Cell-type specific transcriptome and histone modification dynamics during in situ cellular reprogramming in the Arabidopsis stomatal lineage [RNA-Seq]
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE118137 | GEO | 2019/10/08
REPOSITORIES: GEO
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Project description:Plants and plant cells exhibit extraordinary regenerative capacity, yet plant cells stably maintain their identities once acquired. Although this capacity was recognized more than 100 years ago, our mechanistic understanding of the establishment, maintenance, and erasure of cellular identities in plants remains limited. Here we develop a cell-type specific reprogramming system than can be probed at the genome-wide scale for alterations in gene expression and histone modifications before and during reprogramming. We show that the relationship between H3K27me3 and H3K4me3 and gene expression in a single cell type mirrors trends from more complex tissue, and that H3K27me3 dynamics is a critical regulator of guard cell identity. Further, guard cells can sense and resist inappropriate reprogramming, in part via regulation of the wounding response through H3K27me3. The matched single cell-type ChIP-seq and RNA-seq datasets created for this analysis also serve as a resource enabling inquiries into the dynamic and global-scale distribution of histone modifications.
2019-10-08 | GSE118136 | GEO
Project description:In plants, epidermal guard cells integrate and respond to numerous environmental signals to control stomatal pore apertures thereby regulating gas exchange. Chromatin structure controls transcription factor access to the genome, but whether large-scale chromatin remodeling occurs in guard cells during stomatal movements, and in response to the hormone abscisic acid (ABA) in general, remain unknown. Here we isolate guard cell nuclei from Arabidopsis thaliana plants to examine whether the physiological signals, ABA and CO2, regulate guard cell chromatin during stomatal movements. Our cell type specific analyses uncover patterns of chromatin accessibility specific to guard cells and define novel cis-regulatory sequences supporting guard cell specific gene expression. We find that ABA triggers extensive and dynamic chromatin remodeling in guard cells, roots, and mesophyll cells with clear patterns of cell-type specificity. DNA motif analyses uncover binding sites for distinct transcription factors enriched in ABA-induced and ABA-repressed chromatin. We identify the ABF/AREB bZIP-type transcription factors that are required for ABA-triggered chromatin opening in guard cells and implicate the inhibition of a set of bHLH-type transcription factors in controlling ABA-repressed chromatin. Moreover, we demonstrate that ABA and CO2 induce distinct programs of chromatin remodeling. We provide insight into the control of guard cell chromatin dynamics and propose that ABA-induced chromatin remodeling primes the genome for abiotic stress resistance.
2023-12-19 | GSE243470 | GEO
Project description:In plants, epidermal guard cells integrate and respond to numerous environmental signals to control stomatal pore apertures thereby regulating gas exchange. Chromatin structure controls transcription factor access to the genome, but whether large-scale chromatin remodeling occurs in guard cells during stomatal movements, and in response to the hormone abscisic acid (ABA) in general, remain unknown. Here we isolate guard cell nuclei from Arabidopsis thaliana plants to examine whether the physiological signals, ABA and CO2, regulate guard cell chromatin during stomatal movements. Our cell type specific analyses uncover patterns of chromatin accessibility specific to guard cells and define novel cis-regulatory sequences supporting guard cell specific gene expression. We find that ABA triggers extensive and dynamic chromatin remodeling in guard cells, roots, and mesophyll cells with clear patterns of cell-type specificity. DNA motif analyses uncover binding sites for distinct transcription factors enriched in ABA-induced and ABA-repressed chromatin. We identify the ABF/AREB bZIP-type transcription factors that are required for ABA-triggered chromatin opening in guard cells and implicate the inhibition of a set of bHLH-type transcription factors in controlling ABA-repressed chromatin. Moreover, we demonstrate that ABA and CO2 induce distinct programs of chromatin remodeling. We provide insight into the control of guard cell chromatin dynamics and propose that ABA-induced chromatin remodeling primes the genome for abiotic stress resistance.
2023-12-19 | GSE243472 | GEO
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: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:Drought and salt stress severely inhibit plant growth and development. However, the regulatory mechanisms of plants in response to these stresses are not fully understood. Here we find that the expression of a WRKY transcription factor WRKY46 is rapidly induced by drought, salt and oxidative stresses. Mutations of WRKY46 by T-DNA insertion lead to more sensitive to drought and salt stress, whereas, overexpression of WRKY46 exhibits hypersensitive in soil culture with higher water loss rate, but increased tolerance on the agar plates. ABA induced stomatal closing is impaired in the WRKY46 overexpressing line (OV46), which is potentially due to the lower ROS accumulation in the guard cells. Real-time qPCR and GUS activity assay further demonstrate that WRKY46 is expressed in guard cells, but its expression is not affected by dehydration treatment, suggesting different regulatory mechanisms for WRKY46 between guard cells and other WRKY46 expressed tissues. The stomatal movement and conductance assay indicate that WRKY46 is involved in light-dependent stomatal opening. Further microarray analysis reveals that WRKY46 regulates a set of genes involved in cellular osmoprotection and redox homeostasis under dehydration stress. Determinations of ROS and MDA content confirm its role in oxidative detoxification under stress. Furthermore, we find that WRKY46 modulates light-dependent starch metabolism in guard cells via regulating QQS gene expression. Taken together, we demonstrate that WRKY46 plays a role in modulating cellular osmoprotection and redox homeostasis under drought and salt stress, and functions independently in stomatal movement via regulating light-dependent starch metabolism and ROS levels in guard cells. We used microarrays to identify the certain downstream genes regulated by WRKY46 under normal and dehydration conditions.
2015-02-01 | GSE49418 | GEO
Project description:Drought and salt stress severely inhibit plant growth and development. However, the regulatory mechanisms of plants in response to these stresses are not fully understood. Here we find that the expression of a WRKY transcription factor WRKY46 is rapidly induced by drought, salt and oxidative stresses. Mutations of WRKY46 by T-DNA insertion lead to more sensitive to drought and salt stress, whereas, overexpression of WRKY46 exhibits hypersensitive in soil culture with higher water loss rate, but increased tolerance on the agar plates. ABA induced stomatal closing is impaired in the WRKY46 overexpressing line (OV46), which is potentially due to the lower ROS accumulation in the guard cells. Real-time qPCR and GUS activity assay further demonstrate that WRKY46 is expressed in guard cells, but its expression is not affected by dehydration treatment, suggesting different regulatory mechanisms for WRKY46 between guard cells and other WRKY46 expressed tissues. The stomatal movement and conductance assay indicate that WRKY46 is involved in light-dependent stomatal opening. Further microarray analysis reveals that WRKY46 regulates a set of genes involved in cellular osmoprotection and redox homeostasis under dehydration stress. Determinations of ROS and MDA content confirm its role in oxidative detoxification under stress. Furthermore, we find that WRKY46 modulates light-dependent starch metabolism in guard cells via regulating QQS gene expression. Taken together, we demonstrate that WRKY46 plays a role in modulating cellular osmoprotection and redox homeostasis under drought and salt stress, and functions independently in stomatal movement via regulating light-dependent starch metabolism and ROS levels in guard cells. We used microarrays to identify the certain downstream genes regulated by WRKY46 under normal and dehydration conditions. One-week-old Arabidopsis seedlings of wild-type Col-0 (WT) and WRKY46 overexpressing line (46T) with or without dehydration treatment for 1 h were harvested and used for RNA extraction and hybridization to Affymetrix Arabidopsis ATH1 microarrays. The experiment includes 3 biological replicates.
2015-02-01 | E-GEOD-49418 | biostudies-arrayexpress
Project description:Stomata open in response to light and close following exposure to abscisic acid (ABA). They regulate gas exchange between plants and atmosphere, allowing plants to adapt to changing environmental conditions. ABA binding to receptors initiates a signaling cascade that involves protein phosphorylation. Here we show that ABA induced phosphorylation of three basic helix-loop-helix (bHLH) transcription factors, called AKSs (ABA-RESPONSIVE KINASE SUBSTRATES; AKS1, AKS2, AKS3), in Arabidopsis guard cells, and that they facilitated stomatal opening through the transcription of genes encoding inwardly-rectifying K+ channels. aks1aks2-1 double mutant plants showed decreases in light-induced stomatal opening, K+ accumulation in response to light, activity of inwardly-rectifying K+ channels, and transcription of genes encoding major inwardly-rectifying K+ channels. Overexpression of POTASSIUM CHANNEL IN ARABIDOPSIS THALIANA 1 (KAT1), which encodes a major inwardly-rectifying K+ channel in guard cells, rescued the phenotype of aks1aks2-1 plants. AKS1 bound directly to the promoter of KAT1, an interaction that was attenuated after ABA-induced phosphorylation. The ABA agonist pyrabactin induced phosphorylation of AKSs. Our results demonstrate that the AKS family of bHLH transcription factors facilitates stomatal opening through transcription of genes encoding inwardly-rectifying K+ channels, and that ABA suppresses the activity of inwardly-rectifying K+ channel activity by triggering the phosphorylation of these transcription factors. To find the affect of AKS1 and AKS2 transcription factors on gene expression, Arabidopsis guard cell protoplasts from wild type and aks1aks2-1 mutant were compared. Three independent experiments were performed.
2013-06-17 | E-GEOD-46574 | biostudies-arrayexpress
Project description:Stomata open in response to light and close following exposure to abscisic acid (ABA). They regulate gas exchange between plants and atmosphere, allowing plants to adapt to changing environmental conditions. ABA binding to receptors initiates a signaling cascade that involves protein phosphorylation. Here we show that ABA induced phosphorylation of three basic helix-loop-helix (bHLH) transcription factors, called AKSs (ABA-RESPONSIVE KINASE SUBSTRATES; AKS1, AKS2, AKS3), in Arabidopsis guard cells, and that they facilitated stomatal opening through the transcription of genes encoding inwardly-rectifying K+ channels. aks1aks2-1 double mutant plants showed decreases in light-induced stomatal opening, K+ accumulation in response to light, activity of inwardly-rectifying K+ channels, and transcription of genes encoding major inwardly-rectifying K+ channels. Overexpression of POTASSIUM CHANNEL IN ARABIDOPSIS THALIANA 1 (KAT1), which encodes a major inwardly-rectifying K+ channel in guard cells, rescued the phenotype of aks1aks2-1 plants. AKS1 bound directly to the promoter of KAT1, an interaction that was attenuated after ABA-induced phosphorylation. The ABA agonist pyrabactin induced phosphorylation of AKSs. Our results demonstrate that the AKS family of bHLH transcription factors facilitates stomatal opening through transcription of genes encoding inwardly-rectifying K+ channels, and that ABA suppresses the activity of inwardly-rectifying K+ channel activity by triggering the phosphorylation of these transcription factors.
2013-06-17 | GSE46574 | GEO
Project description:Trimethylation of histone H3 lysine27 (H3K27me3) plays critical roles in regulating animal development, and in several cases, H3K27me3 is also required for the proper expression of developmentally important genes in plants. However, the extent to which H3K27me3 regulates plant genes on a genome-wide scale remains unknown. In addition, it is not clear whether the establishment and spreading of H3K27me3 occur through the same mechanisms in plants and animals. Here we identified regions containing H3K27me3 in the genome of the flowering plant Arabidopsis thaliana using a high-density whole-genome tiling microarray. The results suggest that H3K27me3 is a major silencing mechanism in plants that regulates an unexpectedly large number of genes in Arabidopsis (~4,400), and that the maintenance of H3K27me3 is largely independent of other epigenetic pathways such as DNA methylation or RNAi. Unlike in animals where H3K27m3 occupies large genomic regions, we found that H3K27m3 domains in Arabidopsis were largely restricted to the transcribed regions of single genes. Furthermore, unlike in animals systems, H3K27m3 domains were not preferentially associated with low nucleosome density regions. The results suggest that different mechanisms may underlie the establishment and spreading of H3K27me3 in plants and animals. Keywords: ChIP-chip
2007-04-17 | GSE7064 | GEO