Regulation of Stomatal Development by Stomatal Lineage miRNAs
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ABSTRACT:
PROVIDER: PRJNA591466 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10528220.fastq.gz | Fastqsanger.gz | |||
| SRR10528221.fastq.gz | Fastqsanger.gz | |||
| SRR10528222.fastq.gz | Fastqsanger.gz | |||
| SRR10528223.fastq.gz | Fastqsanger.gz | |||
| SRR10528224.fastq.gz | Fastqsanger.gz |
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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:Stomata in the plant epidermis play a critical role in growth and survival by controlling gas exchange, transpiration, and immunity to pathogens. Plants modulate stomatal cell fate and patterning through key transcriptional factors and signaling pathways. MicroRNAs (miRNAs) are known to contribute to developmental plasticity in multicellular organisms; however, no miRNAs appear to target the known regulators of stomatal development. It remains unclear as to whether miRNAs are involved in stomatal development. Here, we report highly dynamic, developmentally stage-specific miRNA expression profiles from stomatal lineage cells. We demonstrate that stomatal lineage miRNAs positively and negatively regulate stomatal formation and patterning to avoid clustered stomata. Target prediction of stomatal lineage miRNAs implicates potential cellular processes in stomatal development. We show that miR399-mediated PHO2 regulation, involved in phosphate homeostasis, contributes to the control of stomatal development. Our study demonstrates that miRNAs constitute a critical component in the regulatory mechanisms controlling stomatal development.
| S-EPMC7084132 | biostudies-literature
Project description:Plant cells are totipotent and hence can dedifferentiate and re-differentiate, making it possible to clone entire plant parts from a single cell. It is hence critical for plant cells to maintain specific cell-states during and after differentiation. Stomata, microscopic valves on the plant epidermis required for efficient gas exchange and water management, have emerged as a powerful model system for understanding how de novo lineage-specific stem cell initiate, proliferate and differentiate into specialized cell types during their development of the plant epidermis. The stomatal lineage emerged from a subpopulation of protodermal cells as meristemoid mother cells (MMCs) that undergoes an asymmetric entry division to give a rise meristemoid and its sister cell called the stomatal-lineage ground cell (SLGC). After several rounds of asymmetric cell division, meristemoids differentiate into round guard mother cells (GMC), which divide symmetrically and terminally differentiate into paired guard cells (GCs). We have adapted the INTACT (Isolation of Nuclei TAgged in Specific Cell Types) system to isolate each stomatal lineage-specific nuclei followed by ATACseq (Assay for Transposase-Accessible Chromatin). We showed that chromatin accessibility is dynamic throughout the stomatal lineage progression. Further, the analysis of TF binding sites in differentially accessible regions led to discover that combinatorial cis-regulatory elements and transcription factor circuits controls lineage specific cell state transition during stomatal development.
2022-12-28 | GSE190753 | GEO
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: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. 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: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:Profiling chromatin accessibility during stomatal development
| PRJNA788402 | ENA
Project description:Purpose: Identify SLGC cell fate by transcriptomes Methods: Cells expressing SLGC markers (BASLp:BRX-YFP, BASLp:myrBRX-YFP and myrBRXp:myrBRX-YFP) and stomatal commitment stage marker (MUTEp:MUTE-YFP) were collected by FACS. 9dpg plants were used for protoplasting and subjected to cell sorting. Around 20,000/sample were cellected and used for library preparation. Results: SLGCs are renriched in mitotic genes. In addition, top candidates, DEK and MYB16 proteins function in SLGC cell divisions. Conclusions: SLGCs are division competent cells and the coordination of cell cycle and transcriptional regulation though DEK is important for maintaining the transition (SLGC) state during stomatal development.
2021-04-05 | GSE129938 | GEO