Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The PLETHORA gene regulatory network guides growth and cell differentiation in Arabidopsis roots

ABSTRACT: Organ formation in animals and plants relies on precise control of cell state transitions to turn stem cell daughters into fully differentiated cells. In plants, cells cannot rearrange due to shared cell walls. Thus, differentiation progression and the accompanying cell expansion must be tightly coordinated across tissues. PLETHORA (PLT) transcription factor gradients are unique in their ability to guide the progression of cell differentiation at different positions in the growing Arabidopsis root, which contrasts with well-described transcription factor gradients in animals specifying distinct cell fates within an essentially static context. To understand the output of the PLT gradient, we studied the gene set transcriptionally controlled by PLTs. Our work reveals how the PLT gradient can regulate cell state by region-specific induction of cell proliferation genes and repression of differentiation. Moreover, PLT targets include major patterning genes and autoregulatory feedback components, enforcing their role as master regulators of organ development. This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE79755 | GEO | 2016/12/06

SECONDARY ACCESSION(S): PRJNA316932

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Induction of pPLT2-PLT2-GR in Quiescent Center (QC) cells

Project description:Organ formation in animals and plants relies on precise control of cell state transitions to turn stem cell daughters into fully differentiated cells. In plants, cells cannot rearrange due to shared cell walls. Thus, differentiation progression and the accompanying cell expansion must be tightly coordinated. PLETHORA (PLT) transcription factor gradients were shown to guide the progression of cell differentiation at different positions in the Arabidopsis root. While well-described transcription factor gradients in animals specify distinct cell fates within an essentially static context, the PLT gradient is unique in its ability to control cell differentiation in a growing organ during continuous production and expansion of cells. To understand the output of these gradients we studied the gene set transcriptionally controlled by PLTs. Our work reveals how the PLT gradient regulates cell state by region-specific induction of cell proliferation genes and repression of differentiation. Moreover, PLT targets include major patterning genes and autoregulatory feedback components, reinforcing their role as master regulators of organ development.

2016-12-06 | GSE79751 | GEO

Chromatin immunoprecipitation and sequencing of pPLT2::PLT2-YFP in the root of plt1plt2 double mutant

2016-12-06 | GSE79754 | GEO

Induction of PLT1, PLT3, PLT4, PLT5 and PLT7 in whole seedlings

2016-12-06 | GSE79753 | GEO

Induction of 35S-PLT2-GR in whole seedlings

2016-12-06 | GSE79752 | GEO

Proteomic study of apheresis platelets made HLA class I deficient for transfusion of refractory patients

Project description:Refractoriness can occur after repeated PLT transfusions because of alloimmunization to HLA class I antigens on transfused PLTs and generation of anti-HLA antibodies that bind to the foreign PLTs and initiate their destruction. Such refractoriness can be overcome by provision of HLA-matched PLTs from HLA typed donors. However, since the procedure is both expensive and time-consuming, an alternative approach is to deplete PLTs of HLA class I molecules by a brief treatment with citric acid, on ice at low pH. This is shown to be feasible without damaging PLT function

2022-02-14 | PXD027893 | Pride

PLETHORA transcription factors promote early embryo development through induction of meristematic potential

Project description:Given that PLTs are key transcription factors in meristems, we hypothesized that loss of activity fails to confer meristematic properties or 'stemness' to the first embryonic cells, leading to developmental arrest. We asked to what degree downstream PLT targets in meristems overlap with those in early embryos. We selected direct PLT target genes by overlaying existing PLT ChIP-seq and DAP-seq datasets. We extended this set with an additional PLT3-DAP experiment on young roots, because previous PLT-DAP data have only low read counts and used leaf material in which PLTs are typically not strongly expressed.

2024-06-14 | GSE228358 | GEO

A microfluidics workflow for spatial analysis of microenvironmental gradient impact on cancer cell phenotypes

Project description:Despite the physiological and pathophysiological significance of microenvironmental gradients, tools for generating such gradients and analysing their impact on cellular phenotypes are lacking. Here we present an integrated microfluidics-based workflow for mimicking extracellular pH gradients characteristic of solid tumors, and studying their multifactorial impact on cancer cells. Our microfluidics device generates a pH gradient across cancer cell 3D cultures in an extracellular matrix. The gradient, validated using pH-sensitive fluorophores can be rapidly controlled to represent spatiotemporal microenvironmental changes, and the device allows high resolution live imaging of, e.g., cell motility and chemotaxis. The device can be reopened, allowing immunofluorescence analysis of phenotypes and spatially resolved analysis of gene expression changes across the pH gradient. The workflow is easily adaptable for other gradients and multiple cell types, making it broadly applicable for integrated analysis of roles of microenvironmental gradients in biology.

2024-05-07 | GSE242233 | GEO

Defective flow space limits the scaling up of turbulence bioreactors for platelet generation

Project description:To complement donor-dependent platelet supplies, we previously developed an ex vivo manufacturing system using iPSC-derived expandable megakaryocytes, imMKCLs, and a turbulent flow bioreactor, VerMES, to generate iPSC-derived platelet products (iPSC-PLTs). However, the tank size of VerMES was limited to 10 L (VerMES10). Here we examined the feasibility of scaling up to 50 L (VerMES50) with reciprocal motion by two impellers. Under optimized turbulence parameters corresponding to VerMES10, VerMES50 elicited iPSC-PLTs with intact in vivo hemostatic function but with less production efficiency. This insufficiency was caused by increased defective turbulent flow space. A computer simulation proposed that designing VerMES50 with three impellers or a new bioreactor with a modified rotating impeller and unique structure reduces this space. These findings indicate that large-scale PLT manufacturing from cultured imMKCLs requires optimization of the tank structure in addition to optimal turbulent energy and shear stress.

2024-03-26 | GSE262455 | GEO

Graded Nodal/Activin Signaling Governs ES Cell Fate Decisions via Differential Recruitment of Phospho-Smad2 to Oct4 and Distinct Target Gene Subsets.

Project description:The Nodal/Activin morphogens are secreted signaling molecules that form concentration gradients during early embryogenesis providing stem cells with positional information and differentiation instructions important for embryonic patterning. The molecular basis driving stem cell interpretation of signaling gradients and the undertaking of distinct cell fate decisions remains poorly understood. We show that perturbation of endogenous Nodal/Activin signaling in ES cells leads to exit from self renewal towards mesendodermal differentiation at high signaling and trophectoderm induction during low signaling. ChIP-seq of Phospho-Smad2, the downstream transcription factor of the Nodal/Activin pathway reveals binding to distinct subsets of target genes in a dose dependent manner including the promoter region of the Oct4 master regulator of stemness. Consequently, both Oct4 mRNA and protein levels are directly driven by graded Nodal/Activin signaling. Hence stem cells interpret and carry out differential Nodal/Activin signaling instructions via a corresponding gradient of Smad2 phosphorylation that selectively titers self renewal against alternative differentiation programs.

2011-01-31 | GSE23581 | GEO

Cellular trajectory analysis links tissue maturation to cellular specialization in the plant meristem [protophloem sieve element cells]

Project description:The mechanisms that allow cells in the plant meristem to coordinate tissue-wide maturation gradients with specialized cell networks are critical for indeterminate growth. Here, we combine long-term imaging, single-cell transcriptomics, genetic analysis, and network modeling to reconstruct the differentiation trajectory of the 20 protophloem cells in the Arabidopsis root. We found that lineage bifurcation and cellular specification are mediated near the stem cell niche by PEAR regulators. However, many PEAR downstream effects are repressed by a broad gradient of PLETHORA transcription factors, which directly inhibit PEARs’ own direct target APL until dissipating seven cells from the stem cell niche. Modeling and molecular epistasis suggest a so-called “seesaw” cascade of sharp transitions in which transcription factors regulating consecutive steps mutually inhibit each other’s targets, ending in programmed enucleation. This analysis provides a mechanistic understanding of how morphogen-like maturation gradients interface with cell-type specific transcriptional regulators to stage cellular differentiation

2021-12-24 | GSE142259 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data