H3K4me3 and H3K27me3 chromatin states in the Arabidopsis shoot phloem companion cells from INTACT reporter lines
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB21285 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2007960.fastq.gz | Fastqsanger.gz | |||
| ERR2007970.fastq.gz | Fastqsanger.gz | |||
| ERR2007961.fastq.gz | Fastqsanger.gz | |||
| ERR2007971.fastq.gz | Fastqsanger.gz | |||
| ERR2007962.fastq.gz | Fastqsanger.gz |
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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.
2019-01-09 | E-MTAB-5737 | biostudies-arrayexpress
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.
2019-01-09 | E-MTAB-5736 | biostudies-arrayexpress
Project description:The precise onset of flowering is crucial to ensure successful plant reproduction. The gene FLOWERING LOCUS T (FT) encodes florigen, a mobile signal that is produced in leaves and initiates flowering in the shoot apical meristem. FT is highly expressed in phloem companion cells that reside in distal leaf regions. Thus far, a detailed molecular characterization of the FT-expressing phloem companion cells has been lacking. Here, we used single-nuclei RNA-seq to investigate gene expression in FT-expressing cells and other phloem companion cells. We discovered that companion cells with high FT expression form a unique cluster and express other genes encoding small proteins, including the anti-florigen BROTHER OF FT (BFT). The promoters of FT and the genes co-expressed with FT were enriched for the consensus binding motif of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR1 (NIGT1). Overexpression of the paralogs NIGT1.2 and NIGT1.4 in transgenic Arabidopsis lines significantly delayed flowering under nitrogen-rich conditions, consistent with NIGT1s acting as nitrogen-dependent FT repressors. Taken together, our results demonstrate that FT-expressing cells show a distinct expression profile that suggests that these cells produce multiple systemic signals to regulate plant growth and development.
2025-10-03 | GSE273032 | GEO
Project description:Transcriptomes and differential gene expression in the Arabidopsis shoot phloem companion cells during flowering
| PRJEB21286 | ENA
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. Keywords: profiles of mobile and stationary Arabidopsis phloem transcripts
2008-09-01 | GSE10247 | GEO
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
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
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
Project description:We investigated the chromatin modifications H3K4me3 and H3K27me3 in the A. thaliana shoot apical meristem using INTACT reporter lines. Samples were collected in two biological replications.
2017-05-21 | E-MTAB-4684 | biostudies-arrayexpress
Project description:Small RNAs regulate numerous biological processes, including intercellular communication and inter-kingdom relationships, yet their tissue-specific functions remain poorly understood. Dissecting these roles requires tools that selectively eliminate small RNAs in defined cell types. Virus-encoded proteins such as P19 have been widely used to neutralize small RNAs owing to their sequestration capacities. However, their restricted binding spectrum to 21-22-nt small RNAs and lack of discrimination between miRNAs and siRNAs limit their utility. Here we show that constitutive expression of RNASE THREE-LIKE1 (RTL1) in Arabidopsis thaliana, previously shown to degrade siRNA precursors but not miRNA precursors, also degrades siRNA duplexes, irrespective of their size, sequence, or sub-cellular localization. Grafting experiments combined with small RNA sequencing revealed that shoot-derived siRNAs accumulate in dcl2 dcl3 dcl4 mutant roots, but are eliminated upon ectopic RTL1 expression, demonstrating that RTL1 efficiently degrades mobile siRNAs in vivo. Because the Arabidopsis endogenous RTL1 is epigenetically silenced in wild-type plants, its ectopic expression under cell type specific promoters enables targeted depletion of siRNAs in selected tissues. As a proof of concept, we show that expression of RTL1 in phloem companion cells delayed, but did not abolish, systemic post-transcriptional gene silencing (PTGS), thus indicating that mobile siRNAs transit through these cells while also using alternative routes. Together, these results establish RTL1 as a powerful tool to dissect siRNA mobility pathways and tissue-specific functions.
2026-04-02 | GSE318321 | GEO