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Identification of Gon4l-associated genomic regions by DamID-seq

ABSTRACT: We report DNA adenine methyltransferase identification (DamID)-sequencing data to identify Gon4l-associated genomic regions in wild-type (WT) tailbud (TB) stage zebrafish embryos. Methylated, and therefore Gon4l-proximal, gDNA was isolated from embryos expressing a Gon4l-Dam fusion and compared to that from embryos expressing GFP-Dam control.

ORGANISM(S): Danio rerio

PROVIDER: GSE96576 | GEO | 2017/09/13

SECONDARY ACCESSION(S): PRJNA379067

REPOSITORIES: GEO

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Genome-wide DNA-binding analysis for Ttk in intestinal progenitor cells and Su(H) in wildtype, seq overexpressed and ttk-RNAi intestinal progenitor cells by DamID

Project description:Purpose: Genome-wide DNA-binding analysis for Ttk in intestinal progenitor cells and comparing Su(H) binding sites between seq overexpressed and ttk-RNAi intestinal progenitor cells in Drosophila midgut by DNA adenine methyltransferase identification(DamID) Methods: Dam(Ctrl) , Ttk-Dam transgenes, Su(H)-Dam, Su(H)-Dam&seq and Su(H)-Dam&ttk-RNAi were expressed in intestinal progenitor cells by esg-Gal4.The guts within 2 days was used for DNA adenine methyltransferase identification (DamID), followed by deep sequencing analysis Results: Ttk suppresses neural specific Notch targets through suppressing Seq in intestinal progenitor cells

2021-02-23 | GSE130941 | GEO

DamID experiment looking at Dichaete-bound regions in 2-7h old Drosophila embryos

Project description:Dichaete is a developmentally important transcription factor, known to be involved in basic biological processes including segmentation and nervous system development among others. The aim of this experiment was to gain further insight into the role of Dichaete during early embryogenesis, by finding out where in the genome it's binding using the DamID technique. 3 independent biological replicates. Embryos between 2-7 h old were collected. The sample embryos contained a Dichaete-Dam methylase fusion, while the control embryos had a Dam methylase only to simulate the background level of methylation not specific to transcription factor binding.

2013-07-22 | E-GEOD-49013 | biostudies-arrayexpress

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2007-07-05 | E-MEXP-864 | 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.

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Identifying targets of DSX with DamID-seq

2014-10-30 | E-GEOD-27269 | biostudies-arrayexpress

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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

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2022-09-30 | GSE214300 | GEO

Identification of Rx2 binding loci in medaka by iDamID-seq

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2016-10-06 | E-MTAB-4610 | biostudies-arrayexpress

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