From compact greens to ascending stems: elucidating the role of ATH1 in regulating internode growth dynamics in
Arabidopsis thaliana
Authors:   , Shokrian Hajibehzad Shahram 
Published: August 2024

Thesis outline
This thesis investigates the mechanisms underlying rosette initiation and robustness, as well as bolting regulation in Arabidopsis thaliana with an emphasis
on ATH1’s role.
Chapter 2: This chapter investigates the molecular mechanisms governing rosette formation in Arabidopsis. We demonstrate that the TALE transcription factor
ATH1, acting downstream of multiple photoreceptors, plays a central role in establishing and maintaining the rosette habit. Our findings reveal that ATH1 induction
is essential for the inactivity of the SAM’s rib zone (RZ), thereby preserving the
compact rosette form. We show that ATH1 likely achieves this by suppressing
photomorphogenesis inhibitors like PIFs, establishing a double negative feedback
loop with PIF4 at the SAM. Additionally, we elucidate the interplay between light
and sugar signals in ATH1 activation, with TOR kinase serving as a key mediator.
This highlights the complex molecular network controlling rosette development
in Arabidopsis.
Chapter 3: In this chapter, we explore the mechanisms that maintain the compact
rosette habit of Arabidopsis thaliana. We employ a multi-faceted approach, utilizing confocal imaging, genetic analyses, RNA sequencing, and pharmacological
studies. Our investigation reveals the interaction between ATH1 and the BAP/D
and HLH/BHLH regulatory modules, which play a crucial role in controlling cell
elongation. We demonstrate that ATH1 contributes to the robustness of the rosette by regulating these modules and limiting cell elongation within the deeper
layers of the SAM. The chapter concludes by elucidating how ATH1 accomplishes
this regulation. We provide evidence that ATH1 suppresses the expression of PRE
genes locally in the shoot apex, thereby maintaining the compact structure of
the rosette.
Chapter 4: This chapter delves into the gene regulatory network governed by
ATH1 within the SAM during the transition from vegetative to reproductive phase.
Utilizing confocal microscopy, we observed a decrease in ATH1 levels at the SAM,
which coincided with the floral transition, RZ activation, and the onset of bolting.
Subsequently, we employed an inducible ATH1-transgenic line for a transcriptomic
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General Introduction
analysis. This analysis enabled us to identify a set of genes expressed in the SAM
that could potentially be involved in bolting. These genes have been designated as
Bolting-Associated genes Controlled by ATH1 (BACA). Further investigation using
gene ontology underscored the significant role of hormonal pathways and cell
division regulators downstream of ATH1 during bolting. Notably, ATH1 appears to
specifically regulate the biosynthesis and signaling of several hormones, including
gibberellin, auxin, brassinosteroid, and ethylene. This regulation influences the
dramatic switch from an acaulescent (stemless) to a caulescent (stem-forming)
growth pattern.
In the final chapter of this thesis, Chapter 5, a summary of the research is presented and discussed in relation to the current understanding within the field.
The discussion in this chapter serves as the conclusion of the work and provides
insight into the significance of the findings