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Most plant roots have multiple cortex layers that make up the bulk of the organ and play key roles in physiology, such as flood tolerance and symbiosis. However, little is known about the formation of cortical layers outside of the highly reduced anatomy of Arabidopsis. Here we use single-cell RNAseq to rapidly generate a cell resolution map of the maize root, revealing an alternative configuration of the tissue formative transcription factor SHORT-ROOT (SHR) adjacent to an expanded cortex. We show that maize SHR protein is hypermobile, moving at least eight cell layers into the cortex. Higher-order SHR mutants in both maize and Setaria have reduced numbers of cortical layers, showing that the SHR pathway controls expansion of cortical tissue to elaborate anatomical complexity.

Most plant roots have multiple cortex layers that make up the bulk of the organ and play key roles in physiology, such as flood tolerance and symbiosis. However, little is known about the formation of cortical layers outside of the highly reduced anatomy of the model Arabidopsis. Here we use single-cell RNAseq to rapidly generate a cell resolution map of the maize root, revealing an alternative configuration of the tissue formative SHORT-ROOT (SHR) signaling pathway adjacent to an expanded cortex. We show that maize SHR protein is hypermobile, moving at least eight cell layers into the cortex. Higher-order SHR mutants in both maize and Setaria have reduced numbers of cortical layers, showing that the SHR pathway controls expansion of cortical tissue in grasses that sets up anatomical complexity and a host of key traits.One sentence summarySingle-cell RNA-seq maps the maize root transcriptome uncovering a mechanism that regulates cortex layer number.

The mechanisms that allow cells in the plant meristem to coordinate tissue-wide maturation gradients with specialized cell networks are critical for indeterminate growth. Here, we reconstructed the protophloem developmental trajectory of 19 cells from cell birth to terminal differentiation at single cell resolution in the Arabidopsis root. We found that cellular specification is mediated near the stem cell niche by PHLOEM EARLY DOF (PEAR) transcription factors. However, the PEAR dependent differentiation program is repressed by a broad gradient of PLETHORA (PLT) transcription factors, which directly inhibit PEARs’ own direct targetALTERED PHLOEM DEVELOPMENT (APL). The dissipation of PLT gradient around 7 cells from the stem cell activates APL expression, and a subsequent transitional network that results in a “seesaw” pattern of mutual inhibition over developmental time. Together, we provide a mechanistic understanding of how morphogen-like maturation gradients interface with cell-type specific transcriptional regulators to stage cellular differentiation.

Pags 1362-1378 Ilustraciones, Postembryonic organogenesis is critical for plant development. Underground, lateral roots (LRs) form the bulk of mature root systems, yet the ontogeny of the LR primordium (LRP) is not clear. In this study, we performed the single-cell RNA sequencing through the first four stages of LR formation in Arabidopsis. Our analysis led to a model in which a single group of precursor cells, with a cell identity different from their pericycle origins, rapidly reprograms and splits into a mixed ground tissue/stem cell niche fate and a vascular precursor fate. The ground tissue and stem cell niche fates soon separate and a subset of more specialized vascular cells form sucrose transporting phloem cells that appear to connect to the primary root. We did not detect cells resembling epidermis or root cap, suggesting that outer tissues may form later, preceding LR emergence. At this stage, some remaining initial precursor cells form the primordium flanks, while the rest create a reservoir of pluripotent cells that are able to replace the LR if damaged. Laser ablation of the central and lateral LRP regions showed that remaining cells restart the sequence of tissue initiation to form a LR. Collectively, our study reveals an ontological hierarchy for LR formation with an early and sequential split of main root tissues and stem cells., This work was funded by the Ministerio de Economı´a y Competitividad (MINECO) of Spain and ERDF (grants BFU2016-80315-P and PID2019- 111523GB-I00 to M.A.M.-R), by the Comunidad de Madrid (CM) and Universidad Politécnica de Madrid (UPM; grant APOYO_JOVENES_ 2Y36R7_20_TRG6W7 [Plant_Stem] to P.P.-G.), the ‘‘Severo Ochoa (SO) Program for Centers of Excellence in R&D’’ from the Agencia Estatal de Investigacio´ n of Spain [SEV-2016-0672 (2017–2021)] to M.A.M.-R and P.P.-G via the CBGP, and by the National Institutes of Health (grant 1R35GM136362) and National Science Foundation (grant 1934388) to K.D.B. L.S.-R. and A.S.-C. were supported by FPI contracts (BES-2017- 080155 and BES-2014-068852, respectively) from MINECO, P.P.-G. by Programa Atraccion Talento from CM (2017-T2/BIO-3453) and SO, and J.C. by a Juan de la Cierva contract from MINECO (FJCI-2016-28607).

Wounding is a trigger for both regeneration and defense in plants, but it is not clear if the two responses are linked by common activation or regulated as tradeoffs. While plant glutamate-like receptors (GLRs) are known to mediate defense, here we implicate GLRs in regeneration through dynamic changes in chromatin and transcription in reprogramming cells near wound sites. We show that genetic and pharmacological inhibition of GLR activity increases regeneration efficiency in multiple organ repair systems and plant species. Perturbation of GLR-mediated function speeds cell division and re-specification of the stem cell niche while dampening defense responses. We show that the GLRs work through salicylic acid (SA) signaling in regeneration, with mutants in the SA receptor NPR1 partially resistant to GLR perturbation and hyper regenerative. These findings reveal a conserved mechanism that regulates a tradeoff between defense and regeneration and offer new strategies to improve regeneration in agriculture and conservation.

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them., National Science Foundation 1916797 David W Ehrhardt, Kenneth D Birnbaum, Seung Yon Rhee; National Science Foundation 2052590 Seung Yon Rhee

Background Characterizing the behaviors of dynamic systems requires capturing them with high temporal and spatial resolution. Owing to its transparency and genetic tractability, the Arabidopsis thaliana root lends itself well to live imaging when combined with cell and tissue-specific fluorescent reporters. We developed a novel 4D imaging method that utilizes simple confocal microscopy and readily available components to track cell divisions in the root stem cell niche and surrounding region for up to 1 week. Results Using this method, we performed a direct measurement of cell division intervals within and around the root stem cell niche. The results reveal a short, steep gradient of cell division rates in proximal stem cells, with progressively more rapid cell division rates from quiescent center (QC), to cells in direct contact with the QC (initials), to their immediate daughters, after which division rates appear to become more homogeneous. Conclusions These results provide a baseline to study how perturbations in signaling could affect cell division patterns in the root meristem. This new setup further allows us to finely analyze meristematic cell division rates that lead to patterning. Electronic supplementary material The online version of this article (10.1186/s13007-019-0417-9) contains supplementary material, which is available to authorized users.

Enormous societal challenges, such as feeding and providing energy for a growing population in a dramatically changing climate, necessitate technological advances in plant science. Plant cells are fundamental organizational units that mediate the production, transport, and storage of our primary food sources, and they sequester a significant proportion of the world's carbon. New technologies allow comprehensive descriptions of cells that could accelerate research across fields of plant science. Complementary to the efforts towards understanding the cellular diversity in human brain and immune systems, a Plant Cell Atlas (PCA) that maps molecular machineries to cellular and subcellular domains, follows their dynamic movements, and describes their interactions would accelerate discovery in plant science and help to solve imminent societal problems.

The genus Selaginella resides in an early branch of the land plant lineage that possesses a vasculature and roots. The majority of the Selaginella root system is shoot borne and emerges through a distinctive structure known as the rhizophore, the organ identity of which has been a long-debated question. The rhizophore of Selaginella moellendorffii - a model for the lycophytes - shows plasticity to develop into a root or shoot up until 8 d after angle meristem emergence, after which it is committed to root fate. We subsequently use morphology and plasticity to define the stage of rhizophore identity. Transcriptomic analysis of the rhizophore during its plastic stage reveals that, despite some resemblance to the root meristem, rhizophore gene expression patterns are largely distinct from both shoot and root meristems. Based on this transcriptomic analysis and on historical anatomical work, we conclude that the rhizophore is a distinct organ with unique features.

Background Reporter methods to quantitatively measure the efficiency and specificity of genome editing tools are important for the development of novel editing techniques and successful applications of available ones. However, the existing methods have major limitations in sensitivity, accuracy, and/or readiness for in vivo applications. Here, we aim to develop a straight-forward method by using nucleotide insertion/deletion resulted from genome editing. In this system, a target sequence with frame-shifting length is inserted after the start codon of a cerulean fluorescence protein (CFP) to inactivate its fluorescence. As such, only a new insertion/deletion event in the target sequence will reactivate the fluorescence. This reporter is therefore termed as “Insertion/deletion-activated frame-shift fluorescence protein”. To increase its traceability, an internal ribosome entry site and a red fluorescence protein mCherryFP are placed downstream of the reporter. The percentage of CFP-positive cells can be quantified by fluorescence measuring devices such as flow cytometer as the readout for genome editing frequency. Results To test the background noise level, sensitivity, and quantitative capacity of this new reporter, we applied this approach to examine the efficiency of genome editing of CRISPR/Cas9 on two different targeting sequences and in three different cell lines, in the presence or absence of guide-RNAs with or without efficiency-compromising mutations. We found that the insertion/deletion-activated frame-shift fluorescence protein has very low background signal, can detect low-efficiency genome editing events driven by mutated guideRNAs, and can quantitatively distinguish genome editing by normal or mutated guideRNA. To further test whether the positive editing event detected by this reporter indeed correspond to genuine insertion/deletion on the genome, we enriched the CFP-positive cells to examine their fluorescence under confocal microscope and to analyze the DNA sequence of the reporter in the genome by Sanger sequencing. We found that the positive events captured by this reporter indeed correlates with genuine DNA insertion/deletion in the expected genome location. Conclusion The insertion/deletion-activated frame-shift fluorescence protein reporter has very low background, high sensitivity, and is quantitative in nature. It will be able to facilitate the development of new genome editing tools as well as the application of existing tools. Electronic supplementary material The online version of this article (10.1186/s12864-019-5963-z) contains supplementary material, which is available to authorized users.

The growing scale and declining cost of single-cell RNA-sequencing (RNA-seq) now permit a repetition of cell sampling that increases the power to detect rare cell states, reconstruct developmental trajectories, and measure phenotype in new terms such as cellular variance. The characterization of anatomy and developmental dynamics has not had an equivalent breakthrough since groundbreaking advances in live fluorescent microscopy. The new resolution obtained by single-cell RNA-seq is a boon to genetics because the novel description of phenotype offers the opportunity to refine gene function and dissect pleiotropy. In addition, the recent pairing of high-throughput genetic perturbation with single-cell RNA-seq has made practical a scale of genetic screening not previously possible.

Maize is one the most widely cultivated crops worldwide and an important model system for the study of genetics and cytogenetics. Although the availability of a genome sequence has enabled new quantitative genomic studies, developing methods to isolate specific types of cells will enable useful approaches for transcriptomic analysis in the crop plant. Fluorescence-activated cell sorting (FACS) is a powerful technique for cell isolation and the study of transcriptional profiles from specific cell populations. The use of FACS on plant cells requires the generation of protoplasts by tissue digestion and cell wall removal. Although some protocols are available, they mainly focus on dicot species and obtaining sufficient protoplasts from inner tissue layers has been challenging in both monocots and dicots. Here, we report a new protocol that dramatically increases protoplast yield from maize for subsequent cell isolation by FACS. This protocol is efficient in generating protoplasts from root and shoot inner layers and can also be applied successfully to Arabidopsis thaliana. © 2018 by John Wiley & Sons, Inc.

Arginylation is an emerging posttranslational modification mediated by arginyltransferase (ATE1) that is essential for mammalian embryogenesis and regulation of the cytoskeleton. Here, we discovered that Ate1 knockout embryonic fibroblasts exhibit tumorigenic properties, including abnormally rapid contact-independent growth, reduced ability to form cell-cell contacts, and chromosomal aberrations. Ate1 knockout fibroblasts can form large colonies in Matrigel and exhibit invasive behavior, unlike wild type fibroblasts. Furthermore, Ate1 knockout cells form tumors in subcutaneous xenograft assays in immunocompromised mice. Abnormal growth in these cells can be partially rescued by reintroduction of stably expressed specific Ate1 isoforms, which also reduce the ability of these cells to form tumors. Tumor array studies and bioinformatics analysis show that Ate1 is down-regulated in several types of human cancer samples at the protein level, and that its transcription level inversely correlates with metastatic progression and patient survival. We conclude that Ate1 knockout results in carcinogenic transformation of cultured fibroblasts, suggesting that in addition to its previously known activities Ate1 gene is essential for tumor suppression and also likely participates in suppression of metastatic growth.

Under saline conditions, higher plants restrict the accumulation of chloride ions (Cl(-)) in the shoot by regulating their transfer from the root symplast into the xylem-associated apoplast. To identify molecular mechanisms underpinning this phenomenon, we undertook a transcriptional screen of salt stressed Arabidopsis (Arabidopsis thaliana) roots. Microarrays, quantitative RT-PCR, and promoter-GUS fusions identified a candidate gene involved in Cl(-) xylem loading from the Nitrate transporter 1/Peptide Transporter family (NPF2.4). This gene was highly expressed in the root stele compared to the cortex, and its expression decreased after exposure to NaCl or abscisic acid. NPF2.4 fused to fluorescent proteins, expressed either transiently or stably, was targeted to the plasma membrane. Electrophysiological analysis of NPF2.4 in Xenopus laevis oocytes suggested that NPF2.4 catalyzed passive Cl(-) efflux out of cells and was much less permeable to NO3(-). Shoot Cl(-) accumulation was decreased following NPF2.4 artificial microRNA knockdown, whereas it was increased by overexpression of NPF2.4. Taken together, these results suggest that NPF2.4 is involved in long-distance transport of Cl(-) in plants, playing a role in the loading and the regulation of Cl(-) loading into the xylem of Arabidopsis roots during salinity stress.

Most prostate cancer cases remain indolent for long periods of time, but metastatic progression quickly worsens the prognosis and leads to mortality. However, little is known about what promotes the metastasis of prostate cancer and there is a lack of effective prognostic indicators, making it immensely difficult to manage options for treatment or surveillance. Arginyltransferase 1 (Ate1) is the enzyme mediating post-translational protein arginylation, which has recently been identified as a master regulator affecting many cancer-relevant pathways including stress response, cell cycle checkpoints, and cell migration/adhesion. However, the precise role of Ate1 in cancer remains unknown. In this study, we found the occurrence of metastasis of prostate cancer is inversely correlated with the levels of Ate1 protein and mRNA in the primary tumor. We also found that metastatic prostate cancer cell lines have a reduced level of Ate1 protein compared to non-metastatic cell lines, and that a depletion of Ate1 drives prostate cancer cells towards more aggressive pro-metastatic phenotypes without affecting proliferation rates. Furthermore, we demonstrated that a reduction of Ate1 can result from chronic stress, and that shRNA-reduced Ate1 increases cellular resistance to stress, and drives spontaneous and stress-induced genomic mutations. Finally, by using a prostate orthotropic xenograft mouse model, we found that a reduction of Ate1 was sufficient to enhance the metastatic phenotypes of prostate cancer cell line PC-3 in vivo. Our study revealed a novel role of Ate1 in suppressing prostate cancer metastasis, which has a profound significance for establishing metastatic indicators for prostate cancer, and for finding potential treatments to prevent its metastasis.

We present a lab that enables students to test the role of genes involved in the regulation of lateral roots growth in the model plant Arabidopsis thaliana. Here, students design an experiment that follows the effects of the hormone auxin on the stimulation of genes involved in the formation of lateral root initials. These genes, known as lateral organ boundary domain containing protein (LBD) genes, are upregulated in the presence of auxin as part of a multistep molecular and biochemically controlled pathway. Depending on which LBD gene is tested, and the stage of root development, expression patterns are localized in a discrete and punctate fashion at the site of lateral root initials (LBD33), or reveal a broader localization pattern (LBD16). Students view expression using the reporter gene GUS (beta-glucuronidase). Before GUS staining, students view root growth in a “pseudo-aseptic” agar-based environment that allows complete visualization of whole root development to determine the proper stage to test molecular expression. © 2014 by The International Union of Biochemistry and Molecular Biology, 42(3):XXXXX–XXXXX, 2014.

The histone acetyltransferase p300 is an important epigenetic factor known to regulate gene silencing, DNA repair, and cell cycle. Altered p300 expression is linked to cancerous phenotypes and has potential as both a biomarker and therapeutic target. Existing anti-cancer therapies such as histone deacetylase inhibitors (vorinostat, valproic acid, trichostatin A) are known to affect p300 levels and activity. Understanding how p300 affects cancerous and metastatic development is crucial to optimizing and advancing these treatments. However, whether p300 acts as a tumor suppressor or promoter is still controversial. To address this issue, we stably knocked down p300 levels in MCF-7, BT 474 and MDA MB 231 to 30-40% endogenous levels to directly examine p300's effects on tumorigenicity. Our experiments show loss of p300 significantly increased cell motility in the scratch assay (p To identify targets of p300 that might regulate its anti-tumor effect, we observed that miR-let-7c was downregulated in KD-p300 MCF-7 by 70% (p Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-06-04.

The architecture of plant roots affects essential functions including nutrient and water uptake, soil anchorage, and symbiotic interactions. Root architecture comprises many features that arise from the growth of the primary and lateral roots. These root features are dictated by the genetic background but are also highly responsive to the environment. Thus, root system architecture (RSA) represents an important and complex trait that is highly variable, affected by genotype × environment interactions, and relevant to survival/performance. Quantification of RSA in Arabidopsis (Arabidopsis thaliana) using plate-based tissue culture is a very common and relatively rapid assay, but quantifying RSA represents an experimental bottleneck when it comes to medium- or high-throughput approaches used in mutant or genotype screens. Here, we present RootScape, a landmark-based allometric method for rapid phenotyping of RSA using Arabidopsis as a case study. Using the software AAMToolbox, we created a 20-point landmark model that captures RSA as one integrated trait and used this model to quantify changes in the RSA of Arabidopsis (Columbia) wild-type plants grown under different hormone treatments. Principal component analysis was used to compare RootScape with conventional methods designed to measure root architecture. This analysis showed that RootScape efficiently captured nearly all the variation in root architecture detected by measuring individual root traits and is 5 to 10 times faster than conventional scoring. We validated RootScape by quantifying the plasticity of RSA in several mutant lines affected in hormone signaling. The RootScape analysis recapitulated previous results that described complex phenotypes in the mutants and identified novel gene × environment interactions.

Plants have a high intrinsic capacity to regenerate from adult tissues, with the ability to reprogram adult cell fates. In contrast, epigenetic mechanisms have the potential to stabilize cell identity and maintain tissue organization. The question is whether epigenetic memory creates a barrier to reprogramming that needs to be erased or circumvented in plant regeneration. Early evidence suggests that, while chromatin dynamics impact gene expression in the meristem, a lasting constraint on cell fate is not established until late stages of plant cell differentiation. It is not yet clear whether the plasticity of plant cells arises from the ability of cells to erase identity memory or to deploy cells that may exhibit cellular specialization but still lack an epigenetic restriction on cell fate alteration.

The root meristem has a centrally located group of mitotically quiescent cells, to which current models assign a stem cell organizer function. However, evidence is emerging for decentralized control of stem cell activity, whereby self-renewing behavior emerges from the lack of cell displacement at the border of opposing differentiation gradients. We term this a "stagnation" model due to its reliance on passive mechanics. The position of stem cells is established by two opposing axes that reciprocally control each other's differentiation. Such broad tissue organization programs would allow plants, like some animal systems, to rapidly reconstitute stem cells from non-stem-cell tissues.

Plants often make the same organ in different development contexts. Roots are a quintessential example, with embryonic, primary, lateral, adventitious, and regenerative roots common to many plants. The cellular origins and early morphologies of different roots can vary greatly, but the adult structures can be remarkably similar. Recent studies have highlighted the diversity of mechanisms that can initiate roots while late patterning mechanisms are frequently shared. In the middle stages when patterning emerges, evidence shows that antagonistic auxin-cytokinin interactions regulate tissue patterns in root embryogenesis, vascular organization, and regeneration but it is not yet clear if a common ontogeny for the root body plan exists.

Plant researchers have speculated about the need for mechanisms to lock-down cell fate in late development. In PRC2 mutants, specialized, endoreplicated root hair cells differentiate normally but later revert to an embryo-like state.

Single-cell transcriptomics has been employed in a growing number of animal studies, but the technique has yet to be widely used in plants. Nonetheless, early studies indicate that single-cell RNA-seq protocols developed for animal cells produce informative datasets in plants. We argue that single-cell transcriptomics has the potential to provide a new perspective on plant problems, such as the nature of the stem cells or initials, the plasticity of plant cells, and the extent of localized cellular responses to environmental inputs. Single-cell experimental outputs require different analytical approaches compared with pooled cell profiles and new tools tailored to single-cell assays are being developed. Here, we highlight promising new single-cell profiling approaches, their limitations as applied to plants, and their potential to address fundamental questions in plant biology.

For the nematode Caenorhabditis elegans, automated selection of animals of specific genotypes from a mixed pool has become essential for genetic interaction or chemical screens. To date, such selection has been accomplished using specialized instruments. However, access to such dedicated equipment is not common. Here we describe live animal fluorescence-activated cell sorting (laFACS), a protocol for automatic selection of live first larval stage (L1) animals using a standard FACS system. We show that FACS can be used for the precise identification of GFP-expressing and non-GFP-expressing subpopulations and can accomplish high-speed sorting of live animals. We have routinely collected 100,000 or more homozygotes from a mixed starting population within 2 h, and with greater than 99% purity. The sorted animals continue to develop normally, making this protocol ideally suited for the isolation of terminal mutants for use in genetic interaction or chemical genetic screens.

Mutagenesis reporters are critical for quantifying genome stability. However, current methods rely on cell survival/death to report mutation, which takes weeks and prevents evaluation of acute or time-dependent changes. Existing methods also have other limitations, such as cell type restrictions. Using our discovery that mCherryFP fluorescence depends on residue Trp98, we replaced this codon with a stop codon to generate a mutation biosensor (termed CherryOFF), with a green fluorescence protein (GFP) as an internal control. We found that the red fluorescence of this biosensor is activated by a specific A/T-G/C nucleotide transition. Compared with the established hypoxanthine phosphoribosyl transferase assay, our reporter has similar or better ability to detect changes of mutation frequency induced by physical/chemical mutagens or manipulation of mutation-related genes. Furthermore, CherryOFF-GFP can report mutagenesis independently of cell-death events, can be adapted to many cell types, and can generate readouts within 1 day for the measurement of acute or time-dependent events.

Plants are under constant attack from insects, microbes, and other physical assaults that damage or remove body parts. Regeneration is one common strategy among plants to repair their body plan. How do organisms that are proficient at regeneration adapt their developmental programs for repatterning tissues? A new body of research employing high resolution imaging together with cell-fate markers has led to new insights into the tissues competent to regenerate and the mechanisms that re-establish pattern. In a parallel to new findings in metazoan systems, recent work in plants shows that regeneration programs commonly thought to rely on dedifferentiated cells do not need to reprogram to a ground state. Imaging studies that track the expression of regulators of the plant's proliferative centers, meristems, in conjunction with mutant analysis have shed new light on the earliest organizational cues during regenerative organ formation. One promise of plant regeneration studies is to reveal the common design attributes of programs that pattern similar organs in different developmental contexts.

SummaryDivision of the Arabidopsis zygote defines two fundamentally different developmental domains, the proembryo and suspensor. The resulting boundary separates domain-specific gene expression, and a signal originating from the proembryo instructs the suspensor to generate the root stem cell niche. While root induction is known to require the phytohormone auxin and the Auxin Response Factor MONOPTEROS, it has remained largely elusive how the two domains involved in this process are initially specified. Here, we show that the GATA factor HANABA TARANU (HAN) is required to position the inductive proembryo boundary. Mutations in HAN cause a coordinated apical shift of gene expression patterns, revealing that HAN regulates transcription in the basal proembryo. Key auxin transporters are affected as early as the 8 cell stage, resulting in apical redistribution of auxin. Remarkably, han embryos eventually organize a root independent of MONOPTEROS and the suspensor around a new boundary marked by the auxin maximum.

Glutamate is believed to be the primary excitatory neurotransmitter in the vertebrate retina, and its fast postsynaptic effects are elicited by activating NMDA-, kainate-, or AMPA-type glutamate receptors. We have characterized the ionotropic glutamate receptors present on retinal horizontal cells of the skate, which possess a unique all-rod retina simplifying synaptic circuitry within the outer plexiform layer (OPL). Isolated external horizontal cells were examined using whole-cell voltage-clamp techniques. Glutamate and its analogues kainate and AMPA, but not NMDA, elicited dose-dependent currents. The AMPA receptor antagonist GYKI 52466 at 100μmabolished glutamate-elicited currents. Desensitization of glutamate currents was removed upon coapplication of cyclothiazide, known to potentiate AMPA receptor responses, but not by concanavalin A, which potentiates kainate receptor responses. The dose–response curve to glutamate was significantly broader in the presence of the desensitization inhibitor cyclothiazide. Polyclonal antibodies directed against AMPA receptor subunits revealed prominent labeling of isolated external horizontal cells with the GluR2/3 and GluR4 antibodies. 1-Naphthylacetyl spermine, known to block calcium-permeable AMPA receptors, significantly reduced glutamate-gated currents of horizontal cells. Downregulation of glutamate responses was induced by increasing extracellular ion concentrations of Zn2+and H+. The present study suggests that Ca2+-permeable AMPA receptors likely play an important role in shaping the synaptic responses of skate horizontal cells and that alterations in extracellular concentrations of calcium, zinc, and hydrogen ions have the potential to regulate the strength of postsynaptic signals mediated by AMPA receptors within the OPL.

Transient genetic modification of plant protoplasts is a straightforward and rapid technique for the study of numerous aspects of plant biology. Recent studies in metazoan systems have utilized cell-based assays to interrogate signal transduction pathways using high-throughput methods. Plant biologists could benefit from new tools that expand the use of cell culture for large-scale analysis of gene function. We have developed a system that employs fluorescent positive selection in combination with flow cytometric analysis and fluorescence-activated cell sorting to isolate responses in the transformed protoplasts exclusively. The system overcomes the drawback that transfected protoplast suspensions are often a heterogeneous mix of cells that have and have not been successfully transformed. This Gateway-compatible system enables high-throughput screening of genetic circuitry using overexpression. The incorporation of a red fluorescent protein selection marker enables combined utilization with widely available green fluorescent protein (GFP) tools. For instance, such a dual labeling approach allows cytometric analysis of GFP reporter gene activation expressly in the transformed cells or fluorescence-activated cell sorting-mediated isolation and downstream examination of overexpression effects in a specific GFP-marked cell population. Here, as an example, novel uses of this system are applied to the study of auxin signaling, exploiting the red fluorescent protein/GFP dual labeling capability. In response to manipulation of the auxin response network through overexpression of dominant negative auxin signaling components, we quantify effects on auxin-responsive DR5∷GFP reporter gene activation as well as profile genome-wide transcriptional changes specifically in cells expressing a root epidermal marker.

Multicellular organisms possessing relatively long life spans are subjected to diverse, constant, and often intense intrinsic and extrinsic challenges to their survival. Animal and plant tissues wear out as part of normal physiological functions and can be lost to predators, disease, and injury. Both kingdoms survive this wide variety of insults by strategies that include the maintenance of adult stem cells or the induction of stem cell potential in differentiated cells. Repatterning mechanisms often deploy embryonic genes, but the question remains in both plants and animals whether regeneration invokes embryogenesis, generic patterning mechanisms, or unique circuitry comprised of well-established patterning genes.

The organs of multicellular species consist of cell types that must function together to perform specific tasks. One critical organ function is responding to internal or external change. Some cell-specific responses to changes in environmental conditions are known, but the scale of cell-specific responses within an entire organ as it perceives an environmental flux has not been well characterized in plants or any other multicellular organism. Here, we use cellular profiling of five Arabidopsis root cell types in response to an influx of a critical resource, nitrogen, to uncover a vast and predominantly cell-specific response. We show that cell-specific profiling increases sensitivity several-fold, revealing highly localized regulation of transcripts that were largely hidden from previous global analyses. The cell-specific data revealed responses that suggested a coordinated developmental response in distinct cell types or tissues. One example is the cell-specific regulation of a transcriptional circuit that we showed mediates lateral root outgrowth in response to nitrogen via microRNA167, linking small RNAs to nitrogen responses. Together, these results reveal a previously cryptic component of cell-specific responses to nitrogen. Thus, the results make an important advance in our understanding of how multicellular organisms cope with environmental change at the cell level.

Summary Plant organogenesis requires control over division planes and anisotropic cell wall growth, which each require spatial patterning of cells. Polyhedral plant cells can display complex patterning in which individual faces are established as biochemically distinct domains by endomembrane trafficking. We now show that, during organogenesis, the Arabidopsis endomembrane system specifies an important additional cellular spatial domain: the geometric edges. Previously unidentified membrane vesicles lying immediately beneath the plasma membrane at cell edges were revealed through localization of RAB-A5c, a plant GTPase of the Rab family of membrane-trafficking regulators. Specific inhibition of RAB-A5c activity grossly perturbed cell geometry in developing lateral organs by interfering independently with growth anisotropy and cytokinesis without disrupting default membrane trafficking. The initial loss of normal cell geometry can be explained by a failure to maintain wall stiffness specifically at geometric edges. RAB-A5c thus meets a requirement to specify this cellular spatial domain during organogenesis., Graphical Abstract, Highlights • Plant cells possess a discrete class of vesicles that marks their geometric edges • These vesicles are defined by a Rab GTPase variant that is unique to plants • Inhibiting the activity of this GTPase disrupts growth anisotropy and morphogenesis • Edge-directed traffic is a crucial patterning principle, augmenting facial polarity, Organogenesis requires plant cells to adjust their shape through coordinated anisotropic growth of shared walls on individual polyhedral faces. Kirchhelle et. al. now show that the geometric edges of cells represent an additional and important spatial domain, specified by a plant Rab GTPase activity that is essential for morphogenesis.

Plants form the basis of the food webs that sustain animal life. Exogenous factors, such as nutrients and sunlight, and endogenous factors, such as hormones, cooperate to control both the growth and the development of plants. We assessed how Arabidopsis thaliana integrated nutrient and hormone signaling pathways to control root growth and development by investigating the effects of combinatorial treatment with the nutrients nitrate and ammonium; the hormones auxin, cytokinin, and abscisic acid; and all binary combinations of these factors. We monitored and integrated short-term genome-wide changes in gene expression over hours and longterm effects on root development and architecture over several days. Our analysis revealed trends in nutrient and hormonal signal cross-talk and feedback, including responses that exhibited logic gate behavior, which means that they were triggered only when specific combinations of signals were present. From the data, we developed a multivariate network model comprising the signaling molecules, the early gene expression modulation, and the subsequent changes in root phenotypes. This multivariate network model pinpoints several genes that play key roles in the control of root development and may help understand how eukaryotes manage multifactorial signaling inputs.

Summary Plant roots can regenerate after excision of their tip, including the stem cell niche. To determine which developmental program mediates such repair, we applied a combination of lineage tracing, single-cell RNA sequencing, and marker analysis to test different models of tissue reassembly. We show that multiple cell types can reconstitute stem cells, demonstrating the latent potential of untreated plant cells. The transcriptome of regenerating cells prior to stem cell activation resembles that of an embryonic root progenitor. Regeneration defects are more severe in embryonic than in adult root mutants. Furthermore, the signaling domains of the hormones auxin and cytokinin mirror their embryonic dynamics and manipulation of both hormones alters the position of new tissues and stem cell niche markers. Our findings suggest that plant root regeneration follows, on a larger scale, the developmental stages of embryonic patterning and is guided by spatial information provided by complementary hormone domains.

Phenotypic plasticity is presumed to be involved in adaptive change toward species diversification. We thus examined how candidate genes underlying natural variation across populations might also mediate plasticity within an individual. Our implementation of an integrative "plasticity space" approach revealed that the root plasticity of a single Arabidopsis accession exposed to distinct environments broadly recapitulates the natural variation "space." Genome-wide association mapping identified the known gene PHOSPHATE 1 (PHO1) and other genes such as Root System Architecture 1 (RSA1) associated with differences in root allometry, a highly plastic trait capturing the distribution of lateral roots along the primary axis. The response of mutants in the Columbia-0 background suggests their involvement in signaling key modulators of root development including auxin, abscisic acid, and nitrate. Moreover, genotype-by-environment interactions for the PHO1 and RSA1 genes in Columbia-0 phenocopy the root allometry of other natural variants. This finding supports a role for plasticity responses in phenotypic evolution in natural environments.

SummaryDevelopmental transitions can be described in terms of morphology and the roles of individual genes, but also in terms of global transcriptional and epigenetic changes. Temporal dissections of transcriptome changes, however, are rare for intact, developing tissues. We used RNA sequencing and microarray platforms to quantify gene expression from labeled cells isolated by fluorescence-activated cell sorting to generate cell-type-specific transcriptomes during development of an adult stem-cell lineage in the Arabidopsis leaf. We show that regulatory modules in this early lineage link cell types that had previously been considered to be under separate control and provide evidence for recruitment of individual members of gene families for different developmental decisions. Because stomata are physiologically important and because stomatal lineage cells exhibit exemplary division, cell fate, and cell signaling behaviors, this dataset serves as a valuable resource for further investigations of fundamental developmental processes.

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Self-referencing H(+)-selective microelectrodes were used to measure extracellular H(+) fluxes from horizontal cells isolated from the skate retina. A standing H(+) flux was detected from quiescent cells, indicating a higher concentration of free hydrogen ions near the extracellular surface of the cell as compared to the surrounding solution. The standing H(+) flux was reduced by removal of extracellular sodium or application of 5-(N-ethyl-N-isopropyl) amiloride (EIPA), suggesting activity of a Na(+)-H(+) exchanger. Glutamate decreased H(+) flux, lowering the concentration of free hydrogen ions around the cell. AMPA/kainate receptor agonists mimicked the response, and the AMPA/kainate receptor antagonist 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) eliminated the effects of glutamate and kainate. Metabotropic glutamate agonists were without effect. Glutamate-induced alterations in H(+) flux required extracellular calcium, and were abolished when cells were bathed in an alkaline Ringer solution. Increasing intracellular calcium by photolysis of the caged calcium compound NP-EGTA also altered extracellular H(+) flux. Immunocytochemical localization of the plasmalemma Ca(2+)-H(+)-ATPase (PMCA pump) revealed intense labelling within the outer plexiform layer and on isolated horizontal cells. Our results suggest that glutamate modulation of H(+) flux arises from calcium entry into cells with subsequent activation of the plasmalemma Ca(2+)-H(+)-ATPase. These neurotransmitter-induced changes in extracellular pH have the potential to play a modulatory role in synaptic processing in the outer retina. However, our findings argue against the hypothesis that hydrogen ions released by horizontal cells normally act as the inhibitory feedback neurotransmitter onto photoreceptor synaptic terminals to create the surround portion of the centre-surround receptive fields of retinal neurones.

A global map of gene expression within an organ can identify genes with coordinated expression in localized domains, thereby relating gene activity to cell fate and tissue specialization. Here, we present localization of expression of more than 22,000 genes in the Arabidopsis root. Gene expression was mapped to 15 different zones of the root that correspond to cell types and tissues at progressive developmental stages. Patterns of gene expression traverse traditional anatomical boundaries and show cassettes of hormonal response. Chromosomal clustering defined some coregulated genes. This expression map correlates groups of genes to specific cell fates and should serve to guide reverse genetics.

The definition of cell identity is a central problem in biology. While single-cell RNA-seq provides a wealth of information regarding cell states, better methods are needed to map their identity, especially during developmental transitions. Here, we use repositories of cell type-specific transcriptomes to quantify identities from single-cell RNA-seq profiles, accurately classifying cells from Arabidopsis root tips and human glioblastoma tumors. We apply our approach to single cells captured from regenerating roots following tip excision. Our technique exposes a previously uncharacterized transient collapse of identity distant from the injury site, demonstrating the biological relevance of a quantitative cell identity index. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0580-x) contains supplementary material, which is available to authorized users.

A bioinformatics approach is used to analyze the degree of conservation between upstream non-coding regions of cauliflower ( Brassica oleracea ) and Arabidopsis. The level of homology suggests that comparison of these two species could reveal functional cis-regulatory elements. There is growing

International audience; The dynamic nature of gene regulatory networks allows cells to rapidly respond to environmental change. However, the underlying temporal connections are missed, even in kinetic studies, as transcription factor (TF) binding within at least one time point is required to identify primary targets. The TF-regulated but unbound genes are dismissed as secondary targets. Instead, we report that these genes comprise transient TF-target interactions most relevant to rapid signal transduction. We temporally perturbed a master TF (Basic Leucine Zipper 1, bZIP1) and the nitrogen (N) signal it transduces and integrated TF regulation and binding data from the same cell samples. Our enabling approach could identify primary TF targets based solely on gene regulation, in the absence of TF binding. We uncovered three classes of primary TF targets: (i) poised (TF-bound but not TF-regulated), (ii) stable (TF-bound and TF-regulated), and (iii) transient (TF-regulated but not TF-bound), the largest class. Unexpectedly, the transient bZIP1 targets are uniquely relevant to rapid N signaling in planta, enriched in dynamic N-responsive genes, and regulated by TF and N signal interactions. These transient targets include early N responders nitrate transporter 2.1 and NIN-like protein 3, bound by bZIP1 at 1-5 min, but not at later time points following TF perturbation. Moreover, promoters of these transient targets are uniquely enriched with cis-regulatory motifs coinherited with bZIP1 binding sites, suggesting a recruitment role for bZIP1. This transient mode of TF action supports a classic, but forgotten, "hit-and-run" transcription model, which enables a "catalyst TF" to activate a large set of targets within minutes of signal perturbation.

An unprecedented opportunity exists to decipher transcriptional regulation by combining computational analysis of large-scale gene expression with knowledge of complete genomic sequence. The logical basis for this research is the now well-established fact that gene expression is controlled by specific interactions between regulatory proteins, transcription factors, and short sequences in the regulatory regions of genes to which they bind, cis elements (Arnone and Davidson 1997). Taking a reverse perspective, several computational techniques have used expression data to help focus the search for cis elements within the vast expanse of genomic sequence (for review, see Zhang 1999). We describe a simple computational approach that identifies cis elements and the factors that are likely to bind them by finding a high correlation between the expression of a given transcription factor and the sum of expression patterns of a group of genes that share a motif in their regulatory regions. Describing the mechanisms behind gene regulation has enormous implications for understanding development and designing therapies for genetic diseases in humans but the first steps are now focused on defining the primary level of regulatory interactions. Microarray technology has permitted genomewide expression data to be collected in a single experiment (Schena et al. 1995; Lockhart et al. 1996; DiRisi et al. 1996). For instance, in Saccharomyces cerevisiae, several public databases exist that report the expression level of virtually every transcript at different points during a developmental or metabolic time course (e.g., Chu et al. 1998; Spellman et al. 1998). With the complete sequence of S. cerevisiae available, it is also possible to retrieve the putative upstream regulatory sequence of any gene. One important approach to identifying cis elements has been to cluster genes according to their expression patterns and then search for potential regulatory motifs in the upstream regions of gene clusters (Brazma et al. 1998; Roth et al. 1998; Spellman et al. 1998; van Heldon 1998; Zhang 1999). Spellman et al. (1998) used cDNA microarrays to measure mRNA transcript levels in synchronized yeast cells at several time points in the cell cycle. Genes were grouped into expression profiles using Pearson correlation and their upstream regions were searched for over-represented, degenerate motifs using a modified Gibbs sampling algorithm. The technique yielded cis elements that are known to play a role in cell-cycle regulation, suggesting it could predict novel binding sites with functional roles. However, motif searching based on clustered genes eliminates useful data when gene regulation is complex. For instance, the expression pattern of a particular gene may be due to a combination of different regulatory elements conferring different effects at different times or in different tissues (Yuh et al. 1998; Flores et al. 2000; Halfon et al. 2000; Xu et al. 2000). Thus, genes may share certain functional cis elements in their regulatory regions but still differ in their overall expression due to other, nonshared, cis elements. In a method developed independently, Bussemaker et al. (2001) assumed that each binding site makes an additive contribution to the expression of a gene in a given experimental setting. That is, Gi = Σj Nij Cj, where Gi is the normalized expression value of gene i at a given experimental point, Nij is the number of times binding site Bj appears on the promoter region of gene i, and Cj is the coefficient for binding site Bj for a particular experiment. An important assumption of this method is that each binding site B contributes the positive or negative influence on expression for every gene as represented by its coefficient. That implies, for example, that if two binding sites B and B‘ happen to have the same coefficients and if a promoter for gene G has both, then replacing each instance of B by B‘ will result in the same expression level of gene G. We have developed a technique that decomposes promoter regions into reading frames of modest length (e.g., 6–7 bp) that represent the entire set of nondegenerate potential cis elements for a given set of expressed genes. For each such motif z, we add other motifs having degeneracy at each possible position of z. Those are the set of potential cis elements. (We conducted some computational experiments with motifs as large as 16, with 10 degenerate elements.) Then, we calculate correlations between the expression of known transcription factors and the composite expression of genes with respect to specific potential cis elements (Fig. ​(Fig.1).1). In an experiment, the composite expression with respect to a motif z is defined as the sum of all expression values of those genes containing z in their promoter regions. The expression pattern of a known transcription factor is then compared with the composite expressions of each potential cis element found in the promoters of the genes under study. The motifs whose composite expression correlates best (over a series of experiments) to a transcription factor constitute the best candidate binding sites for that transcription factor. Figure 1 The method for correlating a transcription factor with a regulatory motif is based on creating a composite expression of genes for each putative cis element. The regulatory region of all expressed genes are scanned and each frame of a given size (in this ... The weighted value of cis element motifs, which we call the composite expression, is not influenced by genes whose promoters have the cis element but are not expressed (in contrast, see Bussemaker et al. 2001). The basis for this formulation is that a cis element may induce expression on some promoters but not on others that, for instance, lack other cis elements needed for expression or contain bound repressor elements. This is one way to account for combinatorial mechanisms in gene regulation. In our algorithm, the composite weight of a cis element is not a measure of how well the motif explains overall expression but rather has meaning only in its correlation to the expression of a single transcription factor over a series of experiments. A critical assumption of our approach is that there is a quantitative response to a transcription factor’s expression level by at least some of its immediate downstream targets. This assumption incorporates two potential effects. (1) As a transcription factor increases in concentration, the mRNAs it induces also increase in concentration (DiRisi et al. 1997; Chu and Herskowitz 1998). For instance, a reporter gene fused to a promoter with GCN4-responsive cis elements showed increases in activity that were proportional to increases in GCN4 mRNA levels during histidine starvation (Albrecht et al. 1998). (2) Alternatively, a transcription factor may induce more genes at a higher concentration, possibly due to low-affinity binding sites requiring high transcription factor concentration for induction (Driever et al. 1989). Another one of our assumptions is that mRNA expression accurately reflects relative levels of transcription factor proteins. Although there is not a strict concordance between RNA expression and protein concentration, numerous studies have shown that there is usually a very good correlation between the RNA expression level of a transcription factor and its protein concentration. Correlations between a transcription factor and a composite expression pattern can be computed with data from a series of microarray experiments, which may be conducted at various times during a developmental process, under differing conditions, or on different cell types in a multicellular organism. Positive correlations predict induction, whereas negative correlations predict repression. At present, we restrict our analysis of program performance to induction and defer repression to future work. Because of the number of correlations that are measured, it is likely that some correlations do in fact arrive by chance. However, we consider false correlations acceptable if the correct binding sites rank within the top 10 highest candidates. Here, we evaluate our program on several data sets from experiments on yeast comparing our results with known transcription factor binding sites.

International audience; Phenotypic plasticity is presumed to be involved in adaptive change toward species diversification. We thus examined how candidate genes underlying natural variation across populations might also mediate plasticity within an individual. Our implementation of an integrative "plasticity space" approach revealed that the root plasticity of a single Arabidopsis accession exposed to distinct environments broadly recapitulates the natural variation "space." Genome-wide association mapping identified the known gene PHOSPHATE 1 (PHO1) and other genes such as Root System Architecture 1 (RSA1) associated with differences in root allometry, a highly plastic trait capturing the distribution of lateral roots along the primary axis. The response of mutants in the Columbia-0 background suggests their involvement in signaling key modulators of root development including auxin, abscisic acid, and nitrate. Moreover, genotype-by-environment interactions for the PHO1 and RSA1 genes in Columbia-0 phenocopy the root allometry of other natural variants. This finding supports a role for plasticity responses in phenotypic evolution in natural environments.

A map of cell type-specific auxin responses The transcriptional response to auxin was analyzed in four root cell types. The newly obtained data were cross-referenced with spatial expression maps to examine auxin's role in regulating gene expression in the root meristem., The majority of the thousands of auxin-responsive genes in the Arabidopsis thaliana root show a spatial bias in their induction or repression by auxin treatment. Auxin promotes the expression of cell-identity markers for the developing xylem and quiescent center, whereas it inhibits markers for the maturing xylem, cortex and trichoblasts. Relative induction or repression by auxin predicts expression along the longitudinal axis of the root., In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin-responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue-specific transcriptional regulation of cell-identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin-response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome-level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development.