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Quantitating transcription factor redundancy: The relative roles of the ELT-2 and ELT-7 GATA factors in the C. elegans endoderm

ABSTRACT: Quantitating transcription factor redundancy: The relative roles of the ELT-2 and ELT-7 GATA factors in the C. elegans endoderm

PROVIDER: PRJNA419208 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6309960.fastq.gz	Fastqsanger.gz
	SRR6309970.fastq.gz	Fastqsanger.gz
	SRR6309961.fastq.gz	Fastqsanger.gz
	SRR6309971.fastq.gz	Fastqsanger.gz
	SRR6309962.fastq.gz	Fastqsanger.gz

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Quantitating transcription factor redundancy: The relative roles of the ELT-2 and ELT-7 GATA factors in the C. elegans endoderm

Project description:Two GATA transcription factors, ELT-2 and ELT-7, function in the differentiation of the Caenorhabditis elegans intestine. Though loss of elt-7 causes no discernable phenotype on its own, it significantly enhances intestinal morphology defects in elt-2 loss-of-function mutants. We sought to identify the cohorts of gene targets unique to or shared by ELT-2 and ELT-7 in an effort to determine the logic underlying their differential impact on intestinal development.

2018-02-22 | GSE107175 | GEO

Quantitating transcription factor redundancy: The relative roles of the ELT-2 and ELT-7 GATA factors in the C. elegans endoderm.

Project description: Not available

| S-EPMC6476323 | biostudies-literature

Defining the Roles and Regulation of the GATA-factor ELT-2 in the C. elegans Endoderm

2016-03-30 | GSE71720 | GEO

Defining the Roles and Regulation of the GATA-factor ELT-2 in the C. elegans Endoderm

Project description:We identified genome-wide sites of occupancy for the intestine-specific transcription factor ELT-2 in L3-staged N2 worm by performing ELT-2 ChIP-seq on whole worms; we performed RNA-seq on L3-staged N2 whole worms To identify DNA regions of direct ELT-2 occupancy, we performed the following ChIP-seq assays 1) ELT-2 ChIP-seq on L3 staged N2 C. elegans worms; 2) H3K4me3 ChIP-seq on matched L3 staged N2 worms; 3) Mock IgG-only ChIP-seq negative control on L3 stage N2 worms. Input DNA was also sequenced for each replicate. In addition, we performed RNA-seq on two replicates of L3 N2 C. elegans worms.

2016-03-30 | E-GEOD-71720 | biostudies-arrayexpress

Genome-wide characterization of the Caenorhabditis elegans intestine GATA transcription factor ELT-2

Project description:ELT-2 is the major transcription factor required for Caenorhabditis elegans intestinal development. It initiates in embryos to promote development then persists after hatching through larval and adult stages. Though the sites of ELT-2 binding are characterized and the transcriptional changes that result from ELT-2 depletion are described, a major missing piece has been the lack of an intestine-specific transcriptome profile over developmental time. We generated this dataset by Fluorescence Activated Cell Sorting (FACS) intestine cells at distinct developmental stages. We analyzed this dataset in conjunction with previously conducted ELT-2 studies to evaluate ELT-2’s role in directing the intestinal regulatory network through development. We found that only 33% of intestine-enriched genes in the embryo were direct targets of ELT-2 but that number increased to 75% by the L3 stage. This suggests additional transcription factors promote intestinal transcription especially in the embryo. Furthermore, only half of ELT-2’s direct target genes were dependent on ELT-2 for their proper expression levels, and an equal proportion of those responded to elt-2 depletion with over-expression as with under-expression. That is, ELT-2 can either activate or repress direct target genes. Indeed, we observed that ELT-2 repressed its own promoter, implicating new models for its autoregulation. Together, our results illustrate that ELT-2 impacts roughly 20 – 50% of intestine-specific genes, that ELT-2 both positively and negatively controls its direct targets, and that our current model of the intestinal regulatory network is incomplete as the factors responsible for directing the expression of many intestinal genes remain unknown.

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Genome-wide characterization of the Caenorhabditis elegans intestine GATA transcription factor ELT-2

Project description:Genome-wide characterization of the Caenorhabditis elegans intestine GATA transcription factor ELT-2

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Dynamic proteomic profiling of extra-embryonic endoderm differentiation in mouse embryonic stem cells

Project description:During mammalian pre-implantation development, the cells of the blastocyst’s inner cell mass differentiate into the epiblast and primitive endoderm lineages, which give rise to the fetus and extra-embryonic tissues, respectively. Extra-embryonic endoderm differentiation can be modeled in vitro by induced expression of GATA transcription factors in mouse embryonic stem cells. Here we use this GATA-inducible system to quantitatively monitor the dynamics of global proteomic changes during the early stages of this differentiation event and also investigate the fully differentiated phenotype, as represented by embryo-derived extra-embryonic endoderm (XEN) cells. Using mass spectrometry-based quantitative proteomic profiling with multivariate data analysis tools, we reproducibly quantified 2,336 proteins across three biological replicates and have identified clusters of proteins characterized by distinct, dynamic temporal abundance profiles. We first used this approach to highlight novel marker candidates of the pluripotent state and extra-embryonic endoderm differentiation. Through functional annotation enrichment analysis, we have shown that the downregulation of chromatin-modifying enzymes, the re-organization of membrane trafficking machinery and the breakdown of cell-cell adhesion are successive steps of the extra-embryonic differentiation process. Thus, applying a range of sophisticated clustering approaches to a time-resolved proteomic dataset has allowed the elucidation of complex biological processes which characterize stem cell differentiation and could establish a general paradigm for the investigation of these processes.

2015-06-13 | PXD001901 | Pride

Mitochondrial stress activates ELT-2-dependent lysosomal proteostasis to extend lifespan in C. elegans

Project description:Mild mitochondrial stress could extend lifespan across species, yet the underlying mechanism remains unclear. Here we show that inhibition of mitochondrial respiration induces a sustained transcriptional program that enhances lysosomal proteolysis during aging in Caenorhabditis elegans. Mechanistically, this response is primarily regulated by the intestinal GATA transcription factor ELT-2, which retains high expression and directly binds to GATA motifs in the promoters of lysosomal protease genes to promote their transcriptional activation. Moreover, we identified R249 within the conserved zinc-finger DNA-binding domain of ELT-2 as a key residue required for its transcriptional activity. Notably, this mitochondrion-ELT-2-lysosome axis operates largely independently of the mitochondrial unfolded protein response (UPRmt) to counteract aging. Furthermore, increased lysosomal activity, as well as the lysosomal proteases CPR-5 and CPR-8, are essential for mitochondrial stress-induced clearance of toxic polyglutamine (polyQ) aggregates and lifespan extension. Together, our findings reveal a previously unrecognized ELT-2-dependent lysosomal proteostasis pathway that acts downstream of mitochondrial stress to maintain protein homeostasis and promote longevity.

2026-05-15 | GSE291671 | GEO

Mitochondrial stress activates ELT-2-dependent lysosomal proteostasis to extend lifespan in C. elegans

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The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network.

Project description: Not available

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