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1.  Plant stem cell maintenance involves direct transcriptional repression of differentiation program 
The plant stem cell regulator WUSCHEL is shown to repress differentiation-promoting transcription factors. This regulatory network is analyzed with a computational model of the three-dimensional shoot stem cell niche and a combination of genetic perturbation and live imaging.
We find that the transcription factor (TF) WUSCHEL (WUS) directly binds to the promoters and represses a group of genes including key TFs involved in differentiation thus keeping them repressed in the stem cells of the plant shoot, a mechanistic logic that is similar to animal stem cell regulation.We use a three-dimensional computational model of the plant shoot stem cell niche to show that the WUS-mediated repression of the differentiation program along with the previously reported activation of its own negative regulator leads to a robust stem cell homeostasis in a dynamic growth environment.Live imaging of target genes upon transient manipulation of WUS levels is combined with model perturbations to validate the proposed network and to connect it with a large body of previous experimental work.
In animal systems, master regulatory transcription factors (TFs) mediate stem cell maintenance through a direct transcriptional repression of differentiation promoting TFs. Whether similar mechanisms operate in plants is not known. In plants, shoot apical meristems serve as reservoirs of stem cells that provide cells for all above ground organs. WUSCHEL, a homeodomain TF produced in cells of the niche, migrates into adjacent cells where it specifies stem cells. Through high-resolution genomic analysis, we show that WUSCHEL represses a large number of genes that are expressed in differentiating cells including a group of differentiation promoting TFs involved in leaf development. We show that WUS directly binds to the regulatory regions of differentiation promoting TFs; KANADI1, KANADI2, ASYMMETRICLEAVES2 and YABBY3 to repress their expression. Predictions from a computational model, supported by live imaging, reveal that WUS-mediated repression prevents premature differentiation of stem cell progenitors, being part of a minimal regulatory network for meristem maintenance. Our work shows that direct transcriptional repression of differentiation promoting TFs is an evolutionarily conserved logic for stem cell regulation.
doi:10.1038/msb.2013.8
PMCID: PMC3658276  PMID: 23549482
central zone; CLAVATA3; shoot apical meristem; stem cell niche; WUSCHEL
2.  Signaling in the Arabidopsis shoot meristem stem cell niche correlates with ligand-dependent trafficking of the CLV1 receptor kinase 
Current biology : CB  2011;21(5):345-352.
Summary
Cell numbers in above-ground meristem types of plants are thought to be maintained by a feedback loop driven by perception of the glycopeptide ligand CLAVATA3 (CLV3) by the CLAVATA1 (CLV1) receptor kinase and the CLV2/CORYNE (CRN) receptor-like complex [1]. CLV3 made in the stem cells at the meristem apex limits the expression level of the stem cell-promoting homeodomain protein WUSCHEL (WUS) in the cells beneath, where CLV1 as well as WUS RNA are localized. WUS downregulation nonautonomously reduces stem cell proliferation. High-level overexpression of CLV3 eliminates the stem cells and causes meristem termination [2], and loss of CLV3 function allows meristem overproliferation [3]. There are many open questions regarding the CLV3/CLV1 interaction, including where in the meristem it occurs, how it is regulated, and how it is that a large range of CLV3 concentrations gives no meristem size phenotype [4]. Here we use genetics and live imaging to examine the cell biology of CLV1 in Arabidopsis meristematic tissue. We demonstrate that plasma membrane-localized CLV1 is reduced in concentration by CLV3, which causes trafficking of CLV1 to lytic vacuoles. We find that changes in CLV2 activity have no detectable effects on CLV1 levels. We also find that CLV3 appears to diffuse broadly in meristems, contrary to a recent sequestration model which states that CLV3 is quantitatively bound by CLV1 in the apical regions of the meristem, allowing continued WUS activity in lower regions [5]. This study provides a new model for CLV1 function in plant stem cell maintenance and suggests that downregulation of plasma membrane-localized CLV1 by its CLV3 ligand can account for the buffering of CLV3 signaling in the maintenance of stem cell pools in plants.
doi:10.1016/j.cub.2011.01.039
PMCID: PMC3072602  PMID: 21333538
3.  Alignment between PIN1 Polarity and Microtubule Orientation in the Shoot Apical Meristem Reveals a Tight Coupling between Morphogenesis and Auxin Transport 
PLoS Biology  2010;8(10):e1000516.
Imaging and computational modeling of the Arabidopsis shoot meristem epidermis suggests that biomechanical signals coordinately regulate auxin efflux carrier distribution and microtubule patterning to orchestrate the extent and directionality of growth.
Morphogenesis during multicellular development is regulated by intercellular signaling molecules as well as by the mechanical properties of individual cells. In particular, normal patterns of organogenesis in plants require coordination between growth direction and growth magnitude. How this is achieved remains unclear. Here we show that in Arabidopsis thaliana, auxin patterning and cellular growth are linked through a correlated pattern of auxin efflux carrier localization and cortical microtubule orientation. Our experiments reveal that both PIN1 localization and microtubule array orientation are likely to respond to a shared upstream regulator that appears to be biomechanical in nature. Lastly, through mathematical modeling we show that such a biophysical coupling could mediate the feedback loop between auxin and its transport that underlies plant phyllotaxis.
Author Summary
The proper development of plant organs such as leaves or flowers depends both on localized growth, which can be controlled by the plant hormone auxin, and directional growth, which is dependent on each cell's microtubule cytoskeleton. In this paper we show that at the shoot apex where organs initiate the orientation of the microtubule cytoskeleton is correlated with the orientation of the auxin transporter PIN1, suggesting coordination between growth patterning at the tissue level and directional growth at the cellular level. Recent work has indicated that mechanical signals play a role in orienting the plant microtubule network, and here we show that such signals can also orient PIN1. In addition, we demonstrate through mathematical modeling that an auxin transport system that is coordinated by mechanical signals akin to those we observed in vivo is sufficient to give rise to the patterns of organ outgrowth found in the plant Arabidopsis thaliana.
doi:10.1371/journal.pbio.1000516
PMCID: PMC2957402  PMID: 20976043

Results 1-3 (3)