Transcriptome analysis of stomatal lineage ground cells (SLGCs)
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE129938 | GEO | 2021/04/05
REPOSITORIES: GEO
Similar Datasets
Project description:Developmental transitions can be described in terms of morphology and individual genes expression patterns, but also in terms of global transcriptional and epigenetic changes. Most of the large-scale studies of such transitions, however, have only been possible in synchronized cell culture systems. Here we generate a cell type specific transcriptome of an adult stem-cell lineage in the Arabidopsis leaf using RNA sequencing and microarrays. RNA profiles of stomatal entry, commitment, and differentiating cells, as well as of mature stomata and the entire aerial epidermis give a comprehensive view of the developmental progression. To obtain pure cell populations corresponding to different stomatal lineage cell types we used Fluorescent Activated Cell Sorting (FACS) in combination with markers of early (SPCHp::SPCH-YFP, SSY), middle (MUTEp::nucGFP, MG), and late (FAMAp::GFP-FAMA, FGF) precursor stages, as well of mature stomata (enhancer trap E1728::GFP, E1728G) and a marker of the entire epidermis (ML1p::YFP-RCI2A, ML1Y). To minimize transcriptional differences due to age, all cell types were sorted from 14-day old aerial rosettes, and the specificity of expression pattern at this common time point confirmed via confocal microscopy. Total RNA was extracted from purified protoplasts (2,000 to 20,000 cells/replicate; 3 replicates/marker line) and transcript abundance measured using ATH1-121501 microarrays.
2015-04-06 | E-GEOD-58855 | biostudies-arrayexpress
Project description:Developmental transitions can be described in terms of morphology and individual genes expression patterns, but also in terms of global transcriptional and epigenetic changes. Most of the large-scale studies of such transitions, however, have only been possible in synchronized cell culture systems. Here we generate a cell type specific transcriptome of an adult stem-cell lineage in the Arabidopsis leaf using RNA sequencing and microarrays. RNA profiles of stomatal entry, commitment, and differentiating cells, as well as of mature stomata and the entire aerial epidermis give a comprehensive view of the developmental progression. To obtain pure cell populations corresponding to different stomatal lineage cell types we used Fluorescent Activated Cell Sorting (FACS) in combination with markers of early (SPCHp::SPCH-YFP, SSY), middle (MUTEp::nucGFP, MG), and late (FAMAp::GFP-FAMA, FGF) precursor stages, as well of mature stomata (enhancer trap E1728::GFP, E1728G) and a marker of the entire epidermis (ML1p::YFP-RCI2A, ML1Y). To minimize transcriptional differences due to age, all cell types were sorted from 10-day old aerial rosettes, and the specificity of expression pattern at this common time point confirmed via confocal microscopy. Total RNA was extracted from purified protoplasts (4,000 to 20,000 cells/replicate; 2 replicates/marker line; 3 replicates/SSY marker line) and transcript abundance measured using RNA sequencing.
2015-04-06 | E-GEOD-58856 | biostudies-arrayexpress
Project description:To identify new regulators of stomatal development, we assay the transcriptomes of plants bearing enriched stomatal lineage cells undergoing active divisions.
2024-03-01 | GSE226455 | GEO
Project description:Stomata are pores in the epidermis of plants that can open and close and allow for gas exchange vital for photosynthesis and regulate transpiration. Stomatal development is driven by a set of conserved bHLH transcription factors (SPCH, MUTE, FAMA, and their heterodimerization partners ICE1, SCRM2), that initiate and promote progression of cell fates in the stomatal lineage. Due to the shared ancestry of SPCH, MUTE and FAMA (subgroup Ia) and ICE1 and SCRM2 (subgroup IIIb) their DNA binding specificity is similar and there is some functional redundancy. However, individual bHLHs also have unique functions. For example, SPCH is required for initiation of the stomatal lineage, while FAMA is responsible for terminal differentiation of the guard cell pair. In grasses, the stomatal complex comprises the guard cell pair, and two flanking subsidiary cells. Recruitment of the latter from neighboring cell filed during development requires expression of MUTE. Remarkably, while MUTE is absolutely required for the promotion of guard mother cell fate in maize and rice, this is not the case in Brachypodium. This suggests that another TF can at least partially substitute for MUTE in this function. While different expression profiles of the bHLH dimers within the stomatal lineage may partially responsible for distinct functions of each pair, it is likely that each pair forms different transcriptional complexes and that interaction with other transcriptional regulators affects the dimer’s binding DNA binding and gene regulation properties. Given the differences in bHLH function between dicots and grasses and even within the grass family, we were interested in elucidating the protein interaction networks of the stomatal lineage regulators in Brachypodium. To this end, we performed co-immunoprecipitation coupled to LC-MS/MS of BdSPCH2-YFP, YFP-BdMUTE, YFP-BdFAMA, YFP-ICE1 and YFP-SCRM2 from the developmental zone of young B. distachyon leaves using GFP-Trap beads. All YFP-fusion proteins were expressed under the endogenous promoter in the Bd21-3 background. The only exception was BdICE1, which was expressed under the ZmUBI promoter, but was nevertheless mostly restricted to the stomatal lineage. As control lines we use the Bd21-3 wild type and a line expressing 3x YFPnls (nuclear YFP) under the MUTE promoter. Comparison of proteins enriched with the bHLH fusion proteins vs. the controls revealed overlapping and distinct putative interactors, which is in agreement with the assumption that these transcription factors have both shared and unique functions. Notably, in addition to the presumed hetero-dimerization partners, we found a number of other bHLH transcription factors that were identified with one or more of the bait proteins. This suggests the presence of a larger bHLH network acting in the stomatal lineage.
2023-03-11 | PXD035582 | Pride
Project description:Cell polarity is used to guide asymmetric divisions and create morphologically diverse cells. We find that two oppositely oriented cortical polarity domains present during the asymmetric divisions in the Arabidopsis stomatal lineage are reconfigured into polar domains marking ventral (pore-forming) and outward facing domains of maturing stomatal guard cells. Proteins that define these opposing polarity domains were used as baits in miniTurboID-based proximity labeling. Among differentially enriched proteins we find SOSEKIs and their effector ANGUSTIFOLIA, protein kinase CKII and LC8-type DYNEIN LIGHT CHAIN1 as polar scaffolds. Using AI-facilitated protein structure prediction models, we identify their potential interaction interfaces. Functional and localization analysis of polarity protein OPL2 and its newly discovered partners suggest a positive interaction with mitotic microtubules and a potential role in cytokinesis. This combination of cutting-edge proteomics and structural modeling with live cell imaging provides insights into how polarity is rewired in different cell types and cell cycle stages.
2024-03-21 | PXD050287 | Pride
Project description:Dynamic cell identities underlie flexible developmental programs. The stomatal lineages in the Arabidopsis leaf epidermis feature asynchronous and indeterminate divisions that can be modulated by environmental cues. The products of these lineages, stomatal guard cells and pavement cells, regulate plant-atmosphere exchanges, and the epidermis as a whole influences overall leaf growth. How flexibility is encoded in development of the stomatal lineage, and how cell fates are coordinated in the leaf are open questions. Here, we offer single-cell transcriptomes to uncover models of cell differentiation within Arabidopsis leaf tissue.
2021-04-05 | GSE167135 | GEO
Project description:We initiated a study to investigate the transcriptional profiles associated with cell states of the stomatal lineage. A stem-cell like precursor of stomata, a meristemoid. reiterates asymmetric divisions and renews itself before differentiating into guard cells. The transient and asynchronous nature of the meristemoid has made it difficult to study its molecular characteristics. Through combinatorial use of genetic resources that either arrest or constitutively drive stomatal cell-state progressions due to loss- or gain-of-function mutations in the key transcription factor genes, SPEECHLESS, MUTE, and SCRM, we obtained seedlings highly enriched in pavement cells, meristemoids, or stomata. Here we present transcriptome and genome-wide trends in gene regulation associated with each cell state and identify molecular signatures associated with meristemoids.
2011-11-08 | GSE29814 | GEO
Project description:Stomata in the plant epidermis play a vital role in growth and survival by controlling gas exchange and immunity to pathogens. A genetic frame of key transcriptional factors and cellular communication has been established, by which plants modulate stomatal cell fate and patterning. miRNAs contribute to functional and developmental plasticity in multicellular organisms. However, it remains very elusive as to whether miRNAs pitch in stomatal development. Here, we reveal dynamic miRNA expression profiles from stomatal lineage cells in a development stage-specific manner and show that stomatal lineage miRNAs positively and negatively regulate stomatal formation and pattern to avoid clustered and paired stomata. Target prediction of stomatal lineage miRNAs suggests potential cellular processes involved in stomatal development. Furthermore, dysregulation of stomatal lineage miRNAs and their target mRNAs disclose unexpected genetic pathways modulating stomatal development. Our study demonstrates that miRNAs constitute an additional layer in the complex regulatory mechanism of stomatal development.
2020-02-03 | GSE140918 | GEO
Project description:We initiated a study to investigate the transcriptional profiles associated with cell states of the stomatal lineage. A stem-cell like precursor of stomata, a meristemoid. reiterates asymmetric divisions and renews itself before differentiating into guard cells. The transient and asynchronous nature of the meristemoid has made it difficult to study its molecular characteristics. Through combinatorial use of genetic resources that either arrest or constitutively drive stomatal cell-state progressions due to loss- or gain-of-function mutations in the key transcription factor genes, SPEECHLESS, MUTE, and SCRM, we obtained seedlings highly enriched in pavement cells, meristemoids, or stomata. Here we present transcriptome and genome-wide trends in gene regulation associated with each cell state and identify molecular signatures associated with meristemoids. 12 samples are included in this study. Three biological replicates of 5-dag seedlings of speechless, scrm-D and scrm-D;mute were compared wild type seedlings for changes in gene expression.
2011-11-08 | E-GEOD-29814 | biostudies-arrayexpress
Project description:Lineage-specific stem cells are critical for the production and maintenance of specific cell types and tissues in multicellular organisms. In higher plants, the initiation and proliferation of stomatal stem cells is controlled by the basic helix-loop-helix transcription factor SPEECHLESS (SPCH). The stomatal stem cells and SPCH, which represent an innovation in seed plants, allow flexibility in the production of stomata, but how SPCH generates these stem cells is unclear. Here, we developed a highly sensitive chromatin immunoprecipitation (ChIP) assay and profiled the cell-type specific genome-wide targets of Arabidopsis SPCH in vivo. We found that SPCH directly controls key and novel regulators that drive cell fate and asymmetric cell divisions and enhances responsiveness to cell-cell communication. Our results provide molecular insights on how a master transcription factor generates an adult stem cell lineage that contributes to the success of land plants. Genome-wide identification of SPCH binidng sites
2014-09-04 | E-GEOD-57497 | biostudies-arrayexpress