Photoperiod-mediated Chromatin Accessibility in the Single Cell Types of Leaf Phloem and Epidermis in Arabidopsis
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ABSTRACT:
PROVIDER: PRJNA597758 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10768872_1.fastq.gz | Fastqsanger.gz | |||
| SRR10768872_2.fastq.gz | Fastqsanger.gz | |||
| SRR10768873_1.fastq.gz | Fastqsanger.gz | |||
| SRR10768873_2.fastq.gz | Fastqsanger.gz | |||
| SRR10768874_1.fastq.gz | Fastqsanger.gz |
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Project description:Photoperiodic control of the phase transition from vegetative to reproductive growth plays a key role in high plants. Although leaves are considered to be the major organs to perceive the day-length signal, it is not clear what the specific responses happen in the vasculature and epidermis tissues. Here, we performed ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) and RNA-seq with purified phloem and epidermis nuclei by applying INTACT (isolation of nuclei tagged in specific cell/tissue types) sorting method. We found that accessible chromatin regions (ACR) in phloem showed higher variations than epidermis during sensing the long-day signal. These cell/condition-type-specific ACR changes are basically related with gene expression. Taken together, our cell type specific studies sheds light on photoperiodic control of the flowering transition and also investigating of plant development mechanism.
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Project description:The cucumber is one of the most important vegetables worldwide and is used as a research model for study of phloem transport, sex determination and temperature-photoperiod physiology. The shoot apex is the most important plant tissue in which the cell fate and organ meristems have been determined. In this study, a series of whole-genome small RNA, degradome and transcriptome analyses were performed on cucumber shoot apical tissues treated with high vs. low temperature and a long vs. short photoperiod.
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Project description:To better understand the function of the phloem in plants, we have combined laser capture microdissection (LCM) and RNA-seq for an in-depth transcriptional profile of phloem-associated cells of both petioles and stems of potato. Out of the 27k transcripts assembled that we identified, approximately 15K were present in phloem-associated cells of petiole and stem with greater than ten reads. Approximately 22% of the transcripts in phloem cells contained at least one binding motif for Pumilio, Nova, or polypyrimidine tract-binding proteins in their downstream sequences. Highlighting the predominance of binding processes identified in the gene ontology analysis of active genes from phloem cells, 78% of the 464 RNA-binding proteins present in the potato genome were detected in our phloem transcriptome. As a reasonable alternative when phloem sap collection is not possible, LCM can be used to isolate RNA from specific cell types, and along with RNA-seq, provides practical access to expression profiles of phloem tissue.
2015-08-02 | E-MTAB-4251 | biostudies-arrayexpress
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: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
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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.
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Project description:Phloem is essential for higher plant development and survival by transporting photosynthetic products and systemic signals from source to sink organs. To date, most phloem studies were performed with the phloem exudate for physiological, transcriptomic or proteomic analyses. However, as yet, no transcriptomic profiling was performed to the phloem tissue itself, probably due to the technique difficulties to access the phloem tissue inside the plant body. In this study, laser microdissection combined with RNA-Seq technology was used to gain phloem-specific transcript profiling in three different organs (pedicle, stalk and fruit) of cucumber, a model plant species for phloem research. We found that transcription factors and biotic/abiotic stress related genes are highly enriched in the sink organs, while cell growth via calcium ion, hormone actions and cell cycle control was largely restricted in the pedicle and stalk, and genes implicated in transporting amino acids and sugars are mostly up-regulated in the pedicle. Further, we found excellent corroboration between phloem-specific gene expression, and physiological characterization with phloem function. In addition, we identified 432 cucumber-unique genes and several phloem-specific markers for future functional studies. This study provides new insights into the molecular genetics of the function of phloem tissue in cucumber, rather than the conventional phloem sap analyses.
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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. Three biological replicates for control WT and apl mutants were used in thes study. Root tissue was protoplasted and sorted using fluorescence-activated cell sorting (FACS). Total RNA was extracted from GFP+ protoplasts.
2014-08-25 | E-GEOD-55222 | biostudies-arrayexpress
Project description:In this study we used a translating ribosome affinity purification strategy to identify phloem and non-phloem associated translatomes in Prunus domesitca L during PPV infection. Three different promoter:His6FLAG-RPL18 lines were used. These included two phloem specific promoters (pSUC2 and pSULTR2;2) as well as the more ubiquitously expressed cauliflower mosaic virus 35S promoter (p35S). Immunopurification of ribosome-mRNA complexes was accomplished by the method described in Reynoso et al. (Plant Functional Genomics: Methods and Protocols, 185-207; 2015). The dataset includes samples from plum leaves taken at 2, 4, 6, and 12 weeks post cold induced dormancy.
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