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Mapping the transcriptional response to auxin in differentiated endodermal cells

ABSTRACT: Mapping the transcriptional response to auxin in differentiated endodermal cells

PROVIDER: PRJNA642797 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12108100.fastq.gz	Fastqsanger.gz
	SRR12108101.fastq.gz	Fastqsanger.gz
	SRR12108102.fastq.gz	Fastqsanger.gz
	SRR12108103.fastq.gz	Fastqsanger.gz
	SRR12108104.fastq.gz	Fastqsanger.gz

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Mapping the transcriptional response to auxin in differentiated endodermal cells

Project description:Here we show that differntiated endodermal cells have a distinct transcriptional response to auxin treatment. We perform a time serie of 10µM NAA treatment and sample at t=0, 2, 4, 8, 16 and 24hrs after NAA treatment. For the time series we compared roots of the solitairy root 1 (slr-1) mutant to the CASP1::shy2-2/slr-1 double mutant. We also provide RNAseq data of slr-1, CASP1::shy2-2 and CASP1::shy2-2/slr-1 at t=0

2021-01-04 | GSE153478 | GEO

Auxin Induced Endodermal to QC Transdifferentiation Time Series and Downsteam of JKD Analysis

Project description:First series collects endodermal cells using the SCR::GFP promoter after treatment with auxin Second series includes comparative samples of jkd vs. wild type plants for specific tissues; QC and meristem In first series, plants are grown under normal conditions, then transferred to auxin analog 2,4-D and endodermis is collected at time points 0hrs, 24hrs, 48hrs, 72hrs, 96 hrs.

2015-01-15 | E-GEOD-61408 | biostudies-arrayexpress

Auxin Induced Endodermal to QC Transdifferentiation Time Series and Downsteam of JKD Analysis

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Transcriptional activation of auxin biosynthesis drives developmental reprogramming of differentiated cells

Project description:Plant cells exhibit remarkable plasticity of their differentiation states, enabling regeneration of whole plants from differentiated somatic cells. How they revert cell fate and express pluripotency, however, remains unclear. Here we show that transcriptional activation of auxin biosynthesis is crucial for reprogramming differentiated leaf cells in Arabidopsis. We demonstrate that intervention of histone acetyltransferases causes severe defects in callus formation from leaf mesophyll protoplasts. Our data suggest that histone acetylation affects transcription of auxin biosynthesis genes. Auxin biosynthesis is in turn required to accomplish initial cell division through the activation of G2/M phase genes mediated by MYB DOMAIN PROTEIN 3-RELATED (MYB3Rs). We further show that AUXIN RESPONSE FACTOR 7 (ARF7)/ARF19 and INDOLE-3-ACETIC ACID INDUCIBLE 3 (IAA3)/IAA18-mediated auxin signaling pathway is responsible for the cell cycle reactivation in protoplasts. These findings provide novel mechanistic insights into how differentiated plant cells revert their fate and reinitiate the cell cycle to exert pluripotency.

2021-10-03 | GSE178645 | GEO

Global RNA expression patterns in endodermal differentiated cells

Project description:This study will analyse the global RNA expression patterns in human iPSC and endodermal differentiated cells.The goal of this project is to investigate genes regulating definitive endodermal differentiation of human iPSC using genetic screening. The differentiation of human iPSC into definitive endoderm is going to be examined by global RNA expression patterns. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2015-06-09 | E-ERAD-363 | biostudies-arrayexpress

Auxin biosynthesis drives developmental reprogramming of differentiated cells

Project description:Plant cells exhibit remarkable plasticity of their differentiation states, enabling regeneration of whole plants from differentiated somatic cells. How they revert cell fate and express pluripotency, however, remains unclear. In this study we demonstrate that transcriptional activation of auxin biosynthesis is crucial for reprogramming differentiated Arabidopsis leaf cells. We demonstrate that interfering with the activity of histone acetyltransferases dramatically reduces callus formation from leaf mesophyll protoplasts. Histone acetylation permits the transcriptional activation of PLETHORAs (PLTs), leading to the induction of their downstream target gene YUCCA1 (YUC1) encoding an enzyme for auxin biosynthesis. Auxin biosynthesis is in turn required to accomplish initial cell division through the activation of G2/M phase genes mediated by MYB DOMAIN PROTEIN 3-RELATED (MYB3Rs). We further show that the AUXIN RESPONSE FACTOR 7 (ARF7)/ARF19 and INDOLE-3-ACETIC ACID INDUCIBLE 3 (IAA3)/IAA18-mediated auxin signaling pathway is responsible for cell cycle reactivation by transcriptionally upregulating MYB3R4. These findings provide a mechanistic model of how differentiated plant cells revert their fate and reinitiate the cell cycle to become pluripotent.

2022-07-07 | GSE204767 | GEO

Auxin biosynthesis drives developmental reprogramming of differentiated cells

Project description:Auxin biosynthesis drives developmental reprogramming of differentiated cells

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Transcriptional activation of auxin biosynthesis drives developmental reprogramming of differentiated cells

Project description:Transcriptional activation of auxin biosynthesis drives developmental reprogramming of differentiated cells

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Transcriptional state during endodermal differentiation

Project description:ChIP-seq was performed to determine the transcriptional activity of genes during endodermal differentiation RNA pol II occupancy and histone marks of elongation and gene repression were analyzed during early endodermal differentiation

2012-09-25 | E-GEOD-41111 | biostudies-arrayexpress

Rocks in the Auxin Stream: Wound induced auxin accumulation and ERF115 expression synergistically drive stem cell regeneration

Project description:Plants are known for their outstanding capacity for recovering from various wounds and injury. However, it remains largely unknown how plants sense diverse forms of injury and canalize existing developmental processes into the execution of a correct regenerative response. Auxin, a cardinal plant hormone with morphogenlike properties, has been previously implicated in recovery from diverse types of wounding and organ loss. Here, through a combination of cellular imaging and in silico modelling, we demonstrate that vascular stem cell death obstructs the polar auxin flux, much alike rocks in a stream, and causes it to accumulate in the endodermis. This in turn grants the endodermal cells the capacity to undergo periclinal cell division that repopulate the vascular stem cell pool. Replenishment of the vasculature by the endodermis depends on the transcription factor ERF115, a wound inducible regulator of stem cell divisions. Although not being the primary inducer, auxin is required to maintain ERF115 expression. Reversely, ERF115 sensitizes cells to auxin by activating ARF5/MONOPTEROS, an auxin responsive transcription factor involved in the global auxin response, tissue patterning and organ formation. Combined, the wound induced auxin accumulation and ERF115 expression grant the endodermal cells stem cell activity. Our work provides a mechanistic model for wound induced stem cell regeneration in which ERF115 acts as a wound-inducible stem cell organizer that interprets wound-induced auxin maxima.

2020-06-30 | GSE139715 | GEO

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