ) and PRS function has been shown to be required for leaf formation in conjunction with auxin transport ( Nakata et al, 2018 ). In the shoot, REV and KAN1 repress PRS expression indirectly and directly, respectively, ( Ram et al, 2020 ).…”

Identification and expression analysis of GARP superfamily genes in response to nitrogen and phosphorus stress in Spirodela polyrhiza

“…Six SpGLK genes belonged to NIGT1 subfamily and were named based on their topological locations in the phylogenetic tree: SpHHO1 ( SpGLK6 ), SpHHO2 ( SpGLK9 ), SpHHO3 ( SpGLK13 ), SpHHO4 / SpNIGT1.1 ( SpGLK25 ), SpHHO5 / SpNIGT1.2 ( SpGLK27 ), and SpHHO6 ( SpGLK28 ). Subgroup IIe harbored 23 KANADI ( KAN ) genes which play key roles in organ positioning, cell type patterning and organ morphogenesis of shoot apical meristem (SAM) [ 49 , 50 ]. Subgroup IIf contained 35 members which functioned to leaf development [ 41 ], including 7 AtGLKs, 11 OsGLKs, 6 CeGLKs, 3 SpGLKs and 4 WaGLKs.…”