RNA-seq analysis of gene expression levels duing callus formation on CIM using WT and lbd16-2
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE101321 | GEO | 2017/08/01
SECONDARY ACCESSION(S): PRJNA393995
REPOSITORIES: GEO
Similar Datasets
Project description:Plant regeneration could be achieved via formation of a pluripotent cell mass termed callus, nature of which is a group of fast-dividing root primordium cells. However, mechanisms that strictly control the stem cell fate transition in regeneration of callus remain elusive. Here we show that the Arabidopsis ISWI type chromatin remodelers specifically promote the second-step cell fate transition from root founder cells to root primordium cells in the leaf-to-callus transition. Leaf explants cultured in CIM from Col-0 or chr11-1 chr17-1 at time 0 and 8 days after culture (8 DAC) were used for RNA preparation. Microarray was performed using the AffymetrixGeneChip system. Three independent experiments were performed.
2014-05-15 | E-GEOD-57145 | biostudies-arrayexpress
Project description:In plant tissue culture, callus forms from detached explants in response to a high-auxin-to-low-cytokinin ratio on callus-inducing medium. Callus is a group of pluripotent cells because it can regenerate either roots or shoots in response to a low level of auxin on root-inducing medium or a high-cytokinin-to-low-auxin ratio on shoot-inducing medium, respectively1. However, our knowledge of the mechanism of pluripotency acquisition during callus formation is limited. On the basis of analyses at the single-cell level, we show that the tissue structure of Arabidopsis thaliana callus on callus-inducing medium is similar to that of the root primordium or root apical meristem, and the middle cell layer with quiescent centre-like transcriptional identity exhibits the ability to regenerate organs. In the middle cell layer, WUSCHEL-RELATED HOMEOBOX5 (WOX5) directly interacts with PLETHORA1 and 2 to promote TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 expression for endogenous auxin production. WOX5 also interacts with the B-type ARABIDOPSIS RESPONSE REGULATOR12 (ARR12) and represses A-type ARRs to break the negative feedback loop in cytokinin signalling. Overall, the promotion of auxin production and the enhancement of cytokinin sensitivity are both required for pluripotency acquisition in the middle cell layer of callus for organ regeneration.
2021-09-08 | GSE156991 | GEO
Project description:Profiling the transcriptome of the early stage of Arabidopsis callus induction variable_1 = root explants variable_2 = aerial organ explants variable_3 = 0 h on callus inducing medium variable_4 = 12 h on callus inducing medium variable_5 = 24 h on callus inducing medium variable_6 = 48 h on callus inducing medium variable_7 = 96 h on callus inducing medium
2012-07-22 | E-GEOD-29543 | biostudies-arrayexpress
Project description:In plant tissue culture, callus forms from detached explants in response to a high-auxin-to-low-cytokinin ratio on callus-inducing medium. Callus is a group of pluripotent cells because it can regenerate either roots or shoots in response to a low level of auxin on root-inducing medium or a high-cytokinin-to-low-auxin ratio on shoot-inducing medium, respectively1. However, our knowledge of the mechanism of pluripotency acquisition during callus formation is limited. On the basis of analyses at the single-cell level, we show that the tissue structure of Arabidopsis thaliana callus on callus-inducing medium is similar to that of the root primordium or root apical meristem, and the middle cell layer with quiescent centre-like transcriptional identity exhibits the ability to regenerate organs. In the middle cell layer, WUSCHEL-RELATED HOMEOBOX5 (WOX5) directly interacts with PLETHORA1 and 2 to promote TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 expression for endogenous auxin production. WOX5 also interacts with the B-type ARABIDOPSIS RESPONSE REGULATOR12 (ARR12) and represses A-type ARRs to break the negative feedback loop in cytokinin signalling. Overall, the promotion of auxin production and the enhancement of cytokinin sensitivity are both required for pluripotency acquisition in the middle cell layer of callus for organ regeneration.
2021-09-08 | GSE178354 | GEO
Project description:In plant tissue culture, callus forms from detached explants in response to a high-auxin-to-low-cytokinin ratio on callus-inducing medium. Callus is a group of pluripotent cells because it can regenerate either roots or shoots in response to a low level of auxin on root-inducing medium or a high-cytokinin-to-low-auxin ratio on shoot-inducing medium, respectively1. However, our knowledge of the mechanism of pluripotency acquisition during callus formation is limited. On the basis of analyses at the single-cell level, we show that the tissue structure of Arabidopsis thaliana callus on callus-inducing medium is similar to that of the root primordium or root apical meristem, and the middle cell layer with quiescent centre-like transcriptional identity exhibits the ability to regenerate organs. In the middle cell layer, WUSCHEL-RELATED HOMEOBOX5 (WOX5) directly interacts with PLETHORA1 and 2 to promote TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 expression for endogenous auxin production. WOX5 also interacts with the B-type ARABIDOPSIS RESPONSE REGULATOR12 (ARR12) and represses A-type ARRs to break the negative feedback loop in cytokinin signalling. Overall, the promotion of auxin production and the enhancement of cytokinin sensitivity are both required for pluripotency acquisition in the middle cell layer of callus for organ regeneration.
2021-09-08 | GSE156990 | GEO
Project description:Plant regeneration could be achieved via formation of a pluripotent cell mass termed callus, nature of which is a group of fast-dividing root primordium cells. However, mechanisms that strictly control the stem cell fate transition in regeneration of callus remain elusive. Here we show that the Arabidopsis ISWI type chromatin remodelers specifically promote the second-step cell fate transition from root founder cells to root primordium cells in the leaf-to-callus transition.
2014-05-15 | GSE57145 | GEO
Project description:Col-0 and ein2-1 seedlings were submerged for 1 hour and then leaf explants was incubated on CIM for 7 days. The upper half of the explants were harvested for the small RNA sequencing.
2022-08-06 | GSE210413 | GEO
Project description:Callus formation is usually a necessary step in regenerating a new plant from detached plant tissues, and the nature of the callus is similar to that of the root meristem. In this study, we intended to address the molecular basis that directs different plant tissues to form the root-meristem-like callus. We found that leaves, but not roots, of the Polycomb group (PcG) double mutant curly leaf-50 swinger-1 lost the ability to form a callus. Using ChIP-chip analysis, we identified genes that are changed markedly in the histone H3 lysine 27 trimethylation (H3K27me3) levels during callus formation from leaf explants. Among these genes, a number of leaf-regulatory genes were repressed through PcG-mediated H3K27me3. Conversely, certain auxin pathway genes and many root-regulatory genes were derepressed through H3K27 demethylation. Our data indicate that genome-wide H3K27me3 reprogramming, through the PcG-mediated H3K27me3 and the H3K27 demethylation pathways, is critical in directing cell fate transition. This submission represents the gene expression component of the study Leaves from 20-day-old seedlings of wild-type Col-0 and 20-DAC calli were used for RNA preparation.
2012-04-06 | E-GEOD-36479 | biostudies-arrayexpress
Project description:Callus formation is usually a necessary step in regenerating a new plant from detached plant tissues, and the nature of the callus is similar to that of the root meristem. In this study, we intended to address the molecular basis that directs different plant tissues to form the root-meristem-like callus. We found that leaves, but not roots, of the Polycomb group (PcG) double mutant curly leaf-50 swinger-1 lost the ability to form a callus. Using ChIP-chip analysis, we identified genes that are changed markedly in the histone H3 lysine 27 trimethylation (H3K27me3) levels during callus formation from leaf explants. Among these genes, a number of leaf-regulatory genes were repressed through PcG-mediated H3K27me3. Conversely, certain auxin pathway genes and many root-regulatory genes were derepressed through H3K27 demethylation. Our data indicate that genome-wide H3K27me3 reprogramming, through the PcG-mediated H3K27me3 and the H3K27 demethylation pathways, is critical in directing cell fate transition. This submission represents the gene expression component of the study
2012-04-07 | GSE36479 | GEO
Project description:Unlike most animal cells, plant cells can easily regenerate new tissues from a wide variety of organs when properly cultured. The common elements that provide varied plant cells with their remarkable regeneration ability are still largely unknown. Here we describe the initial process of Arabidopsis in vitro regeneration, where a pluripotent cell mass termed callus is induced. We demonstrate that callus resembles the tip of a root meristem, even if it is derived from aerial organs such as petals, which clearly shows that callus formation is not a simple reprogramming process backwards to an undifferentiated state as widely believed. Furthermore, callus formation in roots, cotyledons and petals is blocked in mutant plants incapable of lateral root initiation. It thus appears that the ectopic activation of a lateral root development program is a common mechanism in callus formation from multiple organs. Four sets of biologically independent tissue samples were collect for root, cotyledon and petal explants just after being excised from plants (d0) or after ten days on callus-inducing medium (CIM, d10). Samples derived from the same organ were co-hybridized in the array experiments. Dyes used for labeling the RNA populations derived from the individual samples were switched in the replicate experiments to reduce dye-related artefacts.
2010-01-31 | E-GEOD-19863 | biostudies-arrayexpress