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Microarray analysis of gene expression of the Arabidopsis leaf and callus

ABSTRACT: 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

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE36479 | GEO | 2012/04/07

SECONDARY ACCESSION(S): PRJNA153513

REPOSITORIES: GEO

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Microarray analysis of gene expression of the Arabidopsis leaf and callus

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

ChIP-on-chip analysis of H3K27me3 levels in leaves and calli

Project description:In plants, multiple detached tissues are capable of forming a pluripotent cell mass, termed callus, when cultured with appropriate plant hormones. Recent studies demonstrated that callus resembles the tip of a root meristem, even if it is derived from aerial organs. However, the underlying mechanism that guides differentiated organs to form callus is unknown. Here we show that genome-wide reprogramming of histone H3 lysine 27 trimethylation (H3K27me3) is critical in callus formation. During culture of leaf explants, the H3K27me3 level was decreased first at certain auxin-pathway genes, and then increased at the leaf- but decreased at the root-preferentially expressed genes. In addition, only the root but not the leaf explants of the Polycomb group (PcG) mutants can normally form callus. Our data indicate that PcG and H3K27me3 demethylation pathways act separately in reprogramming of H2K27me3 distributions, and also suggest that this is a general mechanism leading to cell fate transition.

2012-01-01 | GSE34596 | GEO

Genome-wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings

Project description:The Polycomb Group (PcG) proteins form two protein complexes, PcG Repressive Complex 1 (PRC1) and PRC2, which are key epigenetic regulators in eukaryotes. PRC2 represses gene expression by catalyzing the trimethylation of histone H3 lysine 27 (H3K27me3). In Arabidopsis (Arabidopsis thaliana), CURLY LEAF (CLF) and SWINGER (SWN) are two major H3K27 methyltransferases and core components of PRC2, playing essential roles in plant growth and development. Despite their importance, genome-wide binding profiles of CLF and SWN have not been determined and compared yet. In this study, we generated transgenic lines expressing GFP-tagged CLF/SWN under their respective native promoters and used them for ChIP-seq analyses to profile the genome-wide distributions of CLF and SWN in Arabidopsis seedlings. We also profiled and compared the global H3K27me3 levels in wild-type (WT) and PcG mutants (clf, swn, and clf swn). Our data show that CLF and SWN bind to almost the same set of genes, except that SWN has a few hundred more targets. Two short DNA sequences, the GAGA-like and Telo-box-like motifs, were found enriched in the CLF and SWN binding regions. The H3K27me3 levels in clf, but not in swn, were markedly reduced compared with WT; and the mark was undetectable in the clf swn double mutant. Further, we profiled the transcriptomes in clf, swn, and clf swn, and compared with that in WT. Thus this work provides a useful resource for the plant epigenetics community for dissecting the functions of PRC2 in plant growth and development.

2019-01-28 | GSE108960 | GEO

Micro-array analysis of WT and AtISWI in callus formation

2014-05-15 | GSE57145 | GEO

Arabidopsis regeneration from multiple tissues occurs via a root development pathway

2010-02-01 | GSE19863 | GEO

Micro-array analysis of WT and AtISWI in callus formation

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

Arabidopsis regeneration from multiple tissues occurs via a root development pathway

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

microRNA profiling of root tissues and root forming explant cultures in Medicago truncatula

Project description:To identify key miRNAs involved in root meristem formation in M. truncatula, deep sequencing was used to compare the miRNA populations dreived from four tissues. These were; root tip tissue, containing the root apical meristem, elongation zone tissue, root forming callus tissue and non-root forming callus tissue. We identified 83 previously reported miRNAs, 24 new to M. truncatula, in 44 families. For the first time in M. truncatula, members of conserved miRNA families mir165, miR181 and miR397 were found. Bioinformatic analysis identified 38 potential novel miRNAs. Many miRNAs were differentially expressed between tissues, particularly RFC and NRFC.

2013-04-03 | GSE45726 | GEO

microRNA profiling of root tissues and root forming explant cultures in Medicago truncatula

2013-04-03 | E-GEOD-45726 | biostudies-arrayexpress

Expression data from Col, brm-1, clf-29 and brm-1 clf-29 14-d-old seedlings

Project description:To understand how actions of the chromatin-remodeler BRAHMA (BRM) and Polycomb Group (PcG) proteins are coordinated during plant development, we performed a genome-wide profiling of trimethylated histone H3 lysine 27 (H3K27me3) in brm mutant seedlings by chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Increased H3K27me3 deposition at several hundred genes was observed in brm mutants and this increase was partially supressed upon removal of the CURLING LEAF (CLF) H3K27me3 methyltransferase. ChIP experiments demonstrated that BRM directly binds to a subset of genes and prevents the inappropriate association of PcG proteins at some of the loci. Together, these results indicate a crucial role of BRM in restricting the inappropriate activity of PcG protein complexes during plant development.

2015-03-09 | GSE53621 | GEO

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