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Genome-wide DNA-binding analysis for E(spl)m8 in intestinal stem cells by DamID

ABSTRACT: Purpose: Genome-wide DNA-binding analysis for E(spl)m8 in intestinal stem cells in Drosophila midgut by DNA adenine methyltransferase identification(DamID) Methods: DNA adenine methyltransferase identification (DamID) on E(spl)m8 driven by Dl-Gal4 Results:

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE102568 | GEO | 2018/02/02

REPOSITORIES: GEO

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Genome-wide DNA-binding analysis for Stat92E in Drosophila testis by DamID

Project description:Purpose: Genome-wide DNA-binding analysis for Stat92E in Drosophila testis cyst cells by DNA adenine methyltransferase identification(DamID).Methods: DNA adenine methyltransferase identification (DamID) on Stat92E driven by c587Gal4ts;hopTum-l

2023-09-10 | GSE226582 | GEO

Genome-wide DNA-binding analysis for Sox100B in intestinal stem cells by DamID

Project description:Purpose: Genome-wide DNA-binding analysis for Sox100B in intestinal stem cells in Drosophila midgut by DNA adenine methyltransferase identification(DamID) Methods: DNA adenine methyltransferase identification (DamID) on Sox100B driven by ESG-Gal4 Results: 5046 significant genomic binding sites, corresponding to 3182 genes were identified via iDamID following Sox100B overexpression in progenitor cells compared to WT. About a third of these genes were in the list of significantly altered genes following Sox100B overexpression and/or depletion.

2020-05-18 | GSE130304 | GEO

Control of neural daughter cell proliferation by multi-level Notch/Su(H)/E(spl)HLH signaling. (PMID: 27070787)

Project description:We expressed DamID and Flag-tagged versions of E(spl)HLH-m5, -m8 and Su(H), in Drosophila embryos and analyzed their DNA-binding by DamID-seq and ChIP-seq. The Notch pathway controls proliferation during development and in adulthood, and is frequently affected in many disorders. However, the genetic sensitivity and multi-layered transcriptional properties of the Notch pathway has made its molecular decoding challenging. Here, we address the complexity of Notch signaling with respect to proliferation, using the developing Drosophila CNS as model. We find that a Notch/Su(H)/E(spl)-HLH cascade specifically controls daughter, but not progenitor proliferation. Additionally, we find that different E(spl)-HLH genes are required in different neuroblast lineages. The Notch/Su(H)/E(spl)-HLH cascade alters daughter proliferation by regulating four key cell cycle factors: Cyclin E, String/Cdc25, E2f and Dacapo (mammalian p21CIP1/p27KIP1/p57Kip2). ChIP and DamID analysis of Su(H) and E(spl)-HLH indicates direct transcriptional regulation of the cell cycle genes, and of the Notch pathway itself. These results point to a multi-level signaling model, and may help shed light on the dichotomous proliferative role of Notch signaling in many other systems.

2019-09-11 | GSE137195 | GEO

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

Identification of Gon4l-associated genomic regions by DamID-seq

Project description: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.

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Identification of HP1 protein binding sites in Drosophila Kc cells using DamID

Project description:Heterochromatin protein HP1 is thought to play key role in chromatin structure and gene regulation. We performed a genome-wide mapping of HP1 target genes in the non-polytenic Drosophila Kc cells by using DamID. This approach is based on the ability of a chromatin protein fused to Escherichia coli DNA adenine methyltransferase (Dam) to methylate the native binding site of the chromatin protein. Dam-fusion proteins are expressed at very low levels to avoid mistargeting. Subsequently, methylated DNA fragments are isolated, labeled (using Cy3 or Cy5) and hybridized to a microarray. Methylated DNA fragments from cells transfected with Dam alone served as reference. Genomic binding sites of the protein can then be identified based on the targeted methylation pattern. For detailed background information on DamID, see: van Steensel, B., Delrow, J. & Henikoff, S. Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet 27, 304-8 (2001); van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8 (2000). We performed three independent replicates. We used for this study a cDNA array developed by the GeneCore facility in EMBL (Heidelberg, Germany), covering the DGC1 and DGC2 cDNA libraries from the Berkeley Drosophila Genome Project, which represents more than 70% of the coding Drosophila genome.

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DamID profiling of proneural transcription factor binding in Drosophila melanogaster wing imaginal discs

2014-01-01 | GSE53009 | GEO

DamID profiling of proneural transcription factor binding in Drosophila melanogaster wing imaginal discs

Project description:Genome-wide identification of the binding sites of the Drosophila transcription factors Achaete, Asense, E(spl)m3-HLH and Senseless in wing imaginal cells using DamID profiling. Each Dam-fusion-derived sample is compared to a control Dam-only sample. Two biological replicates were performed for sca-Asense, neur-Asense, sca-Achaete, neur-Achaete, neur-Sens and sca-E(spl)m3-HLH.

2014-01-01 | E-GEOD-53009 | biostudies-arrayexpress

DNA Adenine Methyltransferase Identification (DamID) Coupled to Next Generation Sequencing For Profiling Lamina Associated Domains

Project description:DNA Adenine Methyltransferase Identification (DamID) Coupled to Next Generation Sequencing For Profiling Lamina Associated Domains

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DamID for Swi6, Rdp1 and Dcr1 in Schizosaccharomyces pombe

Project description:In the fission yeast Schizosaccharomyces pombe, the RNA interference (RNAi) pathway is required to generate small interfering RNAs (siRNAs) that mediate heterochromatic silencing of centromeric repeats. Here we demonstrate that RNAi also functions to repress genomic elements other than constitutive heterochromatin. Using DamID (DNA adenine methyltransferase identification) we show that Dcr1 and Rdp1 physically associate with some euchromatic genes, non-coding RNA (ncRNA) genes, and retrotransposon long terminal repeats (LTRs), and that this association is independent of the Clr4 histone methyltransferase. Physical association of RNAi with chromatin is sufficient to trigger a silencing response but not to assemble heterochromatin. The mode of silencing at the newly identified RNAi targets is consistent with a co-transcriptional gene silencing model as proposed earlier and functions with trace amounts of siRNAs. We anticipate that similar mechanisms could also be operational in other eukaryotes.

2010-09-25 | GSE24360 | GEO

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