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:Transcriptomes and differential gene expression in the Arabidopsis shoot phloem companion cells during flowering
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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: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:Leaves are asymmetric, with differential functionalization of abaxial and adaxial tissues. The bundle sheath (BS) surrounding the vasculature of the C3 crop barley is dorsoventrally differentiated into three domains: adaxial structural, lateral S-type, and abaxial L-type. S-type cells seem to transfer assimilates towards the phloem. Here we used single-cell RNA sequencing to investigate BS differentiation in C4 maize. Abaxial BS (abBS) cells of rank-2 intermediate veins specifically expressed three SWEET sucrose uniporters (SWEET13a, b, and c) and UmamiT amino acid efflux transporters. SWEET13a, b, c were also identified in the phloem parenchyma (PP). Thus maize acquired a unique mechanism for phloem loading in which abBS cells provide the main pathway for apoplasmic sucrose transfer towards the phloem. This pathway predominates in veins responsible for phloem loading (rank-2 intermediate), while rank-1 intermediate and major veins export sucrose from the phloem parenchyma (PP) adjacent to the sieve element companion cell (SE/CC) complex, as in Arabidopsis. We surmise that abBS identity is subject to dorsoventral patterning and has components of PP identity. The observations provide first insights into the unique properties of abBS cells, cells previously considered to fulfill the same functions as other bundle sheath cells (BSCs), and a basis for understanding the C4 syndrome.
2021-03-02 | GSE157757 | GEO
Project description:As a prerequisite for constant growth, plants can produce vascular tissues at different sites in their postembryonic body. In particular, the formation of vascular tissues during longitudinal and radial expansion of growth axes differs fundamentally with respect to its anatomical configuration. This raises the question to which level regulatory mechanisms of vascular tissue formation are shared throughout plant development. Here, we show that, similar as primary phloem formation during longitudinal growth, the cambium-based formation of secondary phloem depends on the function of SMXL genes. Using promoter reporter lines, we observe that SMXL4 and SMXL5 activities are associated with different stages of secondary phloem formation in Arabidopsis stems and that specific loss of SMXL5 function results in the absence of secondary phloem. Interestingly, the additional disruption of SMXL4 activity increases cell proliferation rates in the cambium region without forming secondary phloem. Based on genome-wide transcriptional profiling and expression analyses of phloem-related markers we conclude that early steps of phloem formation are impaired in smxl4;smxl5 double mutants and that additional cambium-derived cells fail in establishing any phloem-related feature. Our results show that molecular mechanisms determining primary and secondary phloem share important features but differ slightly with SMXL5 playing a more dominant role in the formation of secondary phloem.
2019-04-04 | GSE129190 | GEO
Project description:Leaves are asymmetric, with differential functionalization of abaxial and adaxial tissues. The bundle sheath (BS) surrounding the vasculature of the C3 crop barley is dorsoventrally differentiated into three domains: adaxial structural, lateral S-type, and abaxial L-type. S-type cells seem to transfer assimilates towards the phloem. Here we used single-cell RNA sequencing to investigate BS differentiation in C4 maize. Abaxial BS (abBS) cells of rank-2 intermediate veins specifically expressed three SWEET sucrose uniporters (SWEET13a, b, and c) and UmamiT amino acid efflux transporters. SWEET13a, b, c were also identified in the phloem parenchyma (PP). Thus maize acquired a unique mechanism for phloem loading in which abBS cells provide the main pathway for apoplasmic sucrose transfer towards the phloem. This pathway predominates in veins responsible for phloem loading (rank-2 intermediate), while rank-1 intermediate and major veins export sucrose from the phloem parenchyma (PP) adjacent to the sieve element companion cell (SE/CC) complex, as in Arabidopsis. We surmise that abBS identity is subject to dorsoventral patterning and has components of PP identity. The observations provide first insights into the unique properties of abBS cells, cells previously considered to fulfill the same functions as other bundle sheath cells (BSCs), and a basis for understanding the C4 syndrome.
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Project description:We profiled transcripts from sorted phloem cells of wild-type and apl mutants to identify the genes regulated by APL in phloem. We profiled transcripts from sorted phloem cells of wild-type and apl mutants to identify the genes regulated by APL in phloem.
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