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Abstract The precise regulation of stem cells in the shoot apical meristems (SAMs) involves the function of the homeodomain transcription factor (TF)‐WUSCHEL (WUS). WUS has been shown to move from the site of production‐the rib‐meristem (RM), into overlaying cells of the central zone (CZ), where it specifies stem cells and also regulates the transcription ofCLAVATA3 (CLV3). The secreted signalling peptide CLV3 activates a receptor kinase signalling that restrictsWUStranscription and also regulates the nuclear gradient of WUS by offsetting nuclear export. WUS has been shown to regulate bothCLV3levels and spatial activation, restricting its expression to a few cells in the CZ. The HAIRY MERISTEM (HAM), a GRASS‐domain class of TFs expressed in the RM, has been shown to physically interact with WUS and regulateCLV3expression. However, the mechanisms by which this interaction regulatesCLV3expression non‐cell autonomously remain unclear. Here, we show that HAM function is required for regulating the WUS protein stability, and theCLV3expression responds to altered WUS protein levels inhammutants. Thus, HAM proteins non‐cell autonomously regulatesCLV3expression. 

Abstract Regulation of the homeodomain transcription factor WUSCHEL concentration is critical for stem cell homeostasis inArabidopsisshoot apical meristems. WUSCHEL regulates the transcription ofCLAVATA3through a concentration-dependent activation-repression switch.CLAVATA3, a secreted peptide, activates receptor kinase signaling to repressWUSCHELtranscription. Considering the revised regulation,CLAVATA3mediated repression ofWUSCHELtranscription alone will lead to an unstable system. Here we show thatCLAVATA3signaling regulates nuclear-cytoplasmic partitioning ofWUSCHELto control nuclear levels and its diffusion into adjacent cells. Our work also reveals that WUSCHEL directly interacts with EXPORTINS via EAR-like domain which is also required for destabilizing WUSCHEL in the cytoplasm. We develop a combined experimental and computational modeling approach that integratesCLAVATA3-mediated transcriptional repression ofWUSCHELand post-translational control of nuclear levels with the WUSCHEL concentration-dependent regulation ofCLAVATA3. We show that the dual control by the same signal forms a seamless connection between de novo WUSCHEL synthesis and sub-cellular partitioning in providing robustness to the WUSCHEL gradient. 

Tracking plant cells in three-dimensional (3D) tissue captured through light microscopy presents significant challenge due to the large number of densely packed cells, non-uniform growth patterns, and variations in cell division planes across different cell layers. In addition, images of deeper tissue layers are often noisy, and systemic imaging errors further exacerbate the complexity of the task. In this paper, we propose a novel learning-based method DEGAST3D: Learning Deformable 3D GrAph Similarity to Track Plant Cells in Unregistered Time Lapse Images exploits the tightly packed 3D cell structure of plant cells to create a three-dimensional graph for accurate cell tracking. We also propose a novel algorithm for cell division detection and an effective three-dimensional registration, improving state-of-the-art algorithms. On a public dataset, our novel cell pair matching method outperforms the baseline by 6.83%, 5.96%, 6.40% in precision, recall, and F-1 score, respectively. On the same dataset, our proposed novel cell division technique improves the results of the baseline method by 15.38% and 14.78% in terms of recall and Fl-score, respectively. 

In plants, the robust maintenance of tissue structure is crucial to supporting its functionality. The multi-layered shoot apical meristem (SAM) ofArabidopsis,containing stem cells,is an approximately radially symmetric tissue whose shape and structure is maintained throughout the life of the plant. In this paper, a new biologically calibrated pseudo-three-dimensional (P3D) computational model of a longitudinal section of the SAM is developed. It includes anisotropic expansion and division of cells out of the cross-section plane, as well as representation of tension experienced by the SAM epidermis. Results from the experimentally calibrated P3D model provide new insights into maintenance of the structure of the SAM epidermal cell monolayer under tension and quantify dependence of epidermal and subepidermal cell anisotropy on the amount of tension. Moreover, the model simulations revealed that out-of-plane cell growth is important in offsetting cell crowding and regulating mechanical stresses experienced by tunica cells. Predictive model simulations show that tension-determined cell division plane orientation in the apical corpus may be regulating cell and tissue shape distributions needed for maintaining structure of the wild-type SAM. This suggests that cells' responses to local mechanical cues may serve as a mechanism to regulate cell- and tissue-scale patterning. 

Optimally spaced cis-elements of defined affinities regulate concentration-dependent transcriptional switching in stem cells. 

Stem cell maintenance in multilayered shoot apical meristems (SAMs) of plants requires strict regulation of cell growth and division. Exactly how the complex milieu of chemical and mechanical signals interact in the central region of the SAM to regulate cell division plane orientation is not well understood. In this paper, simulations using a newly developed multiscale computational model are combined with experimental studies to suggest and test three hypothesized mechanisms for the regulation of cell division plane orientation and the direction of anisotropic cell expansion in the corpus. Simulations predict that in the Apical corpus, WUSCHEL and cytokinin regulate the direction of anisotropic cell expansion, and cells divide according to tensile stress on the cell wall. In the Basal corpus, model simulations suggest dual roles for WUSCHEL and cytokinin in regulating both the direction of anisotropic cell expansion and cell division plane orientation. Simulation results are followed by a detailed analysis of changes in cell characteristics upon manipulation of WUSCHEL and cytokinin in experiments that support model predictions. Moreover, simulations predict that this layer-specific mechanism maintains both the experimentally observed shape and structure of the SAM as well as the distribution of WUSCHEL in the tissue. This provides an additional link between the roles of WUSCHEL, cytokinin, and mechanical stress in regulating SAM growth and proper stem cell maintenance in the SAM.