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Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID

ABSTRACT: Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID

PROVIDER: PRJNA691926 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13429061.fastq.gz	Fastqsanger.gz
	SRR13429062.fastq.gz	Fastqsanger.gz
	SRR13429063.fastq.gz	Fastqsanger.gz
	SRR13429064.fastq.gz	Fastqsanger.gz
	SRR13429065.fastq.gz	Fastqsanger.gz

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Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID

Project description:In this study we use targeted DamID to assay RNA polymerase occupancy across the genome specifically within the seam cells and hypodermis of C. elegans to identify genes expressed in these cell-types.

2021-08-31 | GSE164775 | GEO

Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID.

Project description:The epidermis of Caenorhabditis elegans is an essential tissue for survival because it contributes to the formation of the cuticle barrier as well as facilitating developmental progression and animal growth. Most of the epidermis consists of the hyp7 hypodermal syncytium, the nuclei of which are largely generated by the seam cells, which exhibit stem cell-like behaviour during development. How seam cell progenitors differ transcriptionally from the differentiated hypodermis is poorly understood. Here, we introduce Targeted DamID (TaDa) in C. elegans as a method for identifying genes expressed within a tissue of interest without cell isolation. We show that TaDa signal enrichment profiles can be used to identify genes transcribed in the epidermis and use this method to resolve differences in gene expression between the seam cells and the hypodermis. Finally, we predict and functionally validate new transcription and chromatin factors acting in seam cell development. These findings provide insights into cell type-specific gene expression profiles likely associated with epidermal cell fate patterning.

| S-EPMC7613258 | biostudies-literature

Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonising the epidermal stem cell fate

Project description:In this study we adapt targeted DamID (TaDa) for use in C.elegans and employ it to identify targets within the epidermis for the transcription factors LIN-22 and NHR-25 that are key epidermal development regulators.

2021-10-05 | GSE163243 | GEO

C. elegans L4 hypodermal RNA polymerase DamID

Project description:To adapt RNA polymerase DamID (RAPID) for FLP-mediated spatial control in Caenorhabditis elegans, we inserted a Dam::rpb-6 fusion gene downstream of a FRT-flanked mCh::his-58 cassette and under control of the hsp-16.41 promoter. We introduced a single copy of this construct into the C. elegans genome and crossed the resulting line with a dpy-7p::FLP driver to enable basal Dam::rpb-6 expression in the hypodermis. Nematodes were cultured at 20 degrees Celcius to ensure low levels of Dam::RPB-6 expression in the hypodermis and total genomic DNA was purified from L4 larvae. DNA from animals expressing GFP::Dam was used to control for unspecific methylation. The genome-wide association profile of Dam::RPB-6 was determined by deep sequencing, which revealed a list of 2331 protein coding genes with FDR < 0.05. Original RAPID reference: Gomez-Saldivar et al (2020) Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans. Genetics 216, 931–945. doi:10.1534/genetics.120.303774

2022-09-30 | GSE214300 | GEO

C. elegans L4 hypodermal RNA polymerase DamID

Project description:C. elegans L4 hypodermal RNA polymerase DamID

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LMN-1-DamID in N2 and set-25(n5021) met-2(n4256) mutant early C. elegans embryos

2012-09-04 | GSE37226 | GEO

Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonising the epidermal stem cell fate

Project description:Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonising the epidermal stem cell fate

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Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans

Project description:Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans

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LMN-1-DamID in N2 and set-25(n5021) met-2(n4256) mutant early C. elegans embryos

Project description:We asked if the perinuclear position of chromosome arms in C. elegans depends on the histone methyltransferases MET-2 and SET-25. To this end, we performed LMN-1-DamID in wild-type (N2) and mutant (set-25 met-2) strains. LMN-1-DamID signal on chromosome arms was significantly reduced in the mutant. Three biological replicas were performed for each genotype. For one replica dyes were swapped. For each replica methylated DNA amplified from a strain expressing LMN-1-Dam was competitively hybridized against DNA amplified from a strain expressing GFP-Dam.

2012-09-04 | E-GEOD-37226 | biostudies-arrayexpress

Targeted DamID Detects Cell Type Specific Histone Modifications in intact tissues or organisms

Project description:Histone modifications play a key role in regulating gene expression and cell fate during development and disease. Current methods for cell-type specific genome-wide profiling of histone modifications require dissociation and isolation of cells and are not compatible with all tissue types. Here we adapt Targeted DamID to recognise specific histone marks, by fusing chromatin binding proteins or single-chain antibodies to Dam, an E. coli DNA adenine methylase. When combined with Targeted DamID (TaDa), this enables cell-type specific chromatin profiling in intact tissues or organisms. We first profiled H3K4me3, H3K9ac, H3K27me3 and H4K20me1 in vivo in neural stem cells of the developing Drosophila brain. Next, we mapped cell-type specific H3K4me3, H3K9ac and H4K20me1 distributions in the developing mouse brain. Finally, we injected RNA encoding DamID constructs into 1-cell stage Xenopus embryos to profile H3K4me3 distribution during gastrulation and neurulation. These results illustrate the versatility of Targeted DamID to profile cell-type specific histone marks throughout the genome in diverse model systems.

2024-10-23 | GSE278272 | GEO

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