The interaction of transcription factors controls the spatial layout of plant aerial stem cell niches

Self-organization underlies developmental robustness in plants

Development is a self-organized process that builds on cells and their interactions. Cells are heterogeneous in gene expression, growth, and division; yet how development is robust despite such heterogeneity is a fascinating question. Here, we review recent progress on this topic, highlighting how developmental robustness is achieved through self-organization. We will first discuss sources of heterogeneity, including stochastic gene expression, heterogeneity in growth rate and direction, and heterogeneity in division rate and precision. We then discuss cellular mechanisms that buffer against such noise, including Paf1C- and miRNA-mediated denoising, spatiotemporal growth averaging and compensation, mechanisms to improve cell division precision, and coordination of growth rate and developmental timing between different parts of an organ. We also discuss cases where such heterogeneity is not buffered but utilized for development. Finally, we highlight potential directions for future studies of noise and developmental robustness.

An updated model of shoot apical meristem regulation by ERECTA family and CLAVATA3 signaling pathways in Arabidopsis

The shoot apical meristem (SAM) gives rise to the aboveground organs of plants. The size of the SAM is relatively constant due to the balance between stem cell replenishment and cell recruitment into new organs. In angiosperms, the transcription factor WUSCHEL (WUS) promotes stem cell proliferation in the central zone of the SAM. WUS forms a negative feedback loop with a signaling pathway activated by CLAVATA3 (CLV3). In the periphery of the SAM, the ERECTA family receptors (ERfs) constrain WUS and CLV3 expression. Here, we show that four ligands of ERfs redundantly inhibit the expression of these two genes. Transcriptome analysis confirmed that WUS and CLV3 are the main targets of ERf signaling and uncovered new ones. Analysis of promoter reporters indicated that the WUS expression domain mostly overlaps with the CLV3 domain and does not shift along the apical-basal axis in clv3 mutants. Our three-dimensional mathematical model captured gene expression distributions at the single-cell level under various perturbed conditions. Based on our findings, CLV3 regulates cellular levels of WUS mostly through autocrine signaling, and ERfs regulate the spatial expression of WUS, preventing its encroachment into the peripheral zone.

Cell signaling in the shoot apical meristem

Distinct from animals, plants maintain organogenesis from specialized tissues termed meristems throughout life. In the shoot apex, the shoot apical meristem (SAM) produces all aerial organs, such as leaves, from its periphery. For this, the SAM needs to precisely balance stem cell renewal and differentiation, which is achieved through dynamic zonation of the SAM, and cell signaling within functional domains is key for SAM functions. The WUSCHEL-CLAVATA feedback loop plays a key role in SAM homeostasis, and recent studies have uncovered new components, expanding our understanding of the spatial expression and signaling mechanism. Advances in polar auxin transport and signaling have contributed to knowledge of the multifaceted roles of auxin in the SAM and organogenesis. Finally, single-cell techniques have expanded our understanding of the cellular functions within the shoot apex at single-cell resolution. In this review, we summarize the most up-to-date understanding of cell signaling in the SAM and focus on the multiple levels of regulation of SAM formation and maintenance.

Promotive effect of phytosulfokine - peptide growth factor - on protoplast cultures development in Fagopyrum tataricum (L.) Gaertn

BACKGROUND

Fagopyrum tataricum (Tartary buckwheat) is a valuable crop of great nutritional importance due to its high level of bioactive compounds. Excellent opportunities to obtain plants with the high level or the desired profile of valuable metabolites may be provided by in vitro cultures. Among known in vitro techniques, protoplast technology is an exciting tool for genetic manipulation to improve crop traits. In that context, protoplast fusion may be applied to generate hybrid cells between different species of Fagopyrum. To apply protoplast cultures to the aforementioned approaches in this research, we established the protoplast-to-plant system in Tartary buckwheat.

RESULTS

In this work, cellulase and pectinase activity enabled protoplast isolation from non-morphogenic and morphogenic callus (MC), reaching, on average, 2.3 × 106 protoplasts per g of fresh weight. However, to release protoplasts from hypocotyls, the key step was the application of driselase in the enzyme mixture. We showed that colony formation could be induced after protoplast embedding in agarose compared to the alginate matrix. Protoplasts cultured in a medium based on Kao and Michayluk supplemented with phytosulfokine (PSK) rebuilt cell walls, underwent repeated mitotic division, formed aggregates, which consequently led to callus formation. Plating efficiency, expressing the number of cell aggregate formed, in 10-day-old protoplast cultures varied from 14% for morphogenic callus to 30% for hypocotyls used as a protoplast source. However plant regeneration via somatic embryogenesis and organogenesis occurred only during the cultivation of MC-derived protoplasts.

CONCLUSIONS

This study demonstrated that the applied protoplast isolation approach facilitated the recovery of viable protoplasts. Moreover, the embedding of protoplasts in an agarose matrix and supplementation of a culture medium with PSK effectively stimulated cell division and further development of Tartary buckwheat protoplast cultures along with the plant regeneration. Together, these results provide the first evidence of developing a protoplast-to-plant system from the MC of Fagopyrum tataricum used as source material. These findings suggest that Tartary buckwheat's protoplast cultures have potential implications for the species' somatic hybridization and genetic improvement.

Stem Cell Basis of Shoot Branching

During their postembryonic development, plants continuously form branches to conquer more space and adapt to changing environments. In seed plants, this is achieved by lateral branching, in which axillary meristems (AMs) initiate at the leaf axils to form axillary buds. The developmental potential of AMs to form shoot branches is the same as that of embryonic shoot apical meristems (SAMs). Recent studies in Arabidopsis thaliana have revealed the cellular origin of AMs and have identified transcription factors and phytohormones that regulate sequential steps leading to AM initiation. In particular, a group of meristematic cells detached from the SAM are key to AM initiation, which constitutes an excellent system for understanding stem cell fate and de novo meristem formation.

Flower Development in Arabidopsis

Like in other angiosperms, the development of flowers in Arabidopsis starts right after the floral transition, when the shoot apical meristem (SAM) stops producing leaves and makes flowers instead. On the flanks of the SAM emerge the flower meristems (FM) that will soon differentiate into the four main floral organs, sepals, petals, stamens, and pistil, stereotypically arranged in concentric whorls. Each phase of flower development-floral transition, floral bud initiation, and floral organ development-is under the control of specific gene networks. In this chapter, we describe these different phases and the gene regulatory networks involved, from the floral transition to the floral termination.

Quantifying Gene Expression Domains in Plant Shoot Apical Meristems

The shoot apical meristem is the plant tissue that produces the plant aerial organs such as flowers and leaves. To better understand how the shoot apical meristem develops and adapts to the environment, imaging developing shoot meristems expressing fluorescence reporters through laser confocal microscopy is becoming increasingly important. Yet, there are not many computational pipelines enabling a systematic and high-throughput characterization of the produced microscopy images. This chapter provides a simple method to analyze 3D images obtained through laser scanning microscopy and quantitatively characterize radially or axially symmetric 3D fluorescence domains expressed in a tissue or organ by a reporter. Then, it presents different computational pipelines aiming at performing high-throughput quantitative image analysis of gene expression in plant inflorescence and floral meristems. This methodology has notably enabled the quantitative characterization of how stem cells respond to environmental perturbations in the Arabidopsis thaliana inflorescence meristem and will open new avenues in the use of quantitative analysis of gene expression in shoot apical meristems. Overall, the presented methodology provides a simple framework to analyze quantitatively gene expression domains from 3D confocal images at the tissue and organ level, which can be applied to shoot meristems and other organs and tissues.

Integrated transcriptomic and metabolic analyses provide insights into the maintenance of embryogenic potential and the biosynthesis of phenolic acids and flavonoids involving transcription factors in Larix kaempferi (Lamb.) Carr

Somatic embryogenesis (SE) techniques have been established for micropropagation or basic research related to plant development in many conifer species. The frequent occurrence of non-embryogenic callus (NEC) during SE has impose constraints on the application of somatic embryogenesis SE in Larix kaempferi (Lamb.) Carr, but the potential regulatory mechanisms are poorly understood. In this study, integrated transcriptomic and metabolomic analyses were performed in embryogenic callus (EC) and NEC originating from a single immature zygotic embryo to better decipher the key molecular and metabolic mechanisms required for embryogenic potential maintenance. The results showed that a total of 13,842 differentially expressed genes (DEGs) were found in EC and NEC, among which many were enriched in plant hormone signal transduction, starch and sucrose metabolism, phenylpropanoid biosynthesis, flavonoid biosynthesis, and the biosynthesis of amino acids pathways. Metabolite profiling showed that 441 differentially accumulated metabolites (DAMs) were identified in EC and NEC. Both EC and NEC had vigorous primary metabolic activities, while most secondary metabolites were upregulated in NEC. Many totipotency-related transcription factor (TF) genes such as BBMs, WUSs, and LEC1 showed higher expression levels in EC compared with NEC, which may result in the higher accumulation of indole 3-acetic acid (IAA) in EC. NEC was characterized by upregulation of genes and metabolites associated with stress responses, such as DEGs involved in jasmonic acid (JA) and ethylene (ETH) biosynthesis and signal transduction pathways, and DEGs and DAMs related to phenylpropanoid and flavonoid biosynthesis. We predicted and analyzed TFs that could target several key co-expressed structural DEGs including two C4H genes, two CcoAOMT genes and three HCT genes involved in phenylpropanoid and flavonoid biosynthesis. Based on the targeted relationship and the co-expression network, two ERFs (Lk23436 and Lk458687), one MYB (Lk34626) and one C2C2-dof (Lk37167) may play an important role in regulating phenolic acid and flavonoid biosynthesis by transcriptionally regulating the expression of these structural genes. This study shows an approach involving integrated transcriptomic and metabolic analyses to obtain insights into molecular events underlying embryogenic potential maintenance and the biosynthesis mechanisms of key metabolites involving TF regulation, which provides valuable information for the improvement of SE efficiency in L. kaempferi.

Function and Regulation of microRNA171 in Plant Stem Cell Homeostasis and Developmental Programing

MicroRNA171 (miR171), a group of 21-nucleotide single-strand small RNAs, is one ancient and conserved microRNA family in land plants. This review focuses on the recent progress in understanding the role of miR171 in plant stem cell homeostasis and developmental patterning, and the regulation of miR171 by developmental cues and environmental signals. Specifically, miR171 regulates shoot meristem activity and phase transition through repressing the HAIRYMERISTEM (HAM) family genes. In the model species Arabidopsis, miR171 serves as a short-range mobile signal, which initiates in the epidermal layer of shoot meristems and moves downwards within a limited distance, to pattern the apical-basal polarity of gene expression and drive stem cell dynamics. miR171 levels are regulated by light and various abiotic stresses, suggesting miR171 may serve as a linkage between environmental factors and cell fate decisions. Furthermore, miR171 family members also demonstrate both conserved and lineage-specific functions in land plants, which are summarized and discussed here.

CLAVATA3 mediated simultaneous control of transcriptional and post-translational processes provides robustness to the WUSCHEL gradient

Regulation of the homeodomain transcription factor WUSCHEL concentration is critical for stem cell homeostasis in Arabidopsis shoot apical meristems. WUSCHEL regulates the transcription of CLAVATA3 through a concentration-dependent activation-repression switch. CLAVATA3, a secreted peptide, activates receptor kinase signaling to repress WUSCHEL transcription. Considering the revised regulation, CLAVATA3 mediated repression of WUSCHEL transcription alone will lead to an unstable system. Here we show that CLAVATA3 signaling regulates nuclear-cytoplasmic partitioning of WUSCHEL to 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 integrates CLAVATA3-mediated transcriptional repression of WUSCHEL and post-translational control of nuclear levels with the WUSCHEL concentration-dependent regulation of CLAVATA3. 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.

Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines

Somatic embryogenesis-mediated plant regeneration is essential for the genetic manipulation of agronomically important traits in upland cotton. Genotype specific recalcitrance to regeneration is a primary challenge in deploying genome editing and incorporating useful transgenes into elite cotton germplasm. In this study, transcriptomes of a semi-recalcitrant cotton (Gossypium hirsutum L.) genotype ‘Coker312’ were analyzed at two critical stages of somatic embryogenesis that include non-embryogenic callus (NEC) and embryogenic callus (EC) cells, and the results were compared to a non-recalcitrant genotype ‘Jin668’. We discovered 305 differentially expressed genes in Coker312, whereas, in Jin668, about 6-fold more genes (2155) were differentially expressed. A total of 154 differentially expressed genes were common between the two genotypes. Gene enrichment analysis of the upregulated genes identified functional categories, such as lipid transport, embryo development, regulation of transcription, sugar transport, and vitamin biosynthesis, among others. In Coker312 EC cells, five major transcription factors were highly upregulated: LEAFY COTYLEDON 1 (LEC1), WUS-related homeobox 5 (WOX5), ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and WRKY2. In Jin668, LEC1, BABY BOOM (BBM), FUS3, and AGAMOUS-LIKE15 (AGL15) were highly expressed in EC cells. We also found that gene expression of these embryogenesis genes was typically higher in Jin668 when compared to Coker312. We conclude that significant differences in the expression of the above genes between Coker312 and Jin668 may be a critical factor affecting the regenerative ability of these genotypes.

Meeting at the DNA: Specifying Cytokinin Responses through Transcription Factor Complex Formation

Cytokinin is a plant hormone regulating numerous biological processes. Its diverse functions are realized through the expression control of specific target genes. The transcription of the immediate early cytokinin target genes is regulated by type-B response regulator proteins (RRBs), which are transcription factors (TFs) of the Myb family. RRB activity is controlled by phosphorylation and protein degradation. Here, we focus on another step of regulation, the interaction of RRBs among each other or with other TFs to form active or repressive TF complexes. Several examples in Arabidopsis thaliana illustrate that RRBs form homodimers or complexes with other TFs to specify the cytokinin response. This increases the variability of the output response and provides opportunities of crosstalk between the cytokinin signaling pathway and other cellular signaling pathways. We propose that a targeted approach is required to uncover the full extent and impact of RRB interaction with other TFs.

What shoots can teach about theories of plant form

Plants generate a large variety of shoot forms with regular geometries. These forms emerge primarily from the activity of a stem cell niche at the shoot tip. Recent efforts have established a theoretical framework of form emergence at the shoot tip, which has empowered the use of modelling in conjunction with biological approaches to begin to disentangle the biochemical and physical mechanisms controlling form development at the shoot tip. Here, we discuss how these advances get us closer to identifying the construction principles of plant shoot tips. Considering the current limits of our knowledge, we propose a roadmap for developing a general theory of form development at the shoot tip.

ERECTA family signaling constrains CLAVATA3 and WUSCHEL to the center of the shoot apical meristem

The shoot apical meristem (SAM) is a reservoir of stem cells that gives rise to all post-embryonic above-ground plant organs. The size of the SAM remains stable over time owing to a precise balance of stem cell replenishment versus cell incorporation into organ primordia. The WUSCHEL (WUS)/CLAVATA (CLV) negative feedback loop is central to SAM size regulation. Its correct function depends on accurate spatial expression of WUS and CLV3 A signaling pathway, consisting of ERECTA family (ERf) receptors and EPIDERMAL PATTERNING FACTOR LIKE (EPFL) ligands, restricts SAM width and promotes leaf initiation. Although ERf receptors are expressed throughout the SAM, EPFL ligands are expressed in its periphery. Our genetic analysis of Arabidopsis demonstrated that ERfs and CLV3 synergistically regulate the size of the SAM, and wus is epistatic to ERf genes. Furthermore, activation of ERf signaling with exogenous EPFLs resulted in a rapid decrease of CLV3 and WUS expression. ERf-EPFL signaling inhibits expression of WUS and CLV3 in the periphery of the SAM, confining them to the center. These findings establish the molecular mechanism for stem cell positioning along the radial axis.

WUSCHEL in the shoot apical meristem: old player, new tricks

The maintenance of the stem cell niche in the shoot apical meristem, the structure that generates all of the aerial organs of the plant, relies on a canonical feedback loop between WUSCHEL (WUS) and CLAVATA3 (CLV3). WUS is a homeodomain transcription factor expressed in the organizing centre that moves to the central zone to promote stem cell fate. CLV3 is a peptide whose expression is induced by WUS in the central zone and that can move back to the organizing centre to inhibit WUS expression. Within the past 20 years since the initial formulation of the CLV-WUS feedback loop, the mechanisms of stem cell maintenance have been intensively studied and the function of WUS has been redefined. In this review, we highlight the most recent advances in our comprehension of the molecular mechanisms of WUS function, of its interaction with other transcription factors and hormonal signals, and of its connection to environmental signals. Through this, we will show how WUS can integrate both internal and external cues to adapt meristem function to the plant environment.

HAM Gene Family and Shoot Meristem Development

Land plants develop highly diversified shoot architectures, all of which are derived from the pluripotent stem cells in shoot apical meristems (SAMs). As sustainable resources for continuous organ formation in the aboveground tissues, SAMs play an important role in determining plant yield and biomass production. In this review, we summarize recent advances in understanding one group of key regulators - the HAIRY MERISTEM (HAM) family GRAS domain proteins - in shoot meristems. We highlight the functions of HAM family members in dictating shoot stem cell initiation and proliferation, the signaling cascade that shapes HAM expression domains in shoot meristems, and the conservation and diversification of HAM family members in land plants. We also discuss future directions that potentially lead to a more comprehensive view of the HAM gene family and stem cell homeostasis in land plants.

Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

Background

Genotype independent transformation and whole plant regeneration through somatic embryogenesis relies heavily on the intrinsic ability of a genotype to regenerate. The critical genetic architecture of non-embryogenic callus (NEC) cells and embryogenic callus (EC) cells in a highly regenerable cotton genotype is unknown.

Results

In this study, gene expression profiles of a highly regenerable Gossypium hirsutum L. cultivar, Jin668, were analyzed at two critical developmental stages during somatic embryogenesis, non-embryogenic callus (NEC) cells and embryogenic callus (EC) cells. The rate of EC formation in Jin668 is 96%. Differential gene expression analysis revealed a total of 5333 differentially expressed genes (DEG) with 2534 genes upregulated and 2799 genes downregulated in EC. A total of 144 genes were unique to NEC cells and 174 genes were unique to EC. Clustering and enrichment analysis identified genes upregulated in EC that function as transcription factors/DNA binding, phytohormone response, oxidative reduction, and regulators of transcription; while genes categorized in methylation pathways were downregulated. Four key transcription factors were identified based on their sharp upregulation in EC tissue; LEAFY COTYLEDON 1 (LEC1), BABY BOOM (BBM), FUSCA (FUS3) and AGAMOUS-LIKE15 with distinguishable subgenome expression bias.

Conclusions

This comparative analysis of NEC and EC transcriptomes gives new insights into the genes involved in somatic embryogenesis in cotton.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12861-020-00230-4.

A mathematical model for understanding synergistic regulations and paradoxical feedbacks in the shoot apical meristem

The shoot apical meristem (SAM) is the primary stem cell niche in plant shoots. Stem cells in the SAM are controlled by an intricate regulatory network, including negative feedback between WUSCHEL (WUS) and CLAVATA3 (CLV3). Recently, we identified a group of signals, Epidermal Patterning Factor-Like (EPFL) proteins, that are produced at the peripheral region and are important for SAM homeostasis. Here, we present a mathematical model for the SAM regulatory network. The model revealed that the SAM uses EPFL and signals such as HAIRY MERISTEM from the middle in a synergistic manner to constrain both WUS and CLV3. We found that interconnected negative and positive feedbacks between WUS and CLV3 ensure stable WUS expression in the SAM when facing perturbations, and the positive feedback loop also maintains distinct cell populations containing WUS on and CLV3 on cells in the apical-basal direction. Furthermore, systematic perturbations of the parameters revealed a tradeoff between optimizations of multiple patterning features. Our results provide a holistic view of the regulation of SAM patterning in multiple dimensions. They give insights into how Arabidopsis integrates signals from lateral and apical-basal axes to control the SAM patterning, and they shed light into design principles that may be widely useful for understanding regulatory networks of stem cell niche.

Molecular and Hormonal Regulation of Leaf Morphogenesis in Arabidopsis

Shoot apical meristems (SAM) are tissues that function as a site of continuous organogenesis, which indicates that a small pool of pluripotent stem cells replenishes into lateral organs. The coordination of intercellular and intracellular networks is essential for maintaining SAM structure and size and also leads to patterning and formation of lateral organs. Leaves initiate from the flanks of SAM and then develop into a flattened structure with variable sizes and forms. This process is mainly regulated by the transcriptional regulators and mechanical properties that modulate leaf development. Leaf initiation along with proper orientation is necessary for photosynthesis and thus vital for plant survival. Leaf development is controlled by different components such as hormones, transcription factors, miRNAs, small peptides, and epigenetic marks. Moreover, the adaxial/abaxial cell fate, lamina growth, and shape of margins are determined by certain regulatory mechanisms. The over-expression and repression of various factors responsible for leaf initiation, development, and shape have been previously studied in several mutants. However, in this review, we collectively discuss how these factors modulate leaf development in the context of leaf initiation, polarity establishment, leaf flattening and shape.

Control of cell fate during axillary meristem initiation

Axillary meristems (AMs) are located in the leaf axil and can establish new growth axes. Whereas their neighboring cells are differentiated, the undifferentiated cells in the AM endow the AM with the same developmental potential as the shoot apical meristem. The AM is, therefore, an excellent system to study stem cell fate maintenance in plants. In this review, we summarize the current knowledge of AM initiation. Recent findings have shown that AMs derive from a stem cell lineage that is maintained in the leaf axil. This review covers AM progenitor cell fate maintenance, reactivation, and meristem establishment. We also highlight recent work that links transcription factors, phytohormones, and epigenetic regulation to AM initiation.

A signal cascade originated from epidermis defines apical-basal patterning of Arabidopsis shoot apical meristems

In multicellular organisms, a long-standing question is how spatial patterns of distinct cell types are initiated and maintained during continuous cell division and proliferation. Along the vertical axis of plant shoot apical meristems (SAMs), stem cells are located at the top while cells specifying the stem cells are located more basally, forming a robust apical-basal pattern. We previously found that in Arabidopsis SAMs, the HAIRY MERISTEM (HAM) family transcription factors form a concentration gradient from the epidermis to the interior cell layers, and this gradient is essential for the stem cell specification and the apical-basal patterning of the SAMs. Here, we uncover that epidermis specific transcription factors, ARABIDOPSIS THALIANA MERISTEM LAYER 1 (ATML1) and its close homolog, define the concentration gradient of HAM in the SAM through activating a group of microRNAs. This study provides a molecular framework linking the epidermis-derived signal to the stem cell homeostasis in plants.

A concentration gradient of HAM transcription factors specifies apical-basal patterning in the Arabidopsis shoot apical meristem. Here, the authors show that epidermal expression of the ATML1 transcription factor defines this concentration gradient via activation of mobile micro RNA.

Transcriptional circuits in control of shoot stem cell homeostasis

Plant shoot apical meristems (SAMs) play essential roles in plant growth and development. Located at the growing tip of a plant stem, these dome-like structures contain stem cells, which serve to perpetuate themselves in an undifferentiated state while continually adding new cells that differentiate and eventually form all above-ground tissues. In a SAM, the pool of stem cells is dynamically maintained through a balance between cell division (self-renewal) and differentiation (loss of stem-cell identity). In the model plant Arabidopsis thaliana, a negative feedback loop between WUSCHEL (WUS) and the CLAVATA3 (CLV3) plays important roles in maintaining the stem cell population. In this review, we highlight recent findings mainly from studies in Arabidopsis, and summarize the research progress on understanding how multiple transcriptional circuits integrate and function at different cell layers to control the WUS-CLV3 loop and stem cell homeostasis.

The Overlapping and Distinct Roles of HAM Family Genes in Arabidopsis Shoot Meristems

In Arabidopsis shoot apical meristems (SAMs), a well-characterized regulatory loop between WUSCHEL (WUS) and CLAVATA3 (CLV3) maintains stem cell homeostasis by regulating the balance between cell proliferation and cell differentiation. WUS proteins, translated in deep cell layers, move into the overlaying stem cells to activate CLV3. The secreted peptide CLV3 then regulates WUS levels through a ligand-receptor mediated signaling cascade. CLV3 is specifically expressed in the stem cells and repressed in the deep cell layers despite presence of the WUS activator, forming an apical-basal polarity along the axis of the SAM. Previously, we proposed and validated a hypothesis that the HAIRY MERISTEM (HAM) family genes regulate this polarity, keeping the expression of CLV3 off in interior cells of the SAM. However, the specific role of each individual member of the HAM family in this process remains to be elucidated. Combining live imaging and molecular genetics, we have dissected the conserved and distinct functions of different HAM family members in control of CLV3 patterning in the SAMs and in the de novo shoot stem cell niches as well.