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Transcriptomes and differential gene expression in the Arabidopsis shoot phloem companion cells during flowering

ABSTRACT: Transcriptomes and differential gene expression in the Arabidopsis shoot phloem companion cells during flowering

PROVIDER: PRJEB21286 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2007980_1.fastq.gz	Fastqsanger.gz
	ERR2007980_2.fastq.gz	Fastqsanger.gz
	ERR2007990_1.fastq.gz	Fastqsanger.gz
	ERR2007990_2.fastq.gz	Fastqsanger.gz
	ERR2007981_1.fastq.gz	Fastqsanger.gz

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Transcriptomes and differential gene expression in the Arabidopsis shoot phloem companion cells during flowering

Project description:We investigated the transcriptomes and differential gene expression at the Arabidopsis shoot phloem companion cells during flowering using INTACT reporter lines. Samples were collected in three biological replications.

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H3K4me3 and H3K27me3 chromatin states in the Arabidopsis shoot phloem companion cells from INTACT reporter lines

Project description:We investigated the chromatin modifications H3K4me3 and H3K27me3 in the A. thaliana shoot phloem companion cells using INTACT reporter lines. Samples were collected in two biological replications.

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Transcriptomes and differential gene expression at the Arabidopsis shoot meristem during flowering

Project description:We investigated the transcriptomes and differential gene expression at the Arabidopsis shoot meristem during flowering using INTACT reporter lines. Samples were collected in four biological replications.

2017-05-21 | E-MTAB-5130 | biostudies-arrayexpress

Transcription profiling of Arabidopsis phloem

Project description:This sudy focuses on the identification of transcripts in the shoot phloem of the model plant Arabidopsis thaliana. Transcripts expressed in the phloem tissue (parenchyma cell, companion cell, sieve element) were excised by laser microdissection pressure catapulting (LMPC). These were compared with transcripts isolated from leaf phloem exudates by EDTA-chelation technique. Optimization of sample harvest resulted in RNA of high quality from both sources. Modifications of the RNA amplification procedure obtained RNA of sufficient yield and quality for microarray experiments. Microarrays (Affymetrix, ATH1) hybridized with RNA derived from phloem tissue by LMPC or phloem sap allowed us to differentiate between phloem located and mobile transcript species. The datasets provide a search criterion for phloem-based signals and will facilitate reverse genetic studies and forward genetic screens for phloem and long distance RNA signaling mutants. Experiment Overall Design: Arabidopsis plants were cultivated under short day conditions (8 h light) until flowering. Phloem tissue was isolated by Lasermicrodissection and Pressure Catapulting (LMPC) and phloem exudate by EDTA-chelation technique. In both experiments poly-A-RNA was extracted and amplified before hybridization of microarrays (Affymetrix, ATH1). For both experiments three LMPC-derived phloem tissue (LMPC-derived phloem_1-3) and three phloem exudate samples (Phloem exudate_1-3) were analysed. Precise protocols of plant growth, sample harvest, RNA extraction and amplification are provided in Deeken et al., 2008.

2008-10-25 | E-GEOD-10247 | biostudies-arrayexpress

Transcriptome analysis of the Arabidopsis phloem

2008-09-01 | GSE10247 | GEO

H3K4me3 and H3K27me3 chromatin states in the Arabidopsis shoot phloem companion cells from INTACT reporter lines

Project description:H3K4me3 and H3K27me3 chromatin states in the Arabidopsis shoot phloem companion cells from INTACT reporter lines

| PRJEB21285 | ENA

Transcriptomes and differential gene expression at the Arabidopsis shoot meristem during flowering

Project description:Transcriptomes and differential gene expression at the Arabidopsis shoot meristem during flowering

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A molecular circuit that creates the phloem pattern

Project description:The vascular system of plants consists of xylem, phloem and procambium in a specific pattern. The phloem consists of sieve elements, the apparatus for bulk flow of photo-assimilates, and companion cells, which mediate transport of photo-assimilates between the sieve elements and surrounding cells and support the biological activities of the sieve element cells. The regulatory mechanisms of vascular development are being uncovered. Here we show that PHLOEM EARLY DOFs (PEARs) and related genes (collectively phloem-Dofs) not only regulate the number of procambium cell files, but also positively regulate phloem differentiation. Overexpression of phloem-Dofs induced cells that expressed either sieve element or companion cell marker genes, which are mutually exclusive. Conversely, disruption of phloem-Dofs caused loss of phloem. Phloem-Dofs induce CLAVATA3/EMBRYO SURROUNDING REGION-RELATED25 (CLE25) and CLE26 peptides, which in turn inhibit expression of phloem-Dofs and phloem formation, forming a negative feedback loop. Disruption of multiple genes for either phloem-expressed CLEs, BARELY ANY MERISTEM (BAM)-class receptors, or their coreceptors, CLAVATA3 INSENSITIVE RECEPTOR KINASEs (CIKs), caused excess formation of phloem cell files. We further show that phloem-Dofs are under positive self and mutual regulation. These positive and negative feedback loops create the proper phloem pattern.

2022-05-05 | GSE166182 | GEO

Global transcriptome analysis identifies genes regulated by FT in the leaf

Project description:Flowering of Arabidopsis thaliana is accelerated by several environmental cues, including exposure to long days. The photoperiod-dependent promotion of flowering involves the transcriptional induction of FLOWERING LOCUS T (FT) in the phloem of the leaf. FT encodes a mobile protein that is transported from the leaves to the shoot apical meristem, where it forms part of a regulatory complex that induces flowering. Whether FT also has biological functions in leaves of wild-type plants remains unclear. In order to address this issue, we first studied the leaf transcriptomic changes associated with its over expression in the companion cells of the phloem. To this end, transgenic A. thaliana plants that misexpress FT from the pGAS1 promoter in a ft-10 tsf-1 double mutant background were employed (pGAS1:FT ft-10 tsf-1). In these transgenic plants, the use of the pGAS1 promoter ensures that the FT transgene is expressed in phloem companion cells of the minor veins, recreating the spatial pattern of expression described for the native gene. In this studuy, the transcriptome of leaves of pGAS1:FT ft-10 tsf-1 transgenic plants was compared to that of ft-10 tsf-1 and Col-0 plants using Tiling Arrays.

2020-02-05 | GSE125054 | GEO

Transcriptome analysis of Arabidopsis shoots and roots whose nitrate levels and IPT3 expression are manipulated in a shoot-specific manner

Project description:In plants, nitrate is suggested to act as an indicator of nitrogen (N) status that modulates N responses under steady-state conditions. Our preceding study suggested that shoot nitrate accumulation alone represses expression of N starvation-inducible genes in shoots and roots. Notably, we observed that shoot nitrate accumulation was accompanied by increases in shoot expression of ISOPENTENYL TRANSFERASE 3 (IPT3) and shoot levels of N6-(Δ2-isopentenyl) adenine (iP)-type CK. IPT3 expression is localized primarily in phloem companion cells, and iP-type CKs, which are synthesized by IPT3, are phloem-mobile. Hence, both local and systemic responses to shoot nitrate status may be regulated by IPT3-synthesized iP-type CKs. Thus, the present study aims to dissect the local/systemic responses to shoot nitrate status and their dependence on shoot IPT3. To achieve this, we developed a novel experimental system to manipulate nitrate levels and IPT3 expression in a shoot-specific manner using grafted plants derived from the plants lacking nitrate reductase and/or IPT3. Using shoots and roots from the grafted plants, RNA-seq analysis was performed.

2024-08-31 | E-MTAB-14302 | biostudies-arrayexpress

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