Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA271499 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1738110.fastq.gz | Fastqsanger.gz | |||
| SRR1738120.fastq.gz | Fastqsanger.gz | |||
| SRR1738130.fastq.gz | Fastqsanger.gz | |||
| SRR1738140.fastq.gz | Fastqsanger.gz | |||
| SRR1738150.fastq.gz | Fastqsanger.gz |
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Project description:The mechanisms ensuring balanced growth remain a critical question in developmental biology. In plants, this balance relies on spatiotemporal integration of hormonal signaling pathways, but the understanding of the precise contribution of each hormone is just beginning to take form. Brassinosteroid (BR) hormone, is shown here to have opposing effects on root meristem size, depending on its site of action. BR is demonstrated to both delay and promote onset of stem cell daughter differentiation, when acting in the outer tissue of the root meristem, the epidermis, and the inner-most tissue, the stele, respectively. To understand the molecular basis of this phenomenon, a comprehensive spatiotemporal translatome mapping of Arabidopsis roots was performed. Analyses of wild type and mutants featuring different distributions of BR, revealed autonomous, tissue-specific gene responses to BR, implying its contrasting tissue-dependent impact on growth. BR-induced genes were primarily detected in epidermal cells of the basal meristem zone and were enriched by auxin-related genes. In contrast, repressed BR genes prevailed in the stele of the apical meristem zone. Furthermore, auxin was found to mediate the growth-promoting impact of BR signaling originating in the epidermis, while BR signaling in the stele buffered this effect. We propose that context-specific BR activity and responses are oppositely interpreted at the organ level, ensuring coherent growth.
2015-01-04 | GSE64410 | GEO
Project description:The mechanisms ensuring balanced growth remain a critical question in developmental biology. In plants, this balance relies on spatiotemporal integration of hormonal signaling pathways, but the understanding of the precise contribution of each hormone is just beginning to take form. Brassinosteroid (BR) hormone, is shown here to have opposing effects on root meristem size, depending on its site of action. BR is demonstrated to both delay and promote onset of stem cell daughter differentiation, when acting in the outer tissue of the root meristem, the epidermis, and the inner-most tissue, the stele, respectively. To understand the molecular basis of this phenomenon, a comprehensive spatiotemporal translatome mapping of Arabidopsis roots was performed. Analyses of wild type and mutants featuring different distributions of BR, revealed autonomous, tissue-specific gene responses to BR, implying its contrasting tissue-dependent impact on growth. BR-induced genes were primarily detected in epidermal cells of the basal meristem zone and were enriched by auxin-related genes. In contrast, repressed BR genes prevailed in the stele of the apical meristem zone. Furthermore, auxin was found to mediate the growth-promoting impact of BR signaling originating in the epidermis, while BR signaling in the stele buffered this effect. We propose that context-specific BR activity and responses are oppositely interpreted at the organ level, ensuring coherent growth. 24 samples of polyribosome-associated mRNA (following 0, 3, and 8 hours of BR treatment, in two biological repetitions), were collected. RNA samples were sequenced on an Illumina HiSeq 2500, to obtain 50 bp single-end reads. These reads were aligned to the TAIR10 assembly of the Arabidopsis thaliana genome, using Tophat2 v2.0.9. Transcript coordinates from the TAIR10 reference set were used to guide the alignment process. After alignment, the numbers of reads per transcript were estimated using HTSeq v0.5.3p3, and DESeq2 v1.2.8 was used to normalize read counts and call differentially expressed genes.
2015-01-04 | E-GEOD-64410 | biostudies-arrayexpress
Project description:Differentiation processes in the primary root meristem are controlled by several signaling pathways that are regulated by phytohormones or by secreted peptides. Long term maintenance of an active root meristem requires that the generation of new root meristem cells and the loss of cells from the meristem due to differentiation is precisely coordinated. Via phenotypic and large scale transcriptome analyses of mutants, we show that the signalling peptide CLE40 and the receptor proteins CLV2 and CRN act in two genetically separable pathways that antagonistically regulate cell differentiation in the proximal root meristem. CLE40 inhibits cell differentiation throughout the primary root meristem by controlling genes with roles in abscisic acid, auxin and cytokinin signalling. CRN and CLV2 jointly control target genes that promote cell differentiation specifically in the transition zone of the proximal root meristem. While CRN and CLV2 are not acting in the CLE40 signaling pathway under normal growth conditions, both proteins are required when the levels of CLE40 or related CLE peptides increase. We show here that two antagonistically acting pathways controlling root meristem differentiation can be activated by the same peptide in a dosage dependent manner.
2014-10-02 | GSE59167 | GEO
Project description:Differentiation processes in the primary root meristem are controlled by several signaling pathways that are regulated by phytohormones or by secreted peptides. Long term maintenance of an active root meristem requires that the generation of new root meristem cells and the loss of cells from the meristem due to differentiation is precisely coordinated. Via phenotypic and large scale transcriptome analyses of mutants, we show that the signalling peptide CLE40 and the receptor proteins CLV2 and CRN act in two genetically separable pathways that antagonistically regulate cell differentiation in the proximal root meristem. CLE40 inhibits cell differentiation throughout the primary root meristem by controlling genes with roles in abscisic acid, auxin and cytokinin signalling. CRN and CLV2 jointly control target genes that promote cell differentiation specifically in the transition zone of the proximal root meristem. While CRN and CLV2 are not acting in the CLE40 signaling pathway under normal growth conditions, both proteins are required when the levels of CLE40 or related CLE peptides increase. We show here that two antagonistically acting pathways controlling root meristem differentiation can be activated by the same peptide in a dosage dependent manner. 3 replicates reference(Col-0), clv2-gabi, cle40-2; 2 replicates crn-3
2014-10-02 | E-GEOD-59167 | biostudies-arrayexpress
Project description:The capacity for sustained cell division is a critical determinant of plant meristem development, and ultimately, organ size. This capacity is diminished in mutants lacking the microtubule-associated protein CLASP, and when brassinosteroid signaling is increased. Here, we discovered that CLASP is both targeted by and promotes activity of the brassinosteroid pathway in Arabidopsis root apical meristems. We show that enhanced brassinosteroid signalling reduces CLASP transcript and protein levels, and dramatically shifts microtubule organization to promote exit from the cell division cycle. Notably, CLASP sustains brassinosteroid signalling by fostering retrieval of endocytosed BRI1 receptors to the plasma membrane through the tethering of SNX1 vesicles to microtubules. clasp-1 null mutants have fewer BRI1 receptors, and impaired BR-mediated transcriptional activity and responses. Global transcript profiling confirmed the collapse of cell cycle activity in clasp-1 and revealed hormone crosstalk. Together, these findings reveal an unprecedented form of negative feedback that supports meristem homeostasis.
2017-05-01 | GSE85262 | GEO
Project description:The root apical meristems (RAM) is established during embryogenesis and serves as a source of stem cells for plant growth and organogenesis. Young roots have a simple structure and meristeamtic and non-meristematic cells can be differentiated based on their location. We have used the Affymetrix Medicago Genome Array GeneChip to compare tissue from the root meristem and non-meristematic tissue to identify meristem specific candidate genes based on changes in gene expression before and after differentiation Experiment Overall Design: Roots were sectioned separating meristematic (root-tip) and non-meristematic root tissue; total RNA was extracted and used for hybridization to Affymetrix arrays
2008-06-16 | E-GEOD-8115 | biostudies-arrayexpress
Project description:In plants, apical meristems allow continuous growth along the body axis. Within the root apical meristem (RAM), a group of slowly dividing quiescent center (QC) cells is thought to limit stem cell activity to directly neighboring cells (Cowels, 1956; van den Berg et al., 1997), thus endowing them with unique properties, distinct from displaced daughters. This binary identity of the stem cells stands in apparent contradiction with the more gradual changes in cell division potential (Bennett and Scheres, 2010) and differentiation (Yamaguchi et al., 2008; 2010; Furuta et al, 2014; Geldner, 2013; Masucci et al., 1996; Dolan and Costa, 2001) that occur as cells move further away from the QC. To address this paradox and to infer molecular organization of the root meristem, we used a whole-genome approach to determine dominant transcriptional patterns along root ontogeny zones. We found that the prevalent patterns are expressed in two opposing gradients. One is characterized by genes associated with development, the other enriched in differentiation genes. We confirmed these transcript gradients, and demonstrate that these translate to gradients in protein accumulation and gradual changes in cellular properties. We also show that gradients are genetically controlled through multiple pathways. Based on these findings, we propose that cells in the Arabidopsis root meristem gradually transition from ‘stemness’ towards differentiation.
2017-10-03 | GSE98097 | GEO
Project description:Plants acquire essential elements from inherently heterogeneous soils, in which phosphate and iron availabilities vary. Consequently, plants developed adaptive strategies to cope with low iron and low phosphate levels, including alternation between root growth enhancement and attenuation. How this adaptive response is achieved remains unclear. Here, we found that low iron accelerates the root growth of Arabidopsis thaliana by activating brassinosteroid signaling, whereas low-phosphate-induced high iron accumulation inhibited it. Altered hormone signaling intensity also modulated iron accumulation in the root elongation and differentiation zones, constituting a feedback response between brassinosteroid and iron. Surprisingly, the early effect of low iron levels on root growth required the brassinosteroid receptor but the hormone ligand was negligible. The brassinosteroid receptor inhibitor BKI1, the transcription factors BES1/BZR1 and the ferroxidase LPR1, stood at the base of this feedback loop. Hence, shared brassinosteroid and iron regulatory components link nutrient status to root morphology, thereby driving the adaptive response.
2018-08-01 | GSE114250 | GEO
Project description:The root apical meristems (RAM) is established during embryogenesis and serves as a source of stem cells for plant growth and organogenesis. Young roots have a simple structure and meristeamtic and non-meristematic cells can be differentiated based on their location. We have used the Affymetrix Medicago Genome Array GeneChip to compare tissue from the root meristem and non-meristematic tissue to identify meristem specific candidate genes based on changes in gene expression before and after differentiation Keywords: Cell type comparison
2007-07-01 | GSE8115 | GEO
Project description:The Arabidopsis basic leucine zipper transcription factor bZIP29 of the bZIP group I TF family, expressed mainly in proliferative tissues, is functionally characterized in this study. In roots, bZIP29 is highly expressed in the quiescent centre and the columella cells of the root apical meristem. Mutant analyses demonstrate that bZIP29 regulates root meristem cell number and root gravitropic responses. RNA-seq transcriptome profiling of the root meristem shows that bZIP29 target genes are linked to cell wall organization, and that gene regulatory networks controlling proper root meristem organization are intensively rewired upon its perturbation.
2016-11-07 | E-MTAB-3755 | biostudies-arrayexpress