Auxin responses in the Arabidopsis stem and cambium
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ABSTRACT:
PROVIDER: PRJNA384225 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5420080.fastq.gz | Fastqsanger.gz | |||
| SRR5420083.fastq.gz | Fastqsanger.gz | |||
| SRR5420084.fastq.gz | Fastqsanger.gz | |||
| SRR5420075.fastq.gz | Fastqsanger.gz | |||
| SRR5420085.fastq.gz | Fastqsanger.gz |
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Project description:In-vitro induced establishment and activity of the interfascicular cambium in Arabidopsis thaliana stems under auxin treatments. We used microarrays to detail the global programme of gene expression underlying the establishment and activity of the interfascicular cambium and identified tissue-speciffic up-regulated genes during this process.
2010-12-31 | GSE22947 | GEO
Project description:In-vitro induced establishment and activity of the interfascicular cambium in Arabidopsis thaliana stems under auxin treatments. We used microarrays to detail the global programme of gene expression underlying the establishment and activity of the interfascicular cambium and identified tissue-speciffic up-regulated genes during this process. Different tissue types from in-vitro auxin treated stems were selected at successive stages of cambium establishment using laser capture microdissection for RNA extraction and hybridization on Affymetrix microarrays. We aimed to obtain genes exclussively upregulated in the interfascicular region responsible for cambium establishment and activity.
2010-12-31 | E-GEOD-22947 | biostudies-arrayexpress
Project description:We performed an analysis of transcriptomic responses to auxin within four distinct tissues of the Arabidopsis thaliana root. This high-resolution dataset shows how different cell types are predisposed to react to auxin with discrete transcriptional responses. The sensitivity provided by the analysis lies in the ability to detect cell-type specific responses diluted in organ-level analyses. This dataset provides a novel resource to examine how auxin, a widespread signal in plant development, influences differentiation and patterning in the plant through tissue-specific transcriptional regulation.
2013-08-06 | GSE35580 | GEO
Project description:Vascular cambium is a secondary meristem which produces xylem (wood) inwards and phloem (bark) outwards. The activity of cambium leads to expansion in the diameters in plants, that is, secondary growth, and thus contributes to biomass increase. The regulation of cambium development is at multilevel including phytohormones and peptide-receptor kinase (CLE41/44-PXY) signalling pathways. However, only limited progress has been made on the transcriptional regulation level. To construct the transcriptional network that regulates cambium development, we performed a genome wide transcript profiling in sorted procambial and cambial cells in Arabidopsis roots. More than 500 genes were identified as cambium abundant genes via comparison against transcriptomes of other Arabidopsis root cell types. We then investigated the roles of almost all the cambial transcription factors (TFs) and some of their homologous genes during secondary growth. Many of the candidate TFs were highly expressed in cambium based on the promoter GUS fusion and in situ hybridization. An unbiased transcriptional regulatory network was constructed using transcript profiling data collected from inducible overexpression lines for selected candidate TFs and a few major nodes were identified in the network including WOX4 and KNAT1. Moreover, the severity of mutant phenotypes was predicted based on the network. Next, we used the predication as a guide and generated over 70 double mutants within the same or among different TF families to explore the genetic interactions of candidate genes. Phenotype characterization on the secondary growth of the mutants and the overexpression lines identified promoters and inhibitors of cambium activity. The phenotypic data also suggested the redundancy within and among TF families because the phenotypes could be enhanced when additional TFs were mutated. We also found that combinations of certain overexpression lines and mutants led to pronounced increase of cell proliferation or xylem differentiation and in the extreme case the formation of ectopic cambium. We herein propose that cambium development is orchestrated by a wide network at the transcriptional level, where each TF has a different contribution to cell proliferation and differentiation.
2019-03-31 | GSE125244 | GEO
Project description:We performed an analysis of transcriptomic responses to auxin within four distinct tissues of the Arabidopsis thaliana root. This high-resolution dataset shows how different cell types are predisposed to react to auxin with discrete transcriptional responses. The sensitivity provided by the analysis lies in the ability to detect cell-type specific responses diluted in organ-level analyses. This dataset provides a novel resource to examine how auxin, a widespread signal in plant development, influences differentiation and patterning in the plant through tissue-specific transcriptional regulation. To analyze the effect of auxin in separate spatial domains of the root, early transcriptional changes in response to auxin treatment were assayed by means of fluorescence activated cell sorting (FACS) and microarray analysis in four tissues of the Arabidopsis root (wild type Col-0). The samples covered inner and outer as well as proximal and distal cell populations; including the stele (reporter line pWOL::GFP), xylem-pole (xp) pericycle (enhancer trap line E3754), epidermis/lateral root cap (reporter line pWER::GFP) and columella (enhancer trap line PET111). One-week-old seedlings of the individual lines were treated with auxin (two hours, 5µM indole-3-acetic acid [IAA]) or mock treated, after which roots were harvested and cells were dissociated by cell wall digestion (1 hour; including 5uM IAA) . GFP-positive cells were sorted and used for microarray transcriptome analysis (as in Bargmann and Birnbaum, Plant Phys. 2010). For comparison, transcriptional responses to auxin were also assayed in intact (undigested) roots.
2013-08-06 | E-GEOD-35580 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2017-05-28 | GSE98193 | GEO
Project description:In plant development, a receptor kinase may be active in disparate cell types, with each requir-ing different signalling outputs. The ERECTA (ER) receptor kinase and its homologs ERL1 and ERL2 exemplify this pleiotropy. In Arabidopsis, they influence stomatal patterning, shoot meristem function, ovule morphogenesis, xylem fiber differentiation, and cell division in the vascular cambium1–6. Such diverse expression and functionality raise the question of how ER signalling can specify such distinct cell behaviours. One explanation is that cell-type specific interactions with co-receptors, ligands, or other proteins modulate signalling. However, little is known about ER interactors in the vascular cambium, a bifacial stem cell niche that generates phloem and xylem. Combinatorial mutations between ER, ERL1 and ERL2 and receptor kinases of a sec-ond family, PXY, PXL1, and PXL2, show severe cambial defects5,7. Here we discovered that PXY and PXL proteins form heterodimers with ER and ERL2. PXY signalling can be manipulated by altering levels of its cognate ligand, TDIF. In genetic analysis, plant lines in which TDIF levels were altered had dramatic phenotypes that required the presence of ER or ERL2. Our results demonstrate that PXY signalling mediated cambium regulation depends on ER signalling and explains ER function in the cambium. Because the cambium produces xylem, which constitutes the wood in vascular plants, our findings position PXY-ER heterodimers at the centre of the ac-cumulation of this versatile biomaterial and carbon sink.
2025-11-07 | GSE263680 | GEO
Project description:In-vivo induced establishment and activity of the interfascicular cambium in Arabidopsis thaliana stems under NPA treatments. We used microarrays to detail the global programme of gene expression underlying the establishment and activity of the interfascicular cambium. 3 mm stem pieces were collected after being in treated with NPA for a week in order to stop the polar auxin transport and induce secondary growth. Collected samples were used for RNA extraction and hybridization on Affymetrix microarrays. We aimed to obtain genes responsible for auxin-induced cambium establishment and activity.
2011-08-31 | E-GEOD-24763 | biostudies-arrayexpress
Project description:The largest reservoir of terrestrial biomass is the wood within plant stems. Consisting of xylem cells, wood is derived from the cambium, a stem cell population that is maintained by non-cell autonomous signalling. The central component of this system is PXY, a receptor protein present on the plasma membrane of cambium cells. Here, we show that PXY protein interacts with a second membrane-localised receptor kinase, ER, to promote cambium fate. Combinatorial mutations between ER, ERL1 and ERL2 and receptor kinases of a second family, PXY, PXL1, and PXL2, show severe cambial defects, but the mechanism underpinning these phenotypes is not known. Here we discovered that PXY and PXL proteins form protein complexes with ER family members. In genetic analyses, plant lines in which PXY signalling was constitutively active had dramatic phenotypic changes that required the presence of ER or ERL2. Our results demonstrate that PXY signalling mediated cambium regulation depends on ER signalling and explains ER function in the cambium. Because the cambium produces xylem, which constitutes the wood in vascular plants, our findings position PXY-ER complexes at the centre of the accumulation of this versatile biomaterial and essential carbon sink.
2025-11-19 | GSE310491 | GEO
Project description:Wood constitutes the majority of terrestrial biomass.Composed of xylem, it arises from one side of the vascular cambium, a bifacial stem cell niche that also produces phloem on the opposing side. It is currently unknown which molecular factors endowcambium stem cell identity. Here we show that TDIF ligand-activated PXY receptors promote the expression of CAMBIUM AINTEGUMENTA-LIKE (CAIL) transcription factors to define cambium stem cell identity inthe Arabidopsisroot. By sequestrating the phloem-originated TDIF, xylem-dependent PXY confines the TDIF signaling front, resulting in the activation of CAIL expression and stem cell identity in only a narrow domain. Our findings show how signals emanating from cells on opposing sides ensure robust yet dynamically adjustable positioning of a bifacial stem cell.
2024-04-24 | GSE264403 | GEO