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

ABSTRACT: 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.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE163243 | GEO | 2021/10/05

REPOSITORIES: GEO

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Targeted DamID in <i>C. elegans</i> reveals a direct role for LIN-22 and NHR-25 in antagonizing the epidermal stem cell fate.

Project description:Transcription factors are key players in gene networks controlling cell fate specification during development. In multicellular organisms, they display complex patterns of expression and binding to their targets, hence, tissue specificity is required in the characterization of transcription factor-target interactions. We introduce here targeted DamID (TaDa) as a method for tissue-specific transcription factor target identification in intact Caenorhabditis elegans animals. We use TaDa to recover targets in the epidermis for two factors, the HES1 homolog LIN-22, and the NR5A1/2 nuclear hormone receptor NHR-25. We demonstrate a direct link between LIN-22 and the Wnt signaling pathway through repression of the Frizzled receptor lin-17. We report a direct role for NHR-25 in promoting cell differentiation via repressing the expression of stem cell-promoting GATA factors. Our results expand our understanding of the epidermal gene network and highlight the potential of TaDa to dissect the architecture of tissue-specific gene regulatory networks.

| S-EPMC8816332 | 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:Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonising the epidermal stem cell fate

| PRJNA685417 | ENA

DamID transcriptional profiling identifies the Snail/Scratch transcription factor Kahuli as an Alk target in the Drosophila visceral mesoderm

Project description:We used targeted DamID (TaDa) to identify Alk targets in embryos overexpressing Jeb versus embryos with abrogated Alk activity, revealing differentially expressed genes, including the Snail/Scratch family transcription factor Kahuli (Kah)

2021-11-20 | GSE188907 | GEO

Sequencing of methylated GATC DNA fragments (Targeted DamID) from seven olfactory neuron populations in Drosophila melanogaster

Project description:This project’s aim was to compare the transcriptional profiles of olfactory sensory neurons in Drosophila melanogaster in order to identify novel genes that specify neuron-specific functions/phenotypes or may otherwise be involved in the development of the olfactory system. The isolation of sufficient numbers of intact olfactory sensory neurons (OSN) from the antenna of Drosophila melanogaster has so far limited single-cell transcriptomic approaches being applied to the adult fly antenna. Targeted DamID (TaDa) provides an alternative approach for profiling transcriptional activity in a cell-specific manor that bypasses the need for isolating OSN. Using the Gal4/UAS system, we applied TaDa to seven OSN populations and compared differences in Pol II occupancy for genes across these datasets.

2021-03-17 | E-MTAB-8935 | biostudies-arrayexpress

Genome-winding binding profile of KDM5 in Drosophila larval prothoracic gland cells via Targeted DamID analysis

Project description:kdm5 is an essential gene in Drosophila that has critical developmental roles in the prothoracic gland cells of the larval ring gland. To profile KDM5 binding within these cells and this developmental stage, we performed Targeted DamID (TaDa). By profiling the nearest genes to significant TaDa peaks (FDR < 0.01), we identified 5815 candidate KDM5 target genes. Interestingly, 42% of these candidate KDM5 target genes appear to be conserved across multiple cellular contexts in Drosophila and span many cellular processes for future investigation.

2023-10-16 | GSE229076 | GEO

C. elegans: wildtype vs nhr-49-/-; wildtype vs nhr-66-/-; wildtype vs nhr-80-/-

Project description:Transcriptional profiling of C. elegans NHR-49, NHR-66 and NHR-80

2012-03-15 | GSE34856 | GEO

Novel CHD8 genomic targets identified in fetal mouse brain by in vivo Targeted DamID

Project description:Sequencing studies of autism spectrum disorder (ASD) cases have revealed a causal role for mutations to chromatin remodeling genes. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeler with one of the highest de novo mutation rates in sporadic ASD. However, the relationship between CHD8 genomic function and autism-relevant biology remains poorly elucidated. CHD8 binding studies have relied on Chromatin Immunoprecipitation followed by sequencing (ChIP-seq), but these datasets exhibit significant variation. ChIP-seq has technical limitations in the context of weak or indirect protein-DNA interactions or when high-performance antibodies are unavailable. Thus, complementary approaches are needed to establish CHD8 genomic targets. Here we used Targeted DamID in utero to characterize CHD8 binding activity in the developing embryonic mouse cortex. CHD8 Targeted DamID followed by sequencing (CHD8 TaDa-seq) revealed binding at previously identified genomic targets as well as at genes sensitive to Chd8 haploinsufficiency. CHD8 TaDa-seq showed greater sensitivity for CHD8 binding near a subset of genes specific to brain development and neuron function. These studies establish TaDa-seq as a useful alternative for mapping protein-DNA interactions in vivo and provide insights into the relationship between chromatin remodeling by CHD8 and autism-relevant pathophysiology associated with CHD8 mutations.

2021-01-18 | GSE165002 | GEO

Targeted DamID reveals differential binding of mammalian pluripotency factors

Project description:The precise control of gene expression by transcription factor networks is critical to organismal development. The predominant approach for mapping transcription factor-chromatin interactions has been chromatin immunoprecipitation (ChIP). However, ChIP requires a large number of homogeneous cells and antisera with high specificity. A second approach, DamID, has the drawback that high levels of Dam methylase are toxic. Here we modify our Targeted DamID approach (TaDa) to enable cell type-specific expression in mammalian systems, generating an inducible system (mammalian TaDa or MaTaDa) to identify protein/DNA interactions in 100 to 1000 times fewer cells than ChIP. We mapped the binding sites of key pluripotency factors, OCT4 and PRDM14, in mouse embryonic stem cells, epiblast-like cells and primordial germ cell-like cells (PGCLCs). PGCLCs are an important system to elucidate primordial germ cell development in mice. We monitored PRDM14 binding during the specification of PGCLCs, identifying direct targets of PRDM14 that are key to understanding its critical role in PGCLC development. We show that MaTaDa is a sensitive and accurate method to assess cell type specific transcription factor binding in limited numbers of cells.

2018-09-05 | GSE101971 | GEO

C. elegans: wildtype vs nhr-49-/-; wildtype vs nhr-66-/-; wildtype vs nhr-80-/-

Project description:Transcriptional profiling of C. elegans NHR-49, NHR-66 and NHR-80 Independent data sets were generated for each mutant vs wildtpe comparison: NHR-49 (N=2), NHR-66 (N=3), NHR-80 (N=4)

2012-03-15 | E-GEOD-34856 | biostudies-arrayexpress

Identification of Transcription Factor NHR-25::GFP Binding Regions in L2

Project description:modENCODE_submission_3835 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP33(official name : OP33 genotype : unc119(ed3);wgIs33(nhr-25::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs33(nhr-25::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene nhr-25; Strain OP33(official name : OP33 genotype : unc119(ed3);wgIs33(nhr-25::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius

2013-07-11 | E-GEOD-48707 | biostudies-arrayexpress

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